Starting phenix.real_space_refine on Tue Mar 12 17:04:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6obj_20015/03_2024/6obj_20015.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6obj_20015/03_2024/6obj_20015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6obj_20015/03_2024/6obj_20015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6obj_20015/03_2024/6obj_20015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6obj_20015/03_2024/6obj_20015.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6obj_20015/03_2024/6obj_20015.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 500 5.49 5 Mg 20 5.21 5 S 180 5.16 5 C 38820 2.51 5 N 11560 2.21 5 O 12980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 63": "OD1" <-> "OD2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ASP 248": "OD1" <-> "OD2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 169": "OE1" <-> "OE2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E ASP 248": "OD1" <-> "OD2" Residue "E TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "G PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 63": "OD1" <-> "OD2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G GLU 169": "OE1" <-> "OE2" Residue "G GLU 170": "OE1" <-> "OE2" Residue "G ASP 201": "OD1" <-> "OD2" Residue "G GLU 234": "OE1" <-> "OE2" Residue "G ASP 248": "OD1" <-> "OD2" Residue "G TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "I PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 63": "OD1" <-> "OD2" Residue "I ARG 84": "NH1" <-> "NH2" Residue "I ARG 152": "NH1" <-> "NH2" Residue "I GLU 166": "OE1" <-> "OE2" Residue "I GLU 169": "OE1" <-> "OE2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "I ASP 201": "OD1" <-> "OD2" Residue "I GLU 234": "OE1" <-> "OE2" Residue "I ASP 248": "OD1" <-> "OD2" Residue "I TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 335": "OE1" <-> "OE2" Residue "K PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 63": "OD1" <-> "OD2" Residue "K ARG 84": "NH1" <-> "NH2" Residue "K ARG 152": "NH1" <-> "NH2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K GLU 169": "OE1" <-> "OE2" Residue "K GLU 170": "OE1" <-> "OE2" Residue "K ASP 201": "OD1" <-> "OD2" Residue "K GLU 234": "OE1" <-> "OE2" Residue "K ASP 248": "OD1" <-> "OD2" Residue "K TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 335": "OE1" <-> "OE2" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 63": "OD1" <-> "OD2" Residue "M ARG 84": "NH1" <-> "NH2" Residue "M ARG 152": "NH1" <-> "NH2" Residue "M GLU 166": "OE1" <-> "OE2" Residue "M GLU 169": "OE1" <-> "OE2" Residue "M GLU 170": "OE1" <-> "OE2" Residue "M ASP 201": "OD1" <-> "OD2" Residue "M GLU 234": "OE1" <-> "OE2" Residue "M ASP 248": "OD1" <-> "OD2" Residue "M TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 335": "OE1" <-> "OE2" Residue "O PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 63": "OD1" <-> "OD2" Residue "O ARG 84": "NH1" <-> "NH2" Residue "O ARG 152": "NH1" <-> "NH2" Residue "O GLU 166": "OE1" <-> "OE2" Residue "O GLU 169": "OE1" <-> "OE2" Residue "O GLU 170": "OE1" <-> "OE2" Residue "O ASP 201": "OD1" <-> "OD2" Residue "O GLU 234": "OE1" <-> "OE2" Residue "O ASP 248": "OD1" <-> "OD2" Residue "O TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 335": "OE1" <-> "OE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 63": "OD1" <-> "OD2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "Q ARG 152": "NH1" <-> "NH2" Residue "Q GLU 166": "OE1" <-> "OE2" Residue "Q GLU 169": "OE1" <-> "OE2" Residue "Q GLU 170": "OE1" <-> "OE2" Residue "Q ASP 201": "OD1" <-> "OD2" Residue "Q GLU 234": "OE1" <-> "OE2" Residue "Q ASP 248": "OD1" <-> "OD2" Residue "Q TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 335": "OE1" <-> "OE2" Residue "S PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 63": "OD1" <-> "OD2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S GLU 166": "OE1" <-> "OE2" Residue "S GLU 169": "OE1" <-> "OE2" Residue "S GLU 170": "OE1" <-> "OE2" Residue "S ASP 201": "OD1" <-> "OD2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "S ASP 248": "OD1" <-> "OD2" Residue "S TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 335": "OE1" <-> "OE2" Residue "U PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 63": "OD1" <-> "OD2" Residue "U ARG 84": "NH1" <-> "NH2" Residue "U ARG 152": "NH1" <-> "NH2" Residue "U GLU 166": "OE1" <-> "OE2" Residue "U GLU 169": "OE1" <-> "OE2" Residue "U GLU 170": "OE1" <-> "OE2" Residue "U ASP 201": "OD1" <-> "OD2" Residue "U GLU 234": "OE1" <-> "OE2" Residue "U ASP 248": "OD1" <-> "OD2" Residue "U TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 335": "OE1" <-> "OE2" Residue "W PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 63": "OD1" <-> "OD2" Residue "W ARG 84": "NH1" <-> "NH2" Residue "W ARG 152": "NH1" <-> "NH2" Residue "W GLU 166": "OE1" <-> "OE2" Residue "W GLU 169": "OE1" <-> "OE2" Residue "W GLU 170": "OE1" <-> "OE2" Residue "W ASP 201": "OD1" <-> "OD2" Residue "W GLU 234": "OE1" <-> "OE2" Residue "W ASP 248": "OD1" <-> "OD2" Residue "W TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 335": "OE1" <-> "OE2" Residue "Y PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 63": "OD1" <-> "OD2" Residue "Y ARG 84": "NH1" <-> "NH2" Residue "Y ARG 152": "NH1" <-> "NH2" Residue "Y GLU 166": "OE1" <-> "OE2" Residue "Y GLU 169": "OE1" <-> "OE2" Residue "Y GLU 170": "OE1" <-> "OE2" Residue "Y ASP 201": "OD1" <-> "OD2" Residue "Y GLU 234": "OE1" <-> "OE2" Residue "Y ASP 248": "OD1" <-> "OD2" Residue "Y TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 335": "OE1" <-> "OE2" Residue "0 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 63": "OD1" <-> "OD2" Residue "0 ARG 84": "NH1" <-> "NH2" Residue "0 ARG 152": "NH1" <-> "NH2" Residue "0 GLU 166": "OE1" <-> "OE2" Residue "0 GLU 169": "OE1" <-> "OE2" Residue "0 GLU 170": "OE1" <-> "OE2" Residue "0 ASP 201": "OD1" <-> "OD2" Residue "0 GLU 234": "OE1" <-> "OE2" Residue "0 ASP 248": "OD1" <-> "OD2" Residue "0 TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 335": "OE1" <-> "OE2" Residue "2 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 63": "OD1" <-> "OD2" Residue "2 ARG 84": "NH1" <-> "NH2" Residue "2 ARG 152": "NH1" <-> "NH2" Residue "2 GLU 166": "OE1" <-> "OE2" Residue "2 GLU 169": "OE1" <-> "OE2" Residue "2 GLU 170": "OE1" <-> "OE2" Residue "2 ASP 201": "OD1" <-> "OD2" Residue "2 GLU 234": "OE1" <-> "OE2" Residue "2 ASP 248": "OD1" <-> "OD2" Residue "2 TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 335": "OE1" <-> "OE2" Residue "4 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 63": "OD1" <-> "OD2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 ARG 152": "NH1" <-> "NH2" Residue "4 GLU 166": "OE1" <-> "OE2" Residue "4 GLU 169": "OE1" <-> "OE2" Residue "4 GLU 170": "OE1" <-> "OE2" Residue "4 ASP 201": "OD1" <-> "OD2" Residue "4 GLU 234": "OE1" <-> "OE2" Residue "4 ASP 248": "OD1" <-> "OD2" Residue "4 TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 335": "OE1" <-> "OE2" Residue "6 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 63": "OD1" <-> "OD2" Residue "6 ARG 84": "NH1" <-> "NH2" Residue "6 ARG 152": "NH1" <-> "NH2" Residue "6 GLU 166": "OE1" <-> "OE2" Residue "6 GLU 169": "OE1" <-> "OE2" Residue "6 GLU 170": "OE1" <-> "OE2" Residue "6 ASP 201": "OD1" <-> "OD2" Residue "6 GLU 234": "OE1" <-> "OE2" Residue "6 ASP 248": "OD1" <-> "OD2" Residue "6 TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 335": "OE1" <-> "OE2" Residue "8 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 63": "OD1" <-> "OD2" Residue "8 ARG 84": "NH1" <-> "NH2" Residue "8 ARG 152": "NH1" <-> "NH2" Residue "8 GLU 166": "OE1" <-> "OE2" Residue "8 GLU 169": "OE1" <-> "OE2" Residue "8 GLU 170": "OE1" <-> "OE2" Residue "8 ASP 201": "OD1" <-> "OD2" Residue "8 GLU 234": "OE1" <-> "OE2" Residue "8 ASP 248": "OD1" <-> "OD2" Residue "8 TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 335": "OE1" <-> "OE2" Residue "a PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 63": "OD1" <-> "OD2" Residue "a ARG 84": "NH1" <-> "NH2" Residue "a ARG 152": "NH1" <-> "NH2" Residue "a GLU 166": "OE1" <-> "OE2" Residue "a GLU 169": "OE1" <-> "OE2" Residue "a GLU 170": "OE1" <-> "OE2" Residue "a ASP 201": "OD1" <-> "OD2" Residue "a GLU 234": "OE1" <-> "OE2" Residue "a ASP 248": "OD1" <-> "OD2" Residue "a TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 335": "OE1" <-> "OE2" Residue "c PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 63": "OD1" <-> "OD2" Residue "c ARG 84": "NH1" <-> "NH2" Residue "c ARG 152": "NH1" <-> "NH2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "c ASP 201": "OD1" <-> "OD2" Residue "c GLU 234": "OE1" <-> "OE2" Residue "c ASP 248": "OD1" <-> "OD2" Residue "c TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 335": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 64060 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC C 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "B" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC D 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC F 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "G" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC H 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC J 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "K" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC L 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC N 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "O" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC P 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC R 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "S" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC T 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "V" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC V 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "W" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "X" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC X 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC Z 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "0" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "1" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC 1 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "3" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC 3 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "4" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "5" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC 5 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "7" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC 7 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "8" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "9" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC 9 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "b" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC b 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "c" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Inner-chain residues flagged as termini: ['pdbres=" DC d 12 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.43, per 1000 atoms: 0.40 Number of scatterers: 64060 At special positions: 0 Unit cell: (140.17, 138.86, 296.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 180 16.00 P 500 15.00 Mg 20 11.99 O 12980 8.00 N 11560 7.00 C 38820 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: 21.16 Conformation dependent library (CDL) restraints added in 7.2 seconds 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12640 Finding SS restraints... Secondary structure from input PDB file: 380 helices and 40 sheets defined 48.2% alpha, 6.8% beta 200 base pairs and 480 stacking pairs defined. Time for finding SS restraints: 18.38 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 38 through 47 removed outlier: 3.734A pdb=" N ALA A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.631A pdb=" N GLU A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 122 removed outlier: 3.914A pdb=" N LYS A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 143 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.677A pdb=" N LEU A 159 " --> pdb=" O TRP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 199 " --> pdb=" O GLU A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 199' Processing helix chain 'A' and resid 201 through 205 removed outlier: 4.061A pdb=" N TRP A 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 205 " --> pdb=" O GLU A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 205' Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 218 " --> pdb=" O PRO A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 218' Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 264 " --> pdb=" O MET A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU B 73 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS B 81 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 143 Processing helix chain 'B' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU B 159 " --> pdb=" O TRP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE B 198 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 199 " --> pdb=" O GLU B 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 195 through 199' Processing helix chain 'B' and resid 201 through 205 removed outlier: 4.062A pdb=" N TRP B 204 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 205 " --> pdb=" O GLU B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 205' Processing helix chain 'B' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 218 " --> pdb=" O PRO B 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 213 through 218' Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL B 259 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 264 " --> pdb=" O MET B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'E' and resid 8 through 13 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.734A pdb=" N ALA E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 Processing helix chain 'E' and resid 69 through 83 removed outlier: 3.631A pdb=" N GLU E 73 " --> pdb=" O GLY E 69 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N HIS E 81 " --> pdb=" O THR E 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS E 96 " --> pdb=" O ASN E 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER E 106 " --> pdb=" O PHE E 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER E 107 " --> pdb=" O GLU E 103 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 143 Processing helix chain 'E' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU E 159 " --> pdb=" O TRP E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE E 198 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN E 199 " --> pdb=" O GLU E 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 195 through 199' Processing helix chain 'E' and resid 201 through 205 removed outlier: 4.062A pdb=" N TRP E 204 " --> pdb=" O ASP E 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG E 205 " --> pdb=" O GLU E 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 201 through 205' Processing helix chain 'E' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU E 218 " --> pdb=" O PRO E 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 213 through 218' Processing helix chain 'E' and resid 223 through 227 Processing helix chain 'E' and resid 231 through 233 No H-bonds generated for 'chain 'E' and resid 231 through 233' Processing helix chain 'E' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL E 259 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 264 " --> pdb=" O MET E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 Processing helix chain 'E' and resid 319 through 334 removed outlier: 3.623A pdb=" N ALA E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 337 No H-bonds generated for 'chain 'E' and resid 335 through 337' Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA G 44 " --> pdb=" O GLN G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN G 60 " --> pdb=" O SER G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU G 73 " --> pdb=" O GLY G 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS G 81 " --> pdb=" O THR G 77 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE G 82 " --> pdb=" O GLU G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA G 98 " --> pdb=" O LYS G 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER G 106 " --> pdb=" O PHE G 102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER G 107 " --> pdb=" O GLU G 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET G 110 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 143 Processing helix chain 'G' and resid 156 through 160 removed outlier: 3.677A pdb=" N LEU G 159 " --> pdb=" O TRP G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU G 166 " --> pdb=" O PRO G 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL G 167 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE G 168 " --> pdb=" O SER G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE G 198 " --> pdb=" O PRO G 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN G 199 " --> pdb=" O GLU G 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 195 through 199' Processing helix chain 'G' and resid 201 through 205 removed outlier: 4.061A pdb=" N TRP G 204 " --> pdb=" O ASP G 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG G 205 " --> pdb=" O GLU G 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 201 through 205' Processing helix chain 'G' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE G 217 " --> pdb=" O ARG G 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU G 218 " --> pdb=" O PRO G 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 213 through 218' Processing helix chain 'G' and resid 223 through 227 Processing helix chain 'G' and resid 231 through 233 No H-bonds generated for 'chain 'G' and resid 231 through 233' Processing helix chain 'G' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL G 259 " --> pdb=" O TYR G 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU G 262 " --> pdb=" O ASN G 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 264 " --> pdb=" O MET G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 291 Processing helix chain 'G' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA G 323 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU G 332 " --> pdb=" O ALA G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 337 No H-bonds generated for 'chain 'G' and resid 335 through 337' Processing helix chain 'I' and resid 8 through 13 Processing helix chain 'I' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA I 44 " --> pdb=" O GLN I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN I 60 " --> pdb=" O SER I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS I 81 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE I 82 " --> pdb=" O GLU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS I 96 " --> pdb=" O ASN I 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA I 98 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER I 106 " --> pdb=" O PHE I 102 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER I 107 " --> pdb=" O GLU I 103 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 143 Processing helix chain 'I' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU I 159 " --> pdb=" O TRP I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU I 166 " --> pdb=" O PRO I 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE I 168 " --> pdb=" O SER I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE I 198 " --> pdb=" O PRO I 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN I 199 " --> pdb=" O GLU I 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 195 through 199' Processing helix chain 'I' and resid 201 through 205 removed outlier: 4.061A pdb=" N TRP I 204 " --> pdb=" O ASP I 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG I 205 " --> pdb=" O GLU I 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 201 through 205' Processing helix chain 'I' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE I 217 " --> pdb=" O ARG I 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU I 218 " --> pdb=" O PRO I 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 213 through 218' Processing helix chain 'I' and resid 223 through 227 Processing helix chain 'I' and resid 231 through 233 No H-bonds generated for 'chain 'I' and resid 231 through 233' Processing helix chain 'I' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL I 259 " --> pdb=" O TYR I 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU I 262 " --> pdb=" O ASN I 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 264 " --> pdb=" O MET I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA I 323 " --> pdb=" O ALA I 319 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU I 332 " --> pdb=" O ALA I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 337 No H-bonds generated for 'chain 'I' and resid 335 through 337' Processing helix chain 'K' and resid 8 through 13 Processing helix chain 'K' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN K 60 " --> pdb=" O SER K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 68 Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU K 73 " --> pdb=" O GLY K 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS K 96 " --> pdb=" O ASN K 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL K 97 " --> pdb=" O ALA K 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA K 98 " --> pdb=" O LYS K 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER K 106 " --> pdb=" O PHE K 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER K 107 " --> pdb=" O GLU K 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET K 110 " --> pdb=" O SER K 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN K 112 " --> pdb=" O ALA K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 143 Processing helix chain 'K' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU K 159 " --> pdb=" O TRP K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU K 166 " --> pdb=" O PRO K 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE K 168 " --> pdb=" O SER K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE K 198 " --> pdb=" O PRO K 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN K 199 " --> pdb=" O GLU K 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 195 through 199' Processing helix chain 'K' and resid 201 through 205 removed outlier: 4.062A pdb=" N TRP K 204 " --> pdb=" O ASP K 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG K 205 " --> pdb=" O GLU K 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 201 through 205' Processing helix chain 'K' and resid 213 through 218 removed outlier: 3.664A pdb=" N ILE K 217 " --> pdb=" O ARG K 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU K 218 " --> pdb=" O PRO K 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 213 through 218' Processing helix chain 'K' and resid 223 through 227 Processing helix chain 'K' and resid 231 through 233 No H-bonds generated for 'chain 'K' and resid 231 through 233' Processing helix chain 'K' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL K 259 " --> pdb=" O TYR K 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU K 262 " --> pdb=" O ASN K 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU K 264 " --> pdb=" O MET K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 291 Processing helix chain 'K' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA K 323 " --> pdb=" O ALA K 319 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU K 332 " --> pdb=" O ALA K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 337 No H-bonds generated for 'chain 'K' and resid 335 through 337' Processing helix chain 'M' and resid 8 through 13 Processing helix chain 'M' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA M 44 " --> pdb=" O GLN M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN M 60 " --> pdb=" O SER M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 68 Processing helix chain 'M' and resid 69 through 83 removed outlier: 3.631A pdb=" N GLU M 73 " --> pdb=" O GLY M 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS M 81 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 122 removed outlier: 3.914A pdb=" N LYS M 96 " --> pdb=" O ASN M 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL M 97 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA M 98 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER M 106 " --> pdb=" O PHE M 102 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER M 107 " --> pdb=" O GLU M 103 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET M 110 " --> pdb=" O SER M 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN M 112 " --> pdb=" O ALA M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 143 Processing helix chain 'M' and resid 156 through 160 removed outlier: 3.677A pdb=" N LEU M 159 " --> pdb=" O TRP M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU M 166 " --> pdb=" O PRO M 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL M 167 " --> pdb=" O GLU M 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE M 168 " --> pdb=" O SER M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE M 198 " --> pdb=" O PRO M 195 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN M 199 " --> pdb=" O GLU M 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 195 through 199' Processing helix chain 'M' and resid 201 through 205 removed outlier: 4.062A pdb=" N TRP M 204 " --> pdb=" O ASP M 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG M 205 " --> pdb=" O GLU M 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 201 through 205' Processing helix chain 'M' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE M 217 " --> pdb=" O ARG M 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU M 218 " --> pdb=" O PRO M 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 213 through 218' Processing helix chain 'M' and resid 223 through 227 Processing helix chain 'M' and resid 231 through 233 No H-bonds generated for 'chain 'M' and resid 231 through 233' Processing helix chain 'M' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL M 259 " --> pdb=" O TYR M 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU M 262 " --> pdb=" O ASN M 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU M 264 " --> pdb=" O MET M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 291 Processing helix chain 'M' and resid 319 through 334 removed outlier: 3.623A pdb=" N ALA M 323 " --> pdb=" O ALA M 319 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU M 332 " --> pdb=" O ALA M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'O' and resid 8 through 13 Processing helix chain 'O' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA O 44 " --> pdb=" O GLN O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN O 60 " --> pdb=" O SER O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 68 Processing helix chain 'O' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU O 73 " --> pdb=" O GLY O 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS O 81 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 122 removed outlier: 3.914A pdb=" N LYS O 96 " --> pdb=" O ASN O 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL O 97 " --> pdb=" O ALA O 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA O 98 " --> pdb=" O LYS O 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER O 106 " --> pdb=" O PHE O 102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER O 107 " --> pdb=" O GLU O 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET O 110 " --> pdb=" O SER O 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN O 112 " --> pdb=" O ALA O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 143 Processing helix chain 'O' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU O 159 " --> pdb=" O TRP O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU O 166 " --> pdb=" O PRO O 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL O 167 " --> pdb=" O GLU O 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 177 through 179 No H-bonds generated for 'chain 'O' and resid 177 through 179' Processing helix chain 'O' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE O 198 " --> pdb=" O PRO O 195 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN O 199 " --> pdb=" O GLU O 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 195 through 199' Processing helix chain 'O' and resid 201 through 205 removed outlier: 4.061A pdb=" N TRP O 204 " --> pdb=" O ASP O 201 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG O 205 " --> pdb=" O GLU O 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 201 through 205' Processing helix chain 'O' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE O 217 " --> pdb=" O ARG O 213 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU O 218 " --> pdb=" O PRO O 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 213 through 218' Processing helix chain 'O' and resid 223 through 227 Processing helix chain 'O' and resid 231 through 233 No H-bonds generated for 'chain 'O' and resid 231 through 233' Processing helix chain 'O' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL O 259 " --> pdb=" O TYR O 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU O 262 " --> pdb=" O ASN O 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU O 264 " --> pdb=" O MET O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 291 Processing helix chain 'O' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA O 323 " --> pdb=" O ALA O 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU O 332 " --> pdb=" O ALA O 328 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 337 No H-bonds generated for 'chain 'O' and resid 335 through 337' Processing helix chain 'Q' and resid 8 through 13 Processing helix chain 'Q' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN Q 60 " --> pdb=" O SER Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 68 Processing helix chain 'Q' and resid 69 through 83 removed outlier: 3.631A pdb=" N GLU Q 73 " --> pdb=" O GLY Q 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS Q 81 " --> pdb=" O THR Q 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE Q 82 " --> pdb=" O GLU Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 122 removed outlier: 3.914A pdb=" N LYS Q 96 " --> pdb=" O ASN Q 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL Q 97 " --> pdb=" O ALA Q 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA Q 98 " --> pdb=" O LYS Q 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER Q 106 " --> pdb=" O PHE Q 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER Q 107 " --> pdb=" O GLU Q 103 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET Q 110 " --> pdb=" O SER Q 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 143 Processing helix chain 'Q' and resid 156 through 160 removed outlier: 3.677A pdb=" N LEU Q 159 " --> pdb=" O TRP Q 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU Q 166 " --> pdb=" O PRO Q 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL Q 167 " --> pdb=" O GLU Q 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 179 No H-bonds generated for 'chain 'Q' and resid 177 through 179' Processing helix chain 'Q' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE Q 198 " --> pdb=" O PRO Q 195 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN Q 199 " --> pdb=" O GLU Q 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 195 through 199' Processing helix chain 'Q' and resid 201 through 205 removed outlier: 4.062A pdb=" N TRP Q 204 " --> pdb=" O ASP Q 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG Q 205 " --> pdb=" O GLU Q 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 201 through 205' Processing helix chain 'Q' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE Q 217 " --> pdb=" O ARG Q 213 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU Q 218 " --> pdb=" O PRO Q 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 213 through 218' Processing helix chain 'Q' and resid 223 through 227 Processing helix chain 'Q' and resid 231 through 233 No H-bonds generated for 'chain 'Q' and resid 231 through 233' Processing helix chain 'Q' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL Q 259 " --> pdb=" O TYR Q 255 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU Q 262 " --> pdb=" O ASN Q 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU Q 264 " --> pdb=" O MET Q 260 " (cutoff:3.500A) Processing helix chain 'Q' and resid 286 through 291 Processing helix chain 'Q' and resid 319 through 334 removed outlier: 3.623A pdb=" N ALA Q 323 " --> pdb=" O ALA Q 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU Q 332 " --> pdb=" O ALA Q 328 " (cutoff:3.500A) Processing helix chain 'Q' and resid 335 through 337 No H-bonds generated for 'chain 'Q' and resid 335 through 337' Processing helix chain 'S' and resid 8 through 13 Processing helix chain 'S' and resid 38 through 47 removed outlier: 3.734A pdb=" N ALA S 44 " --> pdb=" O GLN S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN S 60 " --> pdb=" O SER S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 68 Processing helix chain 'S' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU S 73 " --> pdb=" O GLY S 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS S 81 " --> pdb=" O THR S 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE S 82 " --> pdb=" O GLU S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS S 96 " --> pdb=" O ASN S 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL S 97 " --> pdb=" O ALA S 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA S 98 " --> pdb=" O LYS S 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER S 106 " --> pdb=" O PHE S 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER S 107 " --> pdb=" O GLU S 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET S 110 " --> pdb=" O SER S 106 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN S 112 " --> pdb=" O ALA S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 143 Processing helix chain 'S' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU S 159 " --> pdb=" O TRP S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU S 166 " --> pdb=" O PRO S 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL S 167 " --> pdb=" O GLU S 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE S 168 " --> pdb=" O SER S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 179 No H-bonds generated for 'chain 'S' and resid 177 through 179' Processing helix chain 'S' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE S 198 " --> pdb=" O PRO S 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN S 199 " --> pdb=" O GLU S 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 195 through 199' Processing helix chain 'S' and resid 201 through 205 removed outlier: 4.061A pdb=" N TRP S 204 " --> pdb=" O ASP S 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG S 205 " --> pdb=" O GLU S 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 201 through 205' Processing helix chain 'S' and resid 213 through 218 removed outlier: 3.664A pdb=" N ILE S 217 " --> pdb=" O ARG S 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU S 218 " --> pdb=" O PRO S 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 213 through 218' Processing helix chain 'S' and resid 223 through 227 Processing helix chain 'S' and resid 231 through 233 No H-bonds generated for 'chain 'S' and resid 231 through 233' Processing helix chain 'S' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL S 259 " --> pdb=" O TYR S 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU S 262 " --> pdb=" O ASN S 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU S 264 " --> pdb=" O MET S 260 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 291 Processing helix chain 'S' and resid 319 through 334 removed outlier: 3.623A pdb=" N ALA S 323 " --> pdb=" O ALA S 319 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU S 332 " --> pdb=" O ALA S 328 " (cutoff:3.500A) Processing helix chain 'S' and resid 335 through 337 No H-bonds generated for 'chain 'S' and resid 335 through 337' Processing helix chain 'U' and resid 8 through 13 Processing helix chain 'U' and resid 38 through 47 removed outlier: 3.734A pdb=" N ALA U 44 " --> pdb=" O GLN U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN U 60 " --> pdb=" O SER U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 68 Processing helix chain 'U' and resid 69 through 83 removed outlier: 3.631A pdb=" N GLU U 73 " --> pdb=" O GLY U 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS U 81 " --> pdb=" O THR U 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE U 82 " --> pdb=" O GLU U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 92 through 122 removed outlier: 3.914A pdb=" N LYS U 96 " --> pdb=" O ASN U 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL U 97 " --> pdb=" O ALA U 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA U 98 " --> pdb=" O LYS U 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER U 106 " --> pdb=" O PHE U 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER U 107 " --> pdb=" O GLU U 103 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET U 110 " --> pdb=" O SER U 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN U 112 " --> pdb=" O ALA U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 140 through 143 Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.677A pdb=" N LEU U 159 " --> pdb=" O TRP U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU U 166 " --> pdb=" O PRO U 162 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL U 167 " --> pdb=" O GLU U 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE U 168 " --> pdb=" O SER U 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 179 No H-bonds generated for 'chain 'U' and resid 177 through 179' Processing helix chain 'U' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE U 198 " --> pdb=" O PRO U 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN U 199 " --> pdb=" O GLU U 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 195 through 199' Processing helix chain 'U' and resid 201 through 205 removed outlier: 4.061A pdb=" N TRP U 204 " --> pdb=" O ASP U 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG U 205 " --> pdb=" O GLU U 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 201 through 205' Processing helix chain 'U' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE U 217 " --> pdb=" O ARG U 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU U 218 " --> pdb=" O PRO U 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 213 through 218' Processing helix chain 'U' and resid 223 through 227 Processing helix chain 'U' and resid 231 through 233 No H-bonds generated for 'chain 'U' and resid 231 through 233' Processing helix chain 'U' and resid 253 through 264 removed outlier: 3.700A pdb=" N VAL U 259 " --> pdb=" O TYR U 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU U 262 " --> pdb=" O ASN U 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU U 264 " --> pdb=" O MET U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 286 through 291 Processing helix chain 'U' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA U 323 " --> pdb=" O ALA U 319 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU U 332 " --> pdb=" O ALA U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 335 through 337 No H-bonds generated for 'chain 'U' and resid 335 through 337' Processing helix chain 'W' and resid 8 through 13 Processing helix chain 'W' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA W 44 " --> pdb=" O GLN W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 61 removed outlier: 3.762A pdb=" N ASN W 60 " --> pdb=" O SER W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 68 Processing helix chain 'W' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU W 73 " --> pdb=" O GLY W 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS W 81 " --> pdb=" O THR W 77 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE W 82 " --> pdb=" O GLU W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS W 96 " --> pdb=" O ASN W 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL W 97 " --> pdb=" O ALA W 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA W 98 " --> pdb=" O LYS W 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER W 106 " --> pdb=" O PHE W 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER W 107 " --> pdb=" O GLU W 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET W 110 " --> pdb=" O SER W 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN W 112 " --> pdb=" O ALA W 108 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 143 Processing helix chain 'W' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU W 159 " --> pdb=" O TRP W 156 " (cutoff:3.500A) Processing helix chain 'W' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU W 166 " --> pdb=" O PRO W 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL W 167 " --> pdb=" O GLU W 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 177 through 179 No H-bonds generated for 'chain 'W' and resid 177 through 179' Processing helix chain 'W' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE W 198 " --> pdb=" O PRO W 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN W 199 " --> pdb=" O GLU W 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 195 through 199' Processing helix chain 'W' and resid 201 through 205 removed outlier: 4.062A pdb=" N TRP W 204 " --> pdb=" O ASP W 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG W 205 " --> pdb=" O GLU W 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 201 through 205' Processing helix chain 'W' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE W 217 " --> pdb=" O ARG W 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU W 218 " --> pdb=" O PRO W 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 213 through 218' Processing helix chain 'W' and resid 223 through 227 Processing helix chain 'W' and resid 231 through 233 No H-bonds generated for 'chain 'W' and resid 231 through 233' Processing helix chain 'W' and resid 253 through 264 removed outlier: 3.698A pdb=" N VAL W 259 " --> pdb=" O TYR W 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU W 262 " --> pdb=" O ASN W 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU W 264 " --> pdb=" O MET W 260 " (cutoff:3.500A) Processing helix chain 'W' and resid 286 through 291 Processing helix chain 'W' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA W 323 " --> pdb=" O ALA W 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU W 332 " --> pdb=" O ALA W 328 " (cutoff:3.500A) Processing helix chain 'W' and resid 335 through 337 No H-bonds generated for 'chain 'W' and resid 335 through 337' Processing helix chain 'Y' and resid 8 through 13 Processing helix chain 'Y' and resid 38 through 47 removed outlier: 3.734A pdb=" N ALA Y 44 " --> pdb=" O GLN Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN Y 60 " --> pdb=" O SER Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 68 Processing helix chain 'Y' and resid 69 through 83 removed outlier: 3.631A pdb=" N GLU Y 73 " --> pdb=" O GLY Y 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS Y 81 " --> pdb=" O THR Y 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE Y 82 " --> pdb=" O GLU Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 92 through 122 removed outlier: 3.914A pdb=" N LYS Y 96 " --> pdb=" O ASN Y 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL Y 97 " --> pdb=" O ALA Y 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA Y 98 " --> pdb=" O LYS Y 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER Y 106 " --> pdb=" O PHE Y 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER Y 107 " --> pdb=" O GLU Y 103 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET Y 110 " --> pdb=" O SER Y 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN Y 112 " --> pdb=" O ALA Y 108 " (cutoff:3.500A) Processing helix chain 'Y' and resid 140 through 143 Processing helix chain 'Y' and resid 156 through 160 removed outlier: 3.677A pdb=" N LEU Y 159 " --> pdb=" O TRP Y 156 " (cutoff:3.500A) Processing helix chain 'Y' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU Y 166 " --> pdb=" O PRO Y 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL Y 167 " --> pdb=" O GLU Y 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE Y 168 " --> pdb=" O SER Y 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 179 No H-bonds generated for 'chain 'Y' and resid 177 through 179' Processing helix chain 'Y' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE Y 198 " --> pdb=" O PRO Y 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN Y 199 " --> pdb=" O GLU Y 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 195 through 199' Processing helix chain 'Y' and resid 201 through 205 removed outlier: 4.061A pdb=" N TRP Y 204 " --> pdb=" O ASP Y 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG Y 205 " --> pdb=" O GLU Y 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 201 through 205' Processing helix chain 'Y' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE Y 217 " --> pdb=" O ARG Y 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU Y 218 " --> pdb=" O PRO Y 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 213 through 218' Processing helix chain 'Y' and resid 223 through 227 Processing helix chain 'Y' and resid 231 through 233 No H-bonds generated for 'chain 'Y' and resid 231 through 233' Processing helix chain 'Y' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL Y 259 " --> pdb=" O TYR Y 255 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU Y 262 " --> pdb=" O ASN Y 258 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU Y 264 " --> pdb=" O MET Y 260 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 291 Processing helix chain 'Y' and resid 319 through 334 removed outlier: 3.623A pdb=" N ALA Y 323 " --> pdb=" O ALA Y 319 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU Y 332 " --> pdb=" O ALA Y 328 " (cutoff:3.500A) Processing helix chain 'Y' and resid 335 through 337 No H-bonds generated for 'chain 'Y' and resid 335 through 337' Processing helix chain '0' and resid 8 through 13 Processing helix chain '0' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA 0 44 " --> pdb=" O GLN 0 40 " (cutoff:3.500A) Processing helix chain '0' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN 0 60 " --> pdb=" O SER 0 56 " (cutoff:3.500A) Processing helix chain '0' and resid 63 through 68 Processing helix chain '0' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU 0 73 " --> pdb=" O GLY 0 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS 0 81 " --> pdb=" O THR 0 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE 0 82 " --> pdb=" O GLU 0 78 " (cutoff:3.500A) Processing helix chain '0' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS 0 96 " --> pdb=" O ASN 0 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL 0 97 " --> pdb=" O ALA 0 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA 0 98 " --> pdb=" O LYS 0 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER 0 106 " --> pdb=" O PHE 0 102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER 0 107 " --> pdb=" O GLU 0 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET 0 110 " --> pdb=" O SER 0 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN 0 112 " --> pdb=" O ALA 0 108 " (cutoff:3.500A) Processing helix chain '0' and resid 140 through 143 Processing helix chain '0' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU 0 159 " --> pdb=" O TRP 0 156 " (cutoff:3.500A) Processing helix chain '0' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU 0 166 " --> pdb=" O PRO 0 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL 0 167 " --> pdb=" O GLU 0 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE 0 168 " --> pdb=" O SER 0 164 " (cutoff:3.500A) Processing helix chain '0' and resid 177 through 179 No H-bonds generated for 'chain '0' and resid 177 through 179' Processing helix chain '0' and resid 195 through 199 removed outlier: 3.630A pdb=" N PHE 0 198 " --> pdb=" O PRO 0 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN 0 199 " --> pdb=" O GLU 0 196 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 195 through 199' Processing helix chain '0' and resid 201 through 205 removed outlier: 4.062A pdb=" N TRP 0 204 " --> pdb=" O ASP 0 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG 0 205 " --> pdb=" O GLU 0 202 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 201 through 205' Processing helix chain '0' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE 0 217 " --> pdb=" O ARG 0 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU 0 218 " --> pdb=" O PRO 0 214 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 213 through 218' Processing helix chain '0' and resid 223 through 227 Processing helix chain '0' and resid 231 through 233 No H-bonds generated for 'chain '0' and resid 231 through 233' Processing helix chain '0' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL 0 259 " --> pdb=" O TYR 0 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU 0 262 " --> pdb=" O ASN 0 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 0 264 " --> pdb=" O MET 0 260 " (cutoff:3.500A) Processing helix chain '0' and resid 286 through 291 Processing helix chain '0' and resid 319 through 334 removed outlier: 3.623A pdb=" N ALA 0 323 " --> pdb=" O ALA 0 319 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU 0 332 " --> pdb=" O ALA 0 328 " (cutoff:3.500A) Processing helix chain '0' and resid 335 through 337 No H-bonds generated for 'chain '0' and resid 335 through 337' Processing helix chain '2' and resid 8 through 13 Processing helix chain '2' and resid 38 through 47 removed outlier: 3.734A pdb=" N ALA 2 44 " --> pdb=" O GLN 2 40 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN 2 60 " --> pdb=" O SER 2 56 " (cutoff:3.500A) Processing helix chain '2' and resid 63 through 68 Processing helix chain '2' and resid 69 through 83 removed outlier: 3.631A pdb=" N GLU 2 73 " --> pdb=" O GLY 2 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS 2 81 " --> pdb=" O THR 2 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE 2 82 " --> pdb=" O GLU 2 78 " (cutoff:3.500A) Processing helix chain '2' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS 2 96 " --> pdb=" O ASN 2 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL 2 97 " --> pdb=" O ALA 2 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA 2 98 " --> pdb=" O LYS 2 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER 2 106 " --> pdb=" O PHE 2 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER 2 107 " --> pdb=" O GLU 2 103 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET 2 110 " --> pdb=" O SER 2 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN 2 112 " --> pdb=" O ALA 2 108 " (cutoff:3.500A) Processing helix chain '2' and resid 140 through 143 Processing helix chain '2' and resid 156 through 160 removed outlier: 3.677A pdb=" N LEU 2 159 " --> pdb=" O TRP 2 156 " (cutoff:3.500A) Processing helix chain '2' and resid 161 through 176 removed outlier: 3.673A pdb=" N GLU 2 166 " --> pdb=" O PRO 2 162 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL 2 167 " --> pdb=" O GLU 2 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE 2 168 " --> pdb=" O SER 2 164 " (cutoff:3.500A) Processing helix chain '2' and resid 177 through 179 No H-bonds generated for 'chain '2' and resid 177 through 179' Processing helix chain '2' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE 2 198 " --> pdb=" O PRO 2 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN 2 199 " --> pdb=" O GLU 2 196 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 195 through 199' Processing helix chain '2' and resid 201 through 205 removed outlier: 4.061A pdb=" N TRP 2 204 " --> pdb=" O ASP 2 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG 2 205 " --> pdb=" O GLU 2 202 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 201 through 205' Processing helix chain '2' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE 2 217 " --> pdb=" O ARG 2 213 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU 2 218 " --> pdb=" O PRO 2 214 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 213 through 218' Processing helix chain '2' and resid 223 through 227 Processing helix chain '2' and resid 231 through 233 No H-bonds generated for 'chain '2' and resid 231 through 233' Processing helix chain '2' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL 2 259 " --> pdb=" O TYR 2 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU 2 262 " --> pdb=" O ASN 2 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 2 264 " --> pdb=" O MET 2 260 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 291 Processing helix chain '2' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA 2 323 " --> pdb=" O ALA 2 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU 2 332 " --> pdb=" O ALA 2 328 " (cutoff:3.500A) Processing helix chain '2' and resid 335 through 337 No H-bonds generated for 'chain '2' and resid 335 through 337' Processing helix chain '4' and resid 8 through 13 Processing helix chain '4' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA 4 44 " --> pdb=" O GLN 4 40 " (cutoff:3.500A) Processing helix chain '4' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN 4 60 " --> pdb=" O SER 4 56 " (cutoff:3.500A) Processing helix chain '4' and resid 63 through 68 Processing helix chain '4' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU 4 73 " --> pdb=" O GLY 4 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS 4 81 " --> pdb=" O THR 4 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE 4 82 " --> pdb=" O GLU 4 78 " (cutoff:3.500A) Processing helix chain '4' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS 4 96 " --> pdb=" O ASN 4 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL 4 97 " --> pdb=" O ALA 4 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA 4 98 " --> pdb=" O LYS 4 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER 4 106 " --> pdb=" O PHE 4 102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER 4 107 " --> pdb=" O GLU 4 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET 4 110 " --> pdb=" O SER 4 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN 4 112 " --> pdb=" O ALA 4 108 " (cutoff:3.500A) Processing helix chain '4' and resid 140 through 143 Processing helix chain '4' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU 4 159 " --> pdb=" O TRP 4 156 " (cutoff:3.500A) Processing helix chain '4' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU 4 166 " --> pdb=" O PRO 4 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL 4 167 " --> pdb=" O GLU 4 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE 4 168 " --> pdb=" O SER 4 164 " (cutoff:3.500A) Processing helix chain '4' and resid 177 through 179 No H-bonds generated for 'chain '4' and resid 177 through 179' Processing helix chain '4' and resid 195 through 199 removed outlier: 3.630A pdb=" N PHE 4 198 " --> pdb=" O PRO 4 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN 4 199 " --> pdb=" O GLU 4 196 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 195 through 199' Processing helix chain '4' and resid 201 through 205 removed outlier: 4.062A pdb=" N TRP 4 204 " --> pdb=" O ASP 4 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG 4 205 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 201 through 205' Processing helix chain '4' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE 4 217 " --> pdb=" O ARG 4 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU 4 218 " --> pdb=" O PRO 4 214 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 213 through 218' Processing helix chain '4' and resid 223 through 227 Processing helix chain '4' and resid 231 through 233 No H-bonds generated for 'chain '4' and resid 231 through 233' Processing helix chain '4' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL 4 259 " --> pdb=" O TYR 4 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU 4 262 " --> pdb=" O ASN 4 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 4 264 " --> pdb=" O MET 4 260 " (cutoff:3.500A) Processing helix chain '4' and resid 286 through 291 Processing helix chain '4' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA 4 323 " --> pdb=" O ALA 4 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU 4 332 " --> pdb=" O ALA 4 328 " (cutoff:3.500A) Processing helix chain '4' and resid 335 through 337 No H-bonds generated for 'chain '4' and resid 335 through 337' Processing helix chain '6' and resid 8 through 13 Processing helix chain '6' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA 6 44 " --> pdb=" O GLN 6 40 " (cutoff:3.500A) Processing helix chain '6' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN 6 60 " --> pdb=" O SER 6 56 " (cutoff:3.500A) Processing helix chain '6' and resid 63 through 68 Processing helix chain '6' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU 6 73 " --> pdb=" O GLY 6 69 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS 6 81 " --> pdb=" O THR 6 77 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE 6 82 " --> pdb=" O GLU 6 78 " (cutoff:3.500A) Processing helix chain '6' and resid 92 through 122 removed outlier: 3.914A pdb=" N LYS 6 96 " --> pdb=" O ASN 6 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL 6 97 " --> pdb=" O ALA 6 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA 6 98 " --> pdb=" O LYS 6 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER 6 106 " --> pdb=" O PHE 6 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER 6 107 " --> pdb=" O GLU 6 103 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET 6 110 " --> pdb=" O SER 6 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN 6 112 " --> pdb=" O ALA 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 140 through 143 Processing helix chain '6' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU 6 159 " --> pdb=" O TRP 6 156 " (cutoff:3.500A) Processing helix chain '6' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU 6 166 " --> pdb=" O PRO 6 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL 6 167 " --> pdb=" O GLU 6 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE 6 168 " --> pdb=" O SER 6 164 " (cutoff:3.500A) Processing helix chain '6' and resid 177 through 179 No H-bonds generated for 'chain '6' and resid 177 through 179' Processing helix chain '6' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE 6 198 " --> pdb=" O PRO 6 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN 6 199 " --> pdb=" O GLU 6 196 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 195 through 199' Processing helix chain '6' and resid 201 through 205 removed outlier: 4.062A pdb=" N TRP 6 204 " --> pdb=" O ASP 6 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG 6 205 " --> pdb=" O GLU 6 202 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 201 through 205' Processing helix chain '6' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE 6 217 " --> pdb=" O ARG 6 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU 6 218 " --> pdb=" O PRO 6 214 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 213 through 218' Processing helix chain '6' and resid 223 through 227 Processing helix chain '6' and resid 231 through 233 No H-bonds generated for 'chain '6' and resid 231 through 233' Processing helix chain '6' and resid 253 through 264 removed outlier: 3.700A pdb=" N VAL 6 259 " --> pdb=" O TYR 6 255 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU 6 262 " --> pdb=" O ASN 6 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 6 264 " --> pdb=" O MET 6 260 " (cutoff:3.500A) Processing helix chain '6' and resid 286 through 291 Processing helix chain '6' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA 6 323 " --> pdb=" O ALA 6 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU 6 332 " --> pdb=" O ALA 6 328 " (cutoff:3.500A) Processing helix chain '6' and resid 335 through 337 No H-bonds generated for 'chain '6' and resid 335 through 337' Processing helix chain '8' and resid 8 through 13 Processing helix chain '8' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA 8 44 " --> pdb=" O GLN 8 40 " (cutoff:3.500A) Processing helix chain '8' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN 8 60 " --> pdb=" O SER 8 56 " (cutoff:3.500A) Processing helix chain '8' and resid 63 through 68 Processing helix chain '8' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU 8 73 " --> pdb=" O GLY 8 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS 8 81 " --> pdb=" O THR 8 77 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE 8 82 " --> pdb=" O GLU 8 78 " (cutoff:3.500A) Processing helix chain '8' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS 8 96 " --> pdb=" O ASN 8 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL 8 97 " --> pdb=" O ALA 8 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA 8 98 " --> pdb=" O LYS 8 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER 8 106 " --> pdb=" O PHE 8 102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER 8 107 " --> pdb=" O GLU 8 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET 8 110 " --> pdb=" O SER 8 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN 8 112 " --> pdb=" O ALA 8 108 " (cutoff:3.500A) Processing helix chain '8' and resid 140 through 143 Processing helix chain '8' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU 8 159 " --> pdb=" O TRP 8 156 " (cutoff:3.500A) Processing helix chain '8' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU 8 166 " --> pdb=" O PRO 8 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL 8 167 " --> pdb=" O GLU 8 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE 8 168 " --> pdb=" O SER 8 164 " (cutoff:3.500A) Processing helix chain '8' and resid 177 through 179 No H-bonds generated for 'chain '8' and resid 177 through 179' Processing helix chain '8' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE 8 198 " --> pdb=" O PRO 8 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN 8 199 " --> pdb=" O GLU 8 196 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 195 through 199' Processing helix chain '8' and resid 201 through 205 removed outlier: 4.061A pdb=" N TRP 8 204 " --> pdb=" O ASP 8 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG 8 205 " --> pdb=" O GLU 8 202 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 201 through 205' Processing helix chain '8' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE 8 217 " --> pdb=" O ARG 8 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU 8 218 " --> pdb=" O PRO 8 214 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 213 through 218' Processing helix chain '8' and resid 223 through 227 Processing helix chain '8' and resid 231 through 233 No H-bonds generated for 'chain '8' and resid 231 through 233' Processing helix chain '8' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL 8 259 " --> pdb=" O TYR 8 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU 8 262 " --> pdb=" O ASN 8 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 8 264 " --> pdb=" O MET 8 260 " (cutoff:3.500A) Processing helix chain '8' and resid 286 through 291 Processing helix chain '8' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA 8 323 " --> pdb=" O ALA 8 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU 8 332 " --> pdb=" O ALA 8 328 " (cutoff:3.500A) Processing helix chain '8' and resid 335 through 337 No H-bonds generated for 'chain '8' and resid 335 through 337' Processing helix chain 'a' and resid 8 through 13 Processing helix chain 'a' and resid 38 through 47 removed outlier: 3.734A pdb=" N ALA a 44 " --> pdb=" O GLN a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN a 60 " --> pdb=" O SER a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 68 Processing helix chain 'a' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU a 73 " --> pdb=" O GLY a 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS a 81 " --> pdb=" O THR a 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS a 96 " --> pdb=" O ASN a 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL a 97 " --> pdb=" O ALA a 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA a 98 " --> pdb=" O LYS a 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER a 106 " --> pdb=" O PHE a 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER a 107 " --> pdb=" O GLU a 103 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET a 110 " --> pdb=" O SER a 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN a 112 " --> pdb=" O ALA a 108 " (cutoff:3.500A) Processing helix chain 'a' and resid 140 through 143 Processing helix chain 'a' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU a 159 " --> pdb=" O TRP a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 176 removed outlier: 3.673A pdb=" N GLU a 166 " --> pdb=" O PRO a 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL a 167 " --> pdb=" O GLU a 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE a 168 " --> pdb=" O SER a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 177 through 179 No H-bonds generated for 'chain 'a' and resid 177 through 179' Processing helix chain 'a' and resid 195 through 199 removed outlier: 3.629A pdb=" N PHE a 198 " --> pdb=" O PRO a 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN a 199 " --> pdb=" O GLU a 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 195 through 199' Processing helix chain 'a' and resid 201 through 205 removed outlier: 4.061A pdb=" N TRP a 204 " --> pdb=" O ASP a 201 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG a 205 " --> pdb=" O GLU a 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 201 through 205' Processing helix chain 'a' and resid 213 through 218 removed outlier: 3.663A pdb=" N ILE a 217 " --> pdb=" O ARG a 213 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU a 218 " --> pdb=" O PRO a 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 213 through 218' Processing helix chain 'a' and resid 223 through 227 Processing helix chain 'a' and resid 231 through 233 No H-bonds generated for 'chain 'a' and resid 231 through 233' Processing helix chain 'a' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL a 259 " --> pdb=" O TYR a 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU a 262 " --> pdb=" O ASN a 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU a 264 " --> pdb=" O MET a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 286 through 291 Processing helix chain 'a' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA a 323 " --> pdb=" O ALA a 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU a 332 " --> pdb=" O ALA a 328 " (cutoff:3.500A) Processing helix chain 'a' and resid 335 through 337 No H-bonds generated for 'chain 'a' and resid 335 through 337' Processing helix chain 'c' and resid 8 through 13 Processing helix chain 'c' and resid 38 through 47 removed outlier: 3.733A pdb=" N ALA c 44 " --> pdb=" O GLN c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 56 through 61 removed outlier: 3.761A pdb=" N ASN c 60 " --> pdb=" O SER c 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 63 through 68 Processing helix chain 'c' and resid 69 through 83 removed outlier: 3.630A pdb=" N GLU c 73 " --> pdb=" O GLY c 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS c 81 " --> pdb=" O THR c 77 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE c 82 " --> pdb=" O GLU c 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 92 through 122 removed outlier: 3.913A pdb=" N LYS c 96 " --> pdb=" O ASN c 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL c 97 " --> pdb=" O ALA c 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA c 98 " --> pdb=" O LYS c 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER c 106 " --> pdb=" O PHE c 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER c 107 " --> pdb=" O GLU c 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET c 110 " --> pdb=" O SER c 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN c 112 " --> pdb=" O ALA c 108 " (cutoff:3.500A) Processing helix chain 'c' and resid 140 through 143 Processing helix chain 'c' and resid 156 through 160 removed outlier: 3.676A pdb=" N LEU c 159 " --> pdb=" O TRP c 156 " (cutoff:3.500A) Processing helix chain 'c' and resid 161 through 176 removed outlier: 3.672A pdb=" N GLU c 166 " --> pdb=" O PRO c 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL c 167 " --> pdb=" O GLU c 163 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE c 168 " --> pdb=" O SER c 164 " (cutoff:3.500A) Processing helix chain 'c' and resid 177 through 179 No H-bonds generated for 'chain 'c' and resid 177 through 179' Processing helix chain 'c' and resid 195 through 199 removed outlier: 3.628A pdb=" N PHE c 198 " --> pdb=" O PRO c 195 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN c 199 " --> pdb=" O GLU c 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 195 through 199' Processing helix chain 'c' and resid 201 through 205 removed outlier: 4.062A pdb=" N TRP c 204 " --> pdb=" O ASP c 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG c 205 " --> pdb=" O GLU c 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 201 through 205' Processing helix chain 'c' and resid 213 through 218 removed outlier: 3.664A pdb=" N ILE c 217 " --> pdb=" O ARG c 213 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU c 218 " --> pdb=" O PRO c 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 213 through 218' Processing helix chain 'c' and resid 223 through 227 Processing helix chain 'c' and resid 231 through 233 No H-bonds generated for 'chain 'c' and resid 231 through 233' Processing helix chain 'c' and resid 253 through 264 removed outlier: 3.699A pdb=" N VAL c 259 " --> pdb=" O TYR c 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU c 262 " --> pdb=" O ASN c 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU c 264 " --> pdb=" O MET c 260 " (cutoff:3.500A) Processing helix chain 'c' and resid 286 through 291 Processing helix chain 'c' and resid 319 through 334 removed outlier: 3.624A pdb=" N ALA c 323 " --> pdb=" O ALA c 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU c 332 " --> pdb=" O ALA c 328 " (cutoff:3.500A) Processing helix chain 'c' and resid 335 through 337 No H-bonds generated for 'chain 'c' and resid 335 through 337' Processing sheet with id= 1, first strand: chain 'A' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN A 21 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 36 " --> pdb=" O GLN A 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'A' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL A 193 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE A 235 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 274 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR A 314 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 277 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN B 21 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 36 " --> pdb=" O GLN B 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'B' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL B 193 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE B 235 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 274 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR B 314 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN E 21 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN E 36 " --> pdb=" O GLN E 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'E' and resid 145 through 149 removed outlier: 7.182A pdb=" N VAL E 193 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE E 235 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 274 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR E 314 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL E 277 " --> pdb=" O TYR E 314 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'G' and resid 20 through 22 removed outlier: 3.835A pdb=" N GLN G 21 " --> pdb=" O GLN G 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN G 36 " --> pdb=" O GLN G 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'G' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL G 193 " --> pdb=" O ILE G 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE G 235 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU G 274 " --> pdb=" O SER G 236 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N TYR G 314 " --> pdb=" O PHE G 275 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL G 277 " --> pdb=" O TYR G 314 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'I' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN I 21 " --> pdb=" O GLN I 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN I 36 " --> pdb=" O GLN I 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'I' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL I 193 " --> pdb=" O ILE I 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE I 235 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU I 274 " --> pdb=" O SER I 236 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N TYR I 314 " --> pdb=" O PHE I 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL I 277 " --> pdb=" O TYR I 314 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'K' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN K 21 " --> pdb=" O GLN K 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN K 36 " --> pdb=" O GLN K 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'K' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL K 193 " --> pdb=" O ILE K 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE K 235 " --> pdb=" O VAL K 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU K 274 " --> pdb=" O SER K 236 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N TYR K 314 " --> pdb=" O PHE K 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL K 277 " --> pdb=" O TYR K 314 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'M' and resid 20 through 22 removed outlier: 3.835A pdb=" N GLN M 21 " --> pdb=" O GLN M 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN M 36 " --> pdb=" O GLN M 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'M' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL M 193 " --> pdb=" O ILE M 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE M 235 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU M 274 " --> pdb=" O SER M 236 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR M 314 " --> pdb=" O PHE M 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL M 277 " --> pdb=" O TYR M 314 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'O' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN O 21 " --> pdb=" O GLN O 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN O 36 " --> pdb=" O GLN O 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 15 Processing sheet with id= 16, first strand: chain 'O' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL O 193 " --> pdb=" O ILE O 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE O 235 " --> pdb=" O VAL O 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU O 274 " --> pdb=" O SER O 236 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR O 314 " --> pdb=" O PHE O 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL O 277 " --> pdb=" O TYR O 314 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'Q' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN Q 21 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN Q 36 " --> pdb=" O GLN Q 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'Q' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL Q 193 " --> pdb=" O ILE Q 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE Q 235 " --> pdb=" O VAL Q 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU Q 274 " --> pdb=" O SER Q 236 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR Q 314 " --> pdb=" O PHE Q 275 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL Q 277 " --> pdb=" O TYR Q 314 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'S' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN S 21 " --> pdb=" O GLN S 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN S 36 " --> pdb=" O GLN S 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 'S' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL S 193 " --> pdb=" O ILE S 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE S 235 " --> pdb=" O VAL S 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU S 274 " --> pdb=" O SER S 236 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N TYR S 314 " --> pdb=" O PHE S 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL S 277 " --> pdb=" O TYR S 314 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'U' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN U 21 " --> pdb=" O GLN U 36 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN U 36 " --> pdb=" O GLN U 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'U' and resid 145 through 149 removed outlier: 7.182A pdb=" N VAL U 193 " --> pdb=" O ILE U 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE U 235 " --> pdb=" O VAL U 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU U 274 " --> pdb=" O SER U 236 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR U 314 " --> pdb=" O PHE U 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL U 277 " --> pdb=" O TYR U 314 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'W' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN W 21 " --> pdb=" O GLN W 36 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN W 36 " --> pdb=" O GLN W 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'W' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL W 193 " --> pdb=" O ILE W 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE W 235 " --> pdb=" O VAL W 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU W 274 " --> pdb=" O SER W 236 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N TYR W 314 " --> pdb=" O PHE W 275 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL W 277 " --> pdb=" O TYR W 314 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Y' and resid 20 through 22 removed outlier: 3.835A pdb=" N GLN Y 21 " --> pdb=" O GLN Y 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN Y 36 " --> pdb=" O GLN Y 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain 'Y' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL Y 193 " --> pdb=" O ILE Y 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE Y 235 " --> pdb=" O VAL Y 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU Y 274 " --> pdb=" O SER Y 236 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N TYR Y 314 " --> pdb=" O PHE Y 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL Y 277 " --> pdb=" O TYR Y 314 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '0' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN 0 21 " --> pdb=" O GLN 0 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN 0 36 " --> pdb=" O GLN 0 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain '0' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL 0 193 " --> pdb=" O ILE 0 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE 0 235 " --> pdb=" O VAL 0 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU 0 274 " --> pdb=" O SER 0 236 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR 0 314 " --> pdb=" O PHE 0 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL 0 277 " --> pdb=" O TYR 0 314 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '2' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN 2 21 " --> pdb=" O GLN 2 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN 2 36 " --> pdb=" O GLN 2 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 29 Processing sheet with id= 30, first strand: chain '2' and resid 145 through 149 removed outlier: 7.182A pdb=" N VAL 2 193 " --> pdb=" O ILE 2 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE 2 235 " --> pdb=" O VAL 2 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU 2 274 " --> pdb=" O SER 2 236 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N TYR 2 314 " --> pdb=" O PHE 2 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL 2 277 " --> pdb=" O TYR 2 314 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '4' and resid 20 through 22 removed outlier: 3.835A pdb=" N GLN 4 21 " --> pdb=" O GLN 4 36 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN 4 36 " --> pdb=" O GLN 4 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 31 Processing sheet with id= 32, first strand: chain '4' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL 4 193 " --> pdb=" O ILE 4 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE 4 235 " --> pdb=" O VAL 4 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU 4 274 " --> pdb=" O SER 4 236 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR 4 314 " --> pdb=" O PHE 4 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL 4 277 " --> pdb=" O TYR 4 314 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '6' and resid 20 through 22 removed outlier: 3.835A pdb=" N GLN 6 21 " --> pdb=" O GLN 6 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN 6 36 " --> pdb=" O GLN 6 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 33 Processing sheet with id= 34, first strand: chain '6' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL 6 193 " --> pdb=" O ILE 6 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE 6 235 " --> pdb=" O VAL 6 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU 6 274 " --> pdb=" O SER 6 236 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N TYR 6 314 " --> pdb=" O PHE 6 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL 6 277 " --> pdb=" O TYR 6 314 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '8' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN 8 21 " --> pdb=" O GLN 8 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN 8 36 " --> pdb=" O GLN 8 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain '8' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL 8 193 " --> pdb=" O ILE 8 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE 8 235 " --> pdb=" O VAL 8 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU 8 274 " --> pdb=" O SER 8 236 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR 8 314 " --> pdb=" O PHE 8 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL 8 277 " --> pdb=" O TYR 8 314 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'a' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN a 21 " --> pdb=" O GLN a 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN a 36 " --> pdb=" O GLN a 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'a' and resid 145 through 149 removed outlier: 7.182A pdb=" N VAL a 193 " --> pdb=" O ILE a 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE a 235 " --> pdb=" O VAL a 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU a 274 " --> pdb=" O SER a 236 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR a 314 " --> pdb=" O PHE a 275 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL a 277 " --> pdb=" O TYR a 314 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'c' and resid 20 through 22 removed outlier: 3.834A pdb=" N GLN c 21 " --> pdb=" O GLN c 36 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN c 36 " --> pdb=" O GLN c 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'c' and resid 145 through 149 removed outlier: 7.181A pdb=" N VAL c 193 " --> pdb=" O ILE c 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE c 235 " --> pdb=" O VAL c 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU c 274 " --> pdb=" O SER c 236 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR c 314 " --> pdb=" O PHE c 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL c 277 " --> pdb=" O TYR c 314 " (cutoff:3.500A) 1600 hydrogen bonds defined for protein. 4500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 500 hydrogen bonds 920 hydrogen bond angles 0 basepair planarities 200 basepair parallelities 480 stacking parallelities Total time for adding SS restraints: 23.32 Time building geometry restraints manager: 23.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15546 1.33 - 1.45: 15461 1.45 - 1.57: 34173 1.57 - 1.69: 980 1.69 - 1.81: 320 Bond restraints: 66480 Sorted by residual: bond pdb=" N ARG 8 152 " pdb=" CA ARG 8 152 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.28e-02 6.10e+03 4.96e+00 bond pdb=" N ARG O 152 " pdb=" CA ARG O 152 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.28e-02 6.10e+03 4.95e+00 bond pdb=" N ARG K 152 " pdb=" CA ARG K 152 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.28e-02 6.10e+03 4.95e+00 bond pdb=" N ARG c 152 " pdb=" CA ARG c 152 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.28e-02 6.10e+03 4.95e+00 bond pdb=" N ARG B 152 " pdb=" CA ARG B 152 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.28e-02 6.10e+03 4.92e+00 ... (remaining 66475 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.71: 5018 106.71 - 113.57: 35037 113.57 - 120.42: 27638 120.42 - 127.27: 23224 127.27 - 134.12: 1443 Bond angle restraints: 92360 Sorted by residual: angle pdb=" C ASP Y 155 " pdb=" N TRP Y 156 " pdb=" CA TRP Y 156 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C ARG c 84 " pdb=" N ASP c 85 " pdb=" CA ASP c 85 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C ASP U 155 " pdb=" N TRP U 156 " pdb=" CA TRP U 156 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C ASP I 155 " pdb=" N TRP I 156 " pdb=" CA TRP I 156 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C ASP S 155 " pdb=" N TRP S 156 " pdb=" CA TRP S 156 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 ... (remaining 92355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 31262 17.09 - 34.18: 4557 34.18 - 51.27: 1905 51.27 - 68.37: 696 68.37 - 85.46: 60 Dihedral angle restraints: 38480 sinusoidal: 18900 harmonic: 19580 Sorted by residual: dihedral pdb=" CA GLN 4 129 " pdb=" C GLN 4 129 " pdb=" N PRO 4 130 " pdb=" CA PRO 4 130 " ideal model delta harmonic sigma weight residual 180.00 155.39 24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLN 0 129 " pdb=" C GLN 0 129 " pdb=" N PRO 0 130 " pdb=" CA PRO 0 130 " ideal model delta harmonic sigma weight residual 180.00 155.39 24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLN G 129 " pdb=" C GLN G 129 " pdb=" N PRO G 130 " pdb=" CA PRO G 130 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 38477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 6554 0.040 - 0.080: 2613 0.080 - 0.120: 735 0.120 - 0.160: 178 0.160 - 0.200: 80 Chirality restraints: 10160 Sorted by residual: chirality pdb=" CB VAL Y 145 " pdb=" CA VAL Y 145 " pdb=" CG1 VAL Y 145 " pdb=" CG2 VAL Y 145 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB VAL Q 145 " pdb=" CA VAL Q 145 " pdb=" CG1 VAL Q 145 " pdb=" CG2 VAL Q 145 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CB VAL A 145 " pdb=" CA VAL A 145 " pdb=" CG1 VAL A 145 " pdb=" CG2 VAL A 145 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.94e-01 ... (remaining 10157 not shown) Planarity restraints: 10360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 213 " -0.052 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO G 214 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO G 214 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 214 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 213 " -0.052 5.00e-02 4.00e+02 7.86e-02 9.87e+00 pdb=" N PRO K 214 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO K 214 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO K 214 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG W 213 " -0.052 5.00e-02 4.00e+02 7.85e-02 9.85e+00 pdb=" N PRO W 214 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO W 214 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO W 214 " -0.044 5.00e-02 4.00e+02 ... (remaining 10357 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 63 2.30 - 2.95: 26756 2.95 - 3.60: 91233 3.60 - 4.25: 157701 4.25 - 4.90: 252704 Nonbonded interactions: 528457 Sorted by model distance: nonbonded pdb=" NH1 ARG G 29 " pdb=" O GLY K 61 " model vdw 1.646 2.520 nonbonded pdb=" NH1 ARG O 29 " pdb=" O GLY S 61 " model vdw 1.646 2.520 nonbonded pdb=" NH1 ARG B 29 " pdb=" O GLY O 61 " model vdw 1.646 2.520 nonbonded pdb=" NH1 ARG 0 29 " pdb=" O GLY 4 61 " model vdw 1.646 2.520 nonbonded pdb=" O GLY B 61 " pdb=" NH1 ARG K 29 " model vdw 1.646 2.520 ... (remaining 528452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.050 Extract box with map and model: 6.070 Check model and map are aligned: 0.690 Set scattering table: 0.430 Process input model: 142.000 Find NCS groups from input model: 3.570 Set up NCS constraints: 0.650 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: 0.020 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 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 : 0.005 0.069 66480 Z= 0.318 Angle : 0.755 6.737 92360 Z= 0.434 Chirality : 0.049 0.200 10160 Planarity : 0.008 0.079 10360 Dihedral : 19.632 85.456 25840 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 1.42 % Allowed : 6.03 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.07), residues: 6720 helix: -4.27 (0.04), residues: 2720 sheet: -2.07 (0.15), residues: 640 loop : -2.67 (0.09), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP a 156 HIS 0.002 0.001 HIS 4 278 PHE 0.009 0.001 PHE Q 35 TYR 0.015 0.002 TYR 4 5 ARG 0.004 0.000 ARG O 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1211 time to evaluate : 4.790 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TRP G 126 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP S 126 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP 8 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 131 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.6619 (tpt90) REVERT: A 177 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8523 (mtmt) REVERT: A 203 MET cc_start: 0.8746 (ptm) cc_final: 0.8498 (ptm) REVERT: A 272 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7739 (ttpp) REVERT: B 142 ARG cc_start: 0.7449 (ptt180) cc_final: 0.7198 (mtm110) REVERT: B 203 MET cc_start: 0.8519 (ptm) cc_final: 0.8270 (ptp) REVERT: B 334 MET cc_start: 0.7138 (mmm) cc_final: 0.6889 (mmm) REVERT: E 4 THR cc_start: 0.7106 (p) cc_final: 0.6738 (p) REVERT: E 41 ASN cc_start: 0.6850 (m-40) cc_final: 0.6425 (t0) REVERT: G 63 ASP cc_start: 0.6872 (t0) cc_final: 0.5739 (p0) REVERT: G 66 ASP cc_start: 0.5254 (t0) cc_final: 0.4979 (t0) REVERT: G 159 LEU cc_start: 0.8566 (mt) cc_final: 0.8035 (pp) REVERT: I 121 MET cc_start: 0.8090 (mmp) cc_final: 0.7858 (mmt) REVERT: I 131 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6509 (tpt170) REVERT: I 138 SER cc_start: 0.7210 (OUTLIER) cc_final: 0.6935 (p) REVERT: K 168 ILE cc_start: 0.7749 (mm) cc_final: 0.6935 (mm) REVERT: M 157 VAL cc_start: 0.8076 (t) cc_final: 0.7828 (t) REVERT: M 200 ASN cc_start: 0.7219 (OUTLIER) cc_final: 0.6826 (t0) REVERT: M 260 MET cc_start: 0.7977 (ttm) cc_final: 0.7664 (mtp) REVERT: O 131 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6290 (mtp180) REVERT: O 147 VAL cc_start: 0.7592 (p) cc_final: 0.7269 (t) REVERT: O 321 ASP cc_start: 0.7664 (t70) cc_final: 0.6989 (t70) REVERT: O 334 MET cc_start: 0.7199 (mmm) cc_final: 0.6861 (mmp) REVERT: Q 4 THR cc_start: 0.7040 (p) cc_final: 0.6767 (p) REVERT: Q 41 ASN cc_start: 0.7046 (m-40) cc_final: 0.6628 (t0) REVERT: Q 63 ASP cc_start: 0.4407 (t0) cc_final: 0.4108 (t0) REVERT: S 30 ASN cc_start: 0.7056 (m110) cc_final: 0.6665 (m-40) REVERT: S 63 ASP cc_start: 0.6633 (t0) cc_final: 0.5780 (p0) REVERT: S 66 ASP cc_start: 0.5263 (t0) cc_final: 0.4936 (t0) REVERT: S 131 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6249 (ttt180) REVERT: U 131 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6758 (tpt170) REVERT: U 168 ILE cc_start: 0.7076 (mm) cc_final: 0.6371 (mm) REVERT: W 47 PHE cc_start: 0.6980 (m-80) cc_final: 0.6523 (m-80) REVERT: Y 131 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6684 (tpt90) REVERT: Y 138 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8416 (p) REVERT: Y 142 ARG cc_start: 0.7784 (ptt180) cc_final: 0.7576 (ptp90) REVERT: Y 272 LYS cc_start: 0.7817 (mtpt) cc_final: 0.7466 (ttpp) REVERT: 0 200 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7417 (t0) REVERT: 0 203 MET cc_start: 0.8659 (ptm) cc_final: 0.8419 (ptp) REVERT: 0 272 LYS cc_start: 0.7943 (mtpt) cc_final: 0.7464 (ttmm) REVERT: 2 131 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7299 (ttt-90) REVERT: 4 326 PHE cc_start: 0.8314 (t80) cc_final: 0.8057 (t80) REVERT: 6 4 THR cc_start: 0.7082 (p) cc_final: 0.6868 (p) REVERT: 6 63 ASP cc_start: 0.3478 (t0) cc_final: 0.3010 (t0) REVERT: 6 203 MET cc_start: 0.8194 (ptm) cc_final: 0.7949 (ptm) REVERT: 8 131 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.5198 (tpt170) REVERT: a 4 THR cc_start: 0.7118 (p) cc_final: 0.6739 (p) REVERT: a 138 SER cc_start: 0.7216 (OUTLIER) cc_final: 0.6956 (p) REVERT: a 168 ILE cc_start: 0.6961 (mm) cc_final: 0.5934 (mm) REVERT: c 138 SER cc_start: 0.6648 (OUTLIER) cc_final: 0.6258 (p) REVERT: c 227 GLN cc_start: 0.7361 (tt0) cc_final: 0.7040 (mt0) REVERT: c 262 LEU cc_start: 0.7418 (tt) cc_final: 0.7200 (tt) REVERT: c 321 ASP cc_start: 0.6611 (t70) cc_final: 0.6387 (t0) outliers start: 80 outliers final: 12 residues processed: 1279 average time/residue: 0.6545 time to fit residues: 1364.1081 Evaluate side-chains 662 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 636 time to evaluate : 4.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain I residue 131 ARG Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 200 ASN Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 138 SER Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain U residue 131 ARG Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain Y residue 131 ARG Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain 0 residue 138 SER Chi-restraints excluded: chain 0 residue 200 ASN Chi-restraints excluded: chain 2 residue 131 ARG Chi-restraints excluded: chain 2 residue 138 SER Chi-restraints excluded: chain 4 residue 138 SER Chi-restraints excluded: chain 6 residue 138 SER Chi-restraints excluded: chain 8 residue 131 ARG Chi-restraints excluded: chain 8 residue 138 SER Chi-restraints excluded: chain a residue 138 SER Chi-restraints excluded: chain c residue 138 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 591 optimal weight: 10.0000 chunk 530 optimal weight: 9.9990 chunk 294 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 357 optimal weight: 0.9980 chunk 283 optimal weight: 5.9990 chunk 548 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 333 optimal weight: 8.9990 chunk 408 optimal weight: 5.9990 chunk 635 optimal weight: 0.0050 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 30 ASN A 258 ASN A 278 HIS B 21 GLN B 30 ASN B 258 ASN B 278 HIS B 331 ASN E 21 GLN E 30 ASN E 40 GLN E 258 ASN E 331 ASN G 21 GLN G 25 ASN G 30 ASN G 74 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 ASN G 331 ASN I 21 GLN I 30 ASN I 331 ASN K 21 GLN K 30 ASN K 258 ASN K 331 ASN M 21 GLN M 30 ASN ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 ASN O 21 GLN O 30 ASN ** O 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 258 ASN O 278 HIS O 331 ASN Q 21 GLN Q 30 ASN Q 40 GLN Q 331 ASN S 21 GLN S 25 ASN S 30 ASN S 92 ASN ** S 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 258 ASN S 331 ASN U 21 GLN U 30 ASN U 165 GLN U 258 ASN U 331 ASN W 21 GLN W 30 ASN W 81 HIS W 227 GLN W 258 ASN W 278 HIS W 331 ASN Y 21 GLN Y 30 ASN Y 258 ASN Y 278 HIS Y 331 ASN 0 21 GLN 0 30 ASN 0 258 ASN 0 278 HIS 0 331 ASN 2 21 GLN 2 30 ASN ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 258 ASN 4 21 GLN 4 30 ASN 4 258 ASN 4 278 HIS 4 331 ASN 6 21 GLN 6 30 ASN ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 21 GLN 8 25 ASN 8 92 ASN ** 8 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 258 ASN ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 GLN a 30 ASN a 40 GLN a 165 GLN a 258 ASN a 278 HIS a 331 ASN c 21 GLN c 30 ASN c 258 ASN c 331 ASN Total number of N/Q/H flips: 92 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 66480 Z= 0.296 Angle : 0.690 10.975 92360 Z= 0.371 Chirality : 0.045 0.199 10160 Planarity : 0.007 0.069 10360 Dihedral : 22.695 75.390 13072 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.59 % Favored : 92.26 % Rotamer: Outliers : 2.96 % Allowed : 13.97 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.09), residues: 6720 helix: -2.51 (0.08), residues: 2680 sheet: -2.01 (0.16), residues: 600 loop : -2.10 (0.10), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP O 156 HIS 0.006 0.001 HIS W 81 PHE 0.020 0.002 PHE 8 87 TYR 0.023 0.002 TYR E 64 ARG 0.010 0.001 ARG E 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 564 time to evaluate : 4.861 Fit side-chains TARDY: cannot create tardy model for: "TRP G 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8502 (mtmt) REVERT: B 142 ARG cc_start: 0.7545 (ptt180) cc_final: 0.7333 (mtm110) REVERT: B 203 MET cc_start: 0.8540 (ptm) cc_final: 0.8117 (ptm) REVERT: B 231 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8155 (mm-40) REVERT: E 219 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7773 (mp) REVERT: E 334 MET cc_start: 0.6777 (mmp) cc_final: 0.6497 (mmp) REVERT: E 336 LEU cc_start: 0.8503 (mm) cc_final: 0.8143 (mt) REVERT: G 203 MET cc_start: 0.6699 (ptt) cc_final: 0.6408 (ptp) REVERT: I 138 SER cc_start: 0.8352 (OUTLIER) cc_final: 0.8144 (p) REVERT: K 203 MET cc_start: 0.8127 (ptm) cc_final: 0.7897 (ptm) REVERT: K 262 LEU cc_start: 0.8193 (tp) cc_final: 0.7960 (tt) REVERT: K 272 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7072 (mtpt) REVERT: M 129 GLN cc_start: 0.8908 (tp40) cc_final: 0.8670 (tp-100) REVERT: M 200 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7481 (t0) REVERT: O 321 ASP cc_start: 0.7884 (t70) cc_final: 0.7683 (t70) REVERT: S 25 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7474 (t0) REVERT: S 63 ASP cc_start: 0.8364 (t0) cc_final: 0.8153 (t0) REVERT: W 333 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7412 (tpt90) REVERT: Y 177 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8564 (mtmt) REVERT: Y 203 MET cc_start: 0.8643 (ptm) cc_final: 0.8381 (ptm) REVERT: Y 272 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7765 (ttpp) REVERT: 0 28 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.8047 (m) REVERT: 0 203 MET cc_start: 0.8556 (ptm) cc_final: 0.8041 (ptm) REVERT: 0 297 TYR cc_start: 0.6716 (t80) cc_final: 0.6114 (t80) REVERT: 2 129 GLN cc_start: 0.8910 (tp40) cc_final: 0.8652 (tp-100) REVERT: 4 237 LEU cc_start: 0.8619 (tp) cc_final: 0.8287 (tp) REVERT: 4 260 MET cc_start: 0.8316 (mmm) cc_final: 0.7907 (mmm) REVERT: 8 25 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7865 (t0) REVERT: 8 30 ASN cc_start: 0.7399 (m-40) cc_final: 0.7131 (m-40) REVERT: 8 231 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6522 (mm-40) REVERT: 8 242 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8235 (mttm) REVERT: a 121 MET cc_start: 0.7850 (mmp) cc_final: 0.7512 (mmp) REVERT: a 267 LYS cc_start: 0.8017 (mmtp) cc_final: 0.7797 (mmtm) REVERT: c 168 ILE cc_start: 0.8178 (mm) cc_final: 0.7865 (mm) outliers start: 167 outliers final: 80 residues processed: 683 average time/residue: 0.5664 time to fit residues: 672.6018 Evaluate side-chains 555 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 467 time to evaluate : 4.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain K residue 272 LYS Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 200 ASN Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 122 VAL Chi-restraints excluded: chain Q residue 186 THR Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain S residue 25 ASN Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 299 LEU Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 191 VAL Chi-restraints excluded: chain U residue 192 VAL Chi-restraints excluded: chain U residue 230 VAL Chi-restraints excluded: chain U residue 299 LEU Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain W residue 192 VAL Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain W residue 237 LEU Chi-restraints excluded: chain W residue 268 LEU Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain 0 residue 16 THR Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 138 SER Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 138 SER Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 161 VAL Chi-restraints excluded: chain 4 residue 191 VAL Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 6 residue 138 SER Chi-restraints excluded: chain 6 residue 186 THR Chi-restraints excluded: chain 6 residue 191 VAL Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 23 ILE Chi-restraints excluded: chain 8 residue 25 ASN Chi-restraints excluded: chain 8 residue 242 LYS Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 290 THR Chi-restraints excluded: chain c residue 299 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 353 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 529 optimal weight: 8.9990 chunk 432 optimal weight: 30.0000 chunk 175 optimal weight: 8.9990 chunk 636 optimal weight: 6.9990 chunk 687 optimal weight: 6.9990 chunk 567 optimal weight: 0.9990 chunk 631 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 510 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 HIS E 331 ASN G 92 ASN ** G 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 278 HIS M 224 GLN M 227 GLN M 278 HIS ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 200 ASN Q 331 ASN ** S 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 278 HIS ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 331 ASN ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 224 GLN 6 40 GLN ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 278 HIS ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 331 ASN a 149 ASN c 278 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.7246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 66480 Z= 0.374 Angle : 0.677 10.582 92360 Z= 0.360 Chirality : 0.045 0.297 10160 Planarity : 0.006 0.058 10360 Dihedral : 22.703 78.322 13030 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 3.56 % Allowed : 16.70 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.09), residues: 6720 helix: -1.71 (0.09), residues: 2860 sheet: -2.02 (0.15), residues: 600 loop : -1.96 (0.11), residues: 3260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP 4 156 HIS 0.005 0.001 HIS A 307 PHE 0.028 0.002 PHE 8 87 TYR 0.034 0.002 TYR W 5 ARG 0.007 0.001 ARG c 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 478 time to evaluate : 4.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7004 (p) REVERT: A 255 TYR cc_start: 0.8291 (t80) cc_final: 0.7671 (t80) REVERT: B 132 TYR cc_start: 0.8588 (m-10) cc_final: 0.8332 (m-10) REVERT: B 142 ARG cc_start: 0.7767 (ptt180) cc_final: 0.7332 (mtm110) REVERT: B 203 MET cc_start: 0.8644 (ptm) cc_final: 0.8251 (ptm) REVERT: B 291 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.8592 (m-80) REVERT: E 219 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8674 (mp) REVERT: E 260 MET cc_start: 0.8838 (mmm) cc_final: 0.8588 (mmm) REVERT: G 200 ASN cc_start: 0.8151 (p0) cc_final: 0.7840 (p0) REVERT: I 121 MET cc_start: 0.8332 (mmp) cc_final: 0.7950 (mmp) REVERT: I 172 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8420 (mtt180) REVERT: I 255 TYR cc_start: 0.8556 (t80) cc_final: 0.8156 (t80) REVERT: K 334 MET cc_start: 0.7455 (mmp) cc_final: 0.7172 (mmm) REVERT: M 42 MET cc_start: 0.8160 (ttp) cc_final: 0.7776 (ttp) REVERT: M 297 TYR cc_start: 0.6238 (t80) cc_final: 0.5823 (t80) REVERT: O 116 ARG cc_start: 0.8271 (ttm170) cc_final: 0.8001 (ttm170) REVERT: O 177 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8922 (mmmt) REVERT: Q 200 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7059 (t0) REVERT: S 5 TYR cc_start: 0.8837 (t80) cc_final: 0.8455 (t80) REVERT: S 177 LYS cc_start: 0.9169 (mmmm) cc_final: 0.8893 (mmmt) REVERT: S 231 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7194 (mm-40) REVERT: U 90 ASP cc_start: 0.8071 (t0) cc_final: 0.7866 (t0) REVERT: U 291 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: W 90 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7420 (t0) REVERT: Y 177 LYS cc_start: 0.9072 (mmmt) cc_final: 0.8509 (mtmt) REVERT: Y 272 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7722 (ttpp) REVERT: 0 297 TYR cc_start: 0.6660 (t80) cc_final: 0.6440 (t80) REVERT: 4 260 MET cc_start: 0.8258 (mmm) cc_final: 0.7721 (mmm) REVERT: 6 203 MET cc_start: 0.8667 (ptm) cc_final: 0.8373 (ptm) REVERT: a 203 MET cc_start: 0.8440 (ptt) cc_final: 0.8106 (ttp) REVERT: a 264 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8643 (mt) REVERT: c 168 ILE cc_start: 0.8638 (mm) cc_final: 0.8428 (mm) REVERT: c 193 VAL cc_start: 0.6825 (OUTLIER) cc_final: 0.6609 (p) REVERT: c 219 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8424 (mp) REVERT: c 260 MET cc_start: 0.8582 (mmm) cc_final: 0.8273 (mmm) outliers start: 201 outliers final: 126 residues processed: 643 average time/residue: 0.5890 time to fit residues: 656.6830 Evaluate side-chains 541 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 405 time to evaluate : 4.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 172 ARG Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 64 TYR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 186 THR Chi-restraints excluded: chain O residue 191 VAL Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 122 VAL Chi-restraints excluded: chain Q residue 186 THR Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 197 GLU Chi-restraints excluded: chain Q residue 200 ASN Chi-restraints excluded: chain Q residue 219 LEU Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 321 ASP Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 23 ILE Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 208 ILE Chi-restraints excluded: chain S residue 230 VAL Chi-restraints excluded: chain S residue 318 THR Chi-restraints excluded: chain S residue 321 ASP Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 64 TYR Chi-restraints excluded: chain U residue 186 THR Chi-restraints excluded: chain U residue 191 VAL Chi-restraints excluded: chain U residue 230 VAL Chi-restraints excluded: chain U residue 291 TYR Chi-restraints excluded: chain U residue 318 THR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 159 LEU Chi-restraints excluded: chain W residue 186 THR Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain W residue 290 THR Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 315 VAL Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 16 THR Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 157 VAL Chi-restraints excluded: chain 2 residue 191 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 315 VAL Chi-restraints excluded: chain 4 residue 136 THR Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 161 VAL Chi-restraints excluded: chain 4 residue 186 THR Chi-restraints excluded: chain 4 residue 191 VAL Chi-restraints excluded: chain 4 residue 230 VAL Chi-restraints excluded: chain 4 residue 318 THR Chi-restraints excluded: chain 6 residue 16 THR Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 6 residue 186 THR Chi-restraints excluded: chain 6 residue 191 VAL Chi-restraints excluded: chain 8 residue 23 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 77 THR Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 242 LYS Chi-restraints excluded: chain 8 residue 318 THR Chi-restraints excluded: chain 8 residue 321 ASP Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 219 LEU Chi-restraints excluded: chain c residue 290 THR Chi-restraints excluded: chain c residue 318 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 629 optimal weight: 8.9990 chunk 478 optimal weight: 7.9990 chunk 330 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 303 optimal weight: 8.9990 chunk 427 optimal weight: 2.9990 chunk 639 optimal weight: 6.9990 chunk 676 optimal weight: 20.0000 chunk 333 optimal weight: 9.9990 chunk 605 optimal weight: 0.7980 chunk 182 optimal weight: 0.8980 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 ASN K 278 HIS ** Q 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 224 GLN Q 258 ASN ** S 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 224 GLN ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 149 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.7537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 66480 Z= 0.267 Angle : 0.585 9.276 92360 Z= 0.310 Chirality : 0.042 0.136 10160 Planarity : 0.005 0.052 10360 Dihedral : 22.350 74.140 13020 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.46 % Allowed : 18.07 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.10), residues: 6720 helix: -1.10 (0.10), residues: 2840 sheet: -1.72 (0.17), residues: 500 loop : -1.82 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 156 HIS 0.003 0.001 HIS S 278 PHE 0.016 0.001 PHE M 326 TYR 0.018 0.002 TYR Q 297 ARG 0.011 0.000 ARG 8 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 452 time to evaluate : 4.953 Fit side-chains REVERT: A 138 SER cc_start: 0.8463 (m) cc_final: 0.8136 (p) REVERT: A 177 LYS cc_start: 0.9006 (mmmt) cc_final: 0.8485 (mtmt) REVERT: A 255 TYR cc_start: 0.8304 (t80) cc_final: 0.7892 (t80) REVERT: A 321 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7960 (t70) REVERT: B 142 ARG cc_start: 0.7795 (ptt180) cc_final: 0.7374 (mtm110) REVERT: B 203 MET cc_start: 0.8679 (ptm) cc_final: 0.8267 (ptm) REVERT: B 291 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.8698 (m-80) REVERT: E 8 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7081 (pm20) REVERT: E 219 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8626 (mp) REVERT: G 200 ASN cc_start: 0.8056 (p0) cc_final: 0.7742 (p0) REVERT: I 255 TYR cc_start: 0.8473 (t80) cc_final: 0.8118 (t80) REVERT: K 334 MET cc_start: 0.7412 (mmp) cc_final: 0.7202 (mmm) REVERT: M 260 MET cc_start: 0.8230 (mmm) cc_final: 0.7881 (mmm) REVERT: O 194 LEU cc_start: 0.8331 (tp) cc_final: 0.7972 (tp) REVERT: S 5 TYR cc_start: 0.8742 (t80) cc_final: 0.8312 (t80) REVERT: S 177 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8882 (mmmt) REVERT: S 336 LEU cc_start: 0.8614 (mm) cc_final: 0.8391 (mm) REVERT: U 291 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: Y 255 TYR cc_start: 0.8374 (t80) cc_final: 0.7667 (t80) REVERT: 0 28 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8195 (m) REVERT: 0 203 MET cc_start: 0.8620 (ptm) cc_final: 0.8295 (ptm) REVERT: 0 297 TYR cc_start: 0.6978 (t80) cc_final: 0.6394 (t80) REVERT: 4 116 ARG cc_start: 0.8106 (ttm170) cc_final: 0.7753 (ttm170) REVERT: 4 260 MET cc_start: 0.8262 (mmm) cc_final: 0.7837 (mmm) REVERT: 6 132 TYR cc_start: 0.8183 (m-10) cc_final: 0.7969 (m-10) REVERT: 6 203 MET cc_start: 0.8679 (ptm) cc_final: 0.8220 (ttp) REVERT: c 219 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8350 (mp) outliers start: 195 outliers final: 127 residues processed: 608 average time/residue: 0.5548 time to fit residues: 591.0315 Evaluate side-chains 551 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 417 time to evaluate : 4.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 64 TYR Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 186 THR Chi-restraints excluded: chain O residue 191 VAL Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 122 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 186 THR Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 219 LEU Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 144 GLN Chi-restraints excluded: chain S residue 193 VAL Chi-restraints excluded: chain S residue 318 THR Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 64 TYR Chi-restraints excluded: chain U residue 186 THR Chi-restraints excluded: chain U residue 191 VAL Chi-restraints excluded: chain U residue 230 VAL Chi-restraints excluded: chain U residue 291 TYR Chi-restraints excluded: chain U residue 318 THR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 64 TYR Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 159 LEU Chi-restraints excluded: chain W residue 186 THR Chi-restraints excluded: chain W residue 193 VAL Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 186 THR Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 315 VAL Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 16 THR Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 138 SER Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 2 residue 191 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 315 VAL Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 136 THR Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 161 VAL Chi-restraints excluded: chain 4 residue 186 THR Chi-restraints excluded: chain 4 residue 191 VAL Chi-restraints excluded: chain 4 residue 318 THR Chi-restraints excluded: chain 6 residue 16 THR Chi-restraints excluded: chain 6 residue 136 THR Chi-restraints excluded: chain 6 residue 186 THR Chi-restraints excluded: chain 6 residue 191 VAL Chi-restraints excluded: chain 6 residue 279 THR Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 186 THR Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 275 PHE Chi-restraints excluded: chain 8 residue 318 THR Chi-restraints excluded: chain 8 residue 321 ASP Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 29 ARG Chi-restraints excluded: chain a residue 62 MET Chi-restraints excluded: chain a residue 144 GLN Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 219 LEU Chi-restraints excluded: chain c residue 230 VAL Chi-restraints excluded: chain c residue 264 LEU Chi-restraints excluded: chain c residue 290 THR Chi-restraints excluded: chain c residue 318 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 563 optimal weight: 6.9990 chunk 384 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 503 optimal weight: 0.9990 chunk 279 optimal weight: 8.9990 chunk 577 optimal weight: 8.9990 chunk 467 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 345 optimal weight: 9.9990 chunk 607 optimal weight: 1.9990 chunk 170 optimal weight: 0.0010 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 224 GLN Q 307 HIS ** S 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 200 ASN ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 252 GLN 6 41 ASN ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 331 ASN ** c 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.7767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 66480 Z= 0.242 Angle : 0.568 8.528 92360 Z= 0.302 Chirality : 0.041 0.141 10160 Planarity : 0.005 0.051 10360 Dihedral : 22.315 74.894 13020 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.55 % Allowed : 18.97 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.10), residues: 6720 helix: -0.78 (0.10), residues: 2840 sheet: -1.50 (0.17), residues: 500 loop : -1.73 (0.11), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 156 HIS 0.003 0.001 HIS S 278 PHE 0.013 0.001 PHE M 326 TYR 0.021 0.001 TYR Q 297 ARG 0.006 0.000 ARG 8 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 435 time to evaluate : 5.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 SER cc_start: 0.8559 (m) cc_final: 0.8313 (p) REVERT: A 255 TYR cc_start: 0.8268 (t80) cc_final: 0.7857 (t80) REVERT: A 334 MET cc_start: 0.7678 (mmp) cc_final: 0.7113 (mmp) REVERT: B 142 ARG cc_start: 0.7869 (ptt180) cc_final: 0.7457 (mtm110) REVERT: B 203 MET cc_start: 0.8701 (ptm) cc_final: 0.8262 (ptm) REVERT: B 291 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8699 (m-80) REVERT: E 200 ASN cc_start: 0.7982 (t0) cc_final: 0.7472 (t0) REVERT: E 219 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8579 (mp) REVERT: G 144 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7160 (mt0) REVERT: G 200 ASN cc_start: 0.8216 (p0) cc_final: 0.7974 (p0) REVERT: I 255 TYR cc_start: 0.8478 (t80) cc_final: 0.8162 (t80) REVERT: M 260 MET cc_start: 0.8303 (mmm) cc_final: 0.7989 (mmm) REVERT: M 297 TYR cc_start: 0.6227 (t80) cc_final: 0.5702 (t80) REVERT: O 177 LYS cc_start: 0.9176 (mmmt) cc_final: 0.8805 (mmmt) REVERT: O 194 LEU cc_start: 0.8222 (tp) cc_final: 0.7967 (tp) REVERT: S 5 TYR cc_start: 0.8692 (t80) cc_final: 0.8258 (t80) REVERT: S 177 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8869 (mmmt) REVERT: U 291 TYR cc_start: 0.9114 (OUTLIER) cc_final: 0.8518 (m-80) REVERT: W 159 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7545 (pp) REVERT: W 297 TYR cc_start: 0.6843 (t80) cc_final: 0.6561 (t80) REVERT: Y 177 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8519 (mtmt) REVERT: Y 272 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7526 (ttpp) REVERT: 0 28 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8207 (m) REVERT: 0 297 TYR cc_start: 0.6979 (t80) cc_final: 0.6379 (t80) REVERT: 2 194 LEU cc_start: 0.8726 (tp) cc_final: 0.8434 (tp) REVERT: 2 255 TYR cc_start: 0.8287 (t80) cc_final: 0.8087 (t80) REVERT: 4 116 ARG cc_start: 0.8188 (ttm170) cc_final: 0.7789 (ttm170) REVERT: 4 177 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8867 (mmmt) REVERT: 4 252 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8179 (tm-30) REVERT: 4 260 MET cc_start: 0.8246 (mmm) cc_final: 0.7749 (mmm) REVERT: 6 132 TYR cc_start: 0.8142 (m-10) cc_final: 0.7884 (m-10) REVERT: 6 203 MET cc_start: 0.8707 (ptm) cc_final: 0.8290 (ttp) REVERT: 8 194 LEU cc_start: 0.7942 (tp) cc_final: 0.7558 (tp) REVERT: 8 321 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8168 (m-30) REVERT: 8 334 MET cc_start: 0.7286 (mmp) cc_final: 0.7053 (mmm) REVERT: c 260 MET cc_start: 0.8480 (mmm) cc_final: 0.8106 (mmm) outliers start: 200 outliers final: 149 residues processed: 597 average time/residue: 0.5542 time to fit residues: 583.5590 Evaluate side-chains 576 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 419 time to evaluate : 4.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 64 TYR Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 186 THR Chi-restraints excluded: chain O residue 191 VAL Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain Q residue 4 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 186 THR Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 219 LEU Chi-restraints excluded: chain Q residue 321 ASP Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 186 THR Chi-restraints excluded: chain S residue 193 VAL Chi-restraints excluded: chain S residue 203 MET Chi-restraints excluded: chain S residue 208 ILE Chi-restraints excluded: chain S residue 264 LEU Chi-restraints excluded: chain S residue 318 THR Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 64 TYR Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 186 THR Chi-restraints excluded: chain U residue 191 VAL Chi-restraints excluded: chain U residue 279 THR Chi-restraints excluded: chain U residue 291 TYR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 64 TYR Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 159 LEU Chi-restraints excluded: chain W residue 186 THR Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 73 GLU Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 186 THR Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 315 VAL Chi-restraints excluded: chain Y residue 321 ASP Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 16 THR Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 136 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 138 SER Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 2 residue 191 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 291 TYR Chi-restraints excluded: chain 2 residue 315 VAL Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 136 THR Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 161 VAL Chi-restraints excluded: chain 4 residue 186 THR Chi-restraints excluded: chain 4 residue 191 VAL Chi-restraints excluded: chain 4 residue 230 VAL Chi-restraints excluded: chain 4 residue 252 GLN Chi-restraints excluded: chain 4 residue 318 THR Chi-restraints excluded: chain 6 residue 64 TYR Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 6 residue 136 THR Chi-restraints excluded: chain 6 residue 186 THR Chi-restraints excluded: chain 6 residue 191 VAL Chi-restraints excluded: chain 6 residue 279 THR Chi-restraints excluded: chain 8 residue 23 ILE Chi-restraints excluded: chain 8 residue 186 THR Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 230 VAL Chi-restraints excluded: chain 8 residue 275 PHE Chi-restraints excluded: chain 8 residue 318 THR Chi-restraints excluded: chain 8 residue 321 ASP Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 62 MET Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 144 GLN Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 136 THR Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 264 LEU Chi-restraints excluded: chain c residue 290 THR Chi-restraints excluded: chain c residue 318 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 227 optimal weight: 10.0000 chunk 609 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 397 optimal weight: 0.2980 chunk 167 optimal weight: 5.9990 chunk 677 optimal weight: 9.9990 chunk 562 optimal weight: 0.3980 chunk 313 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 355 optimal weight: 1.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 331 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN ** S 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 331 ASN ** 0 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 224 GLN ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.7925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 66480 Z= 0.230 Angle : 0.558 9.569 92360 Z= 0.296 Chirality : 0.041 0.140 10160 Planarity : 0.005 0.049 10360 Dihedral : 22.267 76.375 13020 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 3.42 % Allowed : 19.34 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.10), residues: 6720 helix: -0.57 (0.10), residues: 2840 sheet: -1.37 (0.17), residues: 500 loop : -1.65 (0.11), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP U 156 HIS 0.003 0.001 HIS 8 278 PHE 0.012 0.001 PHE M 326 TYR 0.024 0.001 TYR A 297 ARG 0.005 0.000 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 452 time to evaluate : 4.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 SER cc_start: 0.8551 (m) cc_final: 0.8318 (p) REVERT: A 177 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8564 (mtmt) REVERT: A 255 TYR cc_start: 0.8229 (t80) cc_final: 0.7823 (t80) REVERT: B 142 ARG cc_start: 0.7859 (ptt180) cc_final: 0.7458 (mtm110) REVERT: B 203 MET cc_start: 0.8709 (ptm) cc_final: 0.8270 (ptm) REVERT: B 291 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.8704 (m-80) REVERT: E 8 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7149 (pm20) REVERT: E 200 ASN cc_start: 0.7974 (t0) cc_final: 0.7468 (t0) REVERT: E 219 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8657 (mp) REVERT: G 144 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7139 (mt0) REVERT: G 200 ASN cc_start: 0.8272 (p0) cc_final: 0.8020 (p0) REVERT: I 121 MET cc_start: 0.8303 (mmp) cc_final: 0.8052 (mmm) REVERT: I 194 LEU cc_start: 0.8402 (tp) cc_final: 0.8116 (tp) REVERT: I 255 TYR cc_start: 0.8483 (t80) cc_final: 0.8063 (t80) REVERT: K 237 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8370 (tt) REVERT: M 42 MET cc_start: 0.8196 (ttm) cc_final: 0.7866 (ttp) REVERT: M 260 MET cc_start: 0.8379 (mmm) cc_final: 0.8054 (mmm) REVERT: O 194 LEU cc_start: 0.8230 (tp) cc_final: 0.8029 (tp) REVERT: Q 255 TYR cc_start: 0.8246 (t80) cc_final: 0.7873 (t80) REVERT: S 5 TYR cc_start: 0.8655 (t80) cc_final: 0.8283 (t80) REVERT: U 291 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8518 (m-80) REVERT: W 86 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: W 159 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7526 (pp) REVERT: W 297 TYR cc_start: 0.6847 (t80) cc_final: 0.6508 (t80) REVERT: Y 177 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8507 (mtmt) REVERT: Y 272 LYS cc_start: 0.7715 (mtpt) cc_final: 0.7321 (ttpp) REVERT: 0 28 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8190 (m) REVERT: 0 194 LEU cc_start: 0.8340 (tp) cc_final: 0.8129 (tp) REVERT: 0 297 TYR cc_start: 0.6880 (t80) cc_final: 0.6282 (t80) REVERT: 2 194 LEU cc_start: 0.8656 (tp) cc_final: 0.8438 (tp) REVERT: 4 86 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.8058 (m-30) REVERT: 4 116 ARG cc_start: 0.8181 (ttm170) cc_final: 0.7796 (ttm170) REVERT: 4 260 MET cc_start: 0.8285 (mmm) cc_final: 0.7781 (mmm) REVERT: 6 132 TYR cc_start: 0.8160 (m-10) cc_final: 0.7885 (m-10) REVERT: 6 203 MET cc_start: 0.8727 (ptm) cc_final: 0.8335 (ttp) REVERT: 6 334 MET cc_start: 0.6683 (mmp) cc_final: 0.6421 (mmp) REVERT: 8 177 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8828 (mmmt) REVERT: 8 203 MET cc_start: 0.8286 (ptp) cc_final: 0.7785 (ttp) REVERT: 8 321 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: 8 334 MET cc_start: 0.7401 (mmp) cc_final: 0.7152 (mmm) REVERT: a 172 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8267 (mtp85) REVERT: a 260 MET cc_start: 0.8278 (tpt) cc_final: 0.8012 (tpt) REVERT: c 208 ILE cc_start: 0.9059 (tp) cc_final: 0.8817 (tt) REVERT: c 219 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8253 (mp) REVERT: c 260 MET cc_start: 0.8487 (mmm) cc_final: 0.8054 (mmm) outliers start: 193 outliers final: 154 residues processed: 602 average time/residue: 0.6148 time to fit residues: 651.8083 Evaluate side-chains 588 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 421 time to evaluate : 4.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 64 TYR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 186 THR Chi-restraints excluded: chain O residue 191 VAL Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain Q residue 4 THR Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 186 THR Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 219 LEU Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 144 GLN Chi-restraints excluded: chain S residue 186 THR Chi-restraints excluded: chain S residue 208 ILE Chi-restraints excluded: chain S residue 318 THR Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 62 MET Chi-restraints excluded: chain U residue 64 TYR Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 186 THR Chi-restraints excluded: chain U residue 191 VAL Chi-restraints excluded: chain U residue 279 THR Chi-restraints excluded: chain U residue 291 TYR Chi-restraints excluded: chain U residue 318 THR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 159 LEU Chi-restraints excluded: chain W residue 186 THR Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain W residue 290 THR Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain Y residue 73 GLU Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 186 THR Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 315 VAL Chi-restraints excluded: chain Y residue 321 ASP Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 16 THR Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 136 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 138 SER Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 2 residue 191 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 291 TYR Chi-restraints excluded: chain 2 residue 315 VAL Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 86 ASP Chi-restraints excluded: chain 4 residue 136 THR Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 161 VAL Chi-restraints excluded: chain 4 residue 191 VAL Chi-restraints excluded: chain 4 residue 230 VAL Chi-restraints excluded: chain 4 residue 318 THR Chi-restraints excluded: chain 6 residue 16 THR Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 6 residue 136 THR Chi-restraints excluded: chain 6 residue 186 THR Chi-restraints excluded: chain 6 residue 191 VAL Chi-restraints excluded: chain 6 residue 279 THR Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 23 ILE Chi-restraints excluded: chain 8 residue 186 THR Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 230 VAL Chi-restraints excluded: chain 8 residue 275 PHE Chi-restraints excluded: chain 8 residue 318 THR Chi-restraints excluded: chain 8 residue 321 ASP Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 62 MET Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 144 GLN Chi-restraints excluded: chain a residue 172 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 321 ASP Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 136 THR Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 219 LEU Chi-restraints excluded: chain c residue 230 VAL Chi-restraints excluded: chain c residue 264 LEU Chi-restraints excluded: chain c residue 290 THR Chi-restraints excluded: chain c residue 297 TYR Chi-restraints excluded: chain c residue 318 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 652 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 494 optimal weight: 10.0000 chunk 383 optimal weight: 10.0000 chunk 570 optimal weight: 2.9990 chunk 378 optimal weight: 9.9990 chunk 674 optimal weight: 9.9990 chunk 422 optimal weight: 0.0000 chunk 411 optimal weight: 9.9990 chunk 311 optimal weight: 4.9990 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 GLN ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN S 200 ASN S 224 GLN U 200 ASN ** U 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 252 GLN 8 144 GLN 8 199 GLN ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 40 GLN ** a 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.8124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 66480 Z= 0.331 Angle : 0.617 12.070 92360 Z= 0.325 Chirality : 0.043 0.152 10160 Planarity : 0.005 0.054 10360 Dihedral : 22.442 78.116 13020 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 3.79 % Allowed : 19.95 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.10), residues: 6720 helix: -0.73 (0.10), residues: 2940 sheet: -1.32 (0.17), residues: 500 loop : -1.82 (0.11), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 156 HIS 0.004 0.001 HIS S 278 PHE 0.018 0.001 PHE Q 35 TYR 0.029 0.002 TYR E 297 ARG 0.008 0.000 ARG I 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 421 time to evaluate : 4.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 SER cc_start: 0.8463 (m) cc_final: 0.8252 (p) REVERT: A 177 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8567 (mtmt) REVERT: A 194 LEU cc_start: 0.8898 (tp) cc_final: 0.8576 (tp) REVERT: A 255 TYR cc_start: 0.8281 (t80) cc_final: 0.7813 (t80) REVERT: B 177 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8739 (mmmt) REVERT: B 203 MET cc_start: 0.8724 (ptm) cc_final: 0.8277 (ptm) REVERT: B 291 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: E 8 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: E 200 ASN cc_start: 0.8005 (t0) cc_final: 0.7462 (t0) REVERT: E 219 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8650 (mp) REVERT: G 144 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7333 (mt0) REVERT: G 200 ASN cc_start: 0.8270 (p0) cc_final: 0.8066 (p0) REVERT: I 121 MET cc_start: 0.8359 (mmp) cc_final: 0.8085 (mmm) REVERT: I 194 LEU cc_start: 0.8439 (tp) cc_final: 0.8112 (tp) REVERT: I 255 TYR cc_start: 0.8502 (t80) cc_final: 0.8057 (t80) REVERT: K 172 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8377 (mtp85) REVERT: K 237 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8292 (tt) REVERT: M 297 TYR cc_start: 0.6388 (t80) cc_final: 0.6145 (t80) REVERT: O 193 VAL cc_start: 0.7199 (OUTLIER) cc_final: 0.6773 (m) REVERT: O 194 LEU cc_start: 0.8381 (tp) cc_final: 0.8027 (tp) REVERT: O 336 LEU cc_start: 0.8211 (pp) cc_final: 0.7804 (mt) REVERT: Q 177 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8687 (mtmt) REVERT: S 5 TYR cc_start: 0.8747 (t80) cc_final: 0.8307 (t80) REVERT: S 177 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8938 (mmmt) REVERT: U 172 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8409 (mtp85) REVERT: U 177 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8717 (mmmt) REVERT: U 291 TYR cc_start: 0.9140 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: W 86 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: W 159 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7416 (pp) REVERT: W 177 LYS cc_start: 0.9216 (mmmt) cc_final: 0.9012 (mmmt) REVERT: W 297 TYR cc_start: 0.7029 (t80) cc_final: 0.6711 (t80) REVERT: Y 138 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.7958 (p) REVERT: 0 28 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8314 (m) REVERT: 0 297 TYR cc_start: 0.7004 (t80) cc_final: 0.6448 (t80) REVERT: 4 252 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: 6 132 TYR cc_start: 0.8233 (m-10) cc_final: 0.7989 (m-10) REVERT: 6 203 MET cc_start: 0.8666 (ptm) cc_final: 0.8314 (ttp) REVERT: 6 264 LEU cc_start: 0.8930 (tt) cc_final: 0.8664 (mt) REVERT: 8 203 MET cc_start: 0.8212 (ptp) cc_final: 0.7758 (ttp) REVERT: 8 334 MET cc_start: 0.7551 (mmp) cc_final: 0.7026 (mmm) REVERT: c 219 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8272 (mp) REVERT: c 260 MET cc_start: 0.8496 (mmm) cc_final: 0.8064 (mmm) outliers start: 214 outliers final: 178 residues processed: 595 average time/residue: 0.5441 time to fit residues: 570.2483 Evaluate side-chains 601 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 408 time to evaluate : 4.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 64 TYR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 172 ARG Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 186 THR Chi-restraints excluded: chain O residue 191 VAL Chi-restraints excluded: chain O residue 193 VAL Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain Q residue 4 THR Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 186 THR Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 219 LEU Chi-restraints excluded: chain Q residue 321 ASP Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 144 GLN Chi-restraints excluded: chain S residue 186 THR Chi-restraints excluded: chain S residue 200 ASN Chi-restraints excluded: chain S residue 208 ILE Chi-restraints excluded: chain S residue 264 LEU Chi-restraints excluded: chain S residue 318 THR Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 62 MET Chi-restraints excluded: chain U residue 64 TYR Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 172 ARG Chi-restraints excluded: chain U residue 186 THR Chi-restraints excluded: chain U residue 191 VAL Chi-restraints excluded: chain U residue 230 VAL Chi-restraints excluded: chain U residue 291 TYR Chi-restraints excluded: chain U residue 318 THR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 159 LEU Chi-restraints excluded: chain W residue 186 THR Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain W residue 290 THR Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 73 GLU Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 186 THR Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 315 VAL Chi-restraints excluded: chain Y residue 321 ASP Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 16 THR Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 136 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 138 SER Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 2 residue 191 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 291 TYR Chi-restraints excluded: chain 2 residue 315 VAL Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 104 ILE Chi-restraints excluded: chain 4 residue 136 THR Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 161 VAL Chi-restraints excluded: chain 4 residue 186 THR Chi-restraints excluded: chain 4 residue 191 VAL Chi-restraints excluded: chain 4 residue 230 VAL Chi-restraints excluded: chain 4 residue 252 GLN Chi-restraints excluded: chain 4 residue 318 THR Chi-restraints excluded: chain 6 residue 16 THR Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 6 residue 136 THR Chi-restraints excluded: chain 6 residue 159 LEU Chi-restraints excluded: chain 6 residue 186 THR Chi-restraints excluded: chain 6 residue 191 VAL Chi-restraints excluded: chain 6 residue 279 THR Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 23 ILE Chi-restraints excluded: chain 8 residue 136 THR Chi-restraints excluded: chain 8 residue 138 SER Chi-restraints excluded: chain 8 residue 144 GLN Chi-restraints excluded: chain 8 residue 186 THR Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 230 VAL Chi-restraints excluded: chain 8 residue 242 LYS Chi-restraints excluded: chain 8 residue 275 PHE Chi-restraints excluded: chain 8 residue 318 THR Chi-restraints excluded: chain 8 residue 321 ASP Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 62 MET Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 144 GLN Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 321 ASP Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 136 THR Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 203 MET Chi-restraints excluded: chain c residue 219 LEU Chi-restraints excluded: chain c residue 264 LEU Chi-restraints excluded: chain c residue 290 THR Chi-restraints excluded: chain c residue 297 TYR Chi-restraints excluded: chain c residue 318 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 417 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 402 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 428 optimal weight: 0.3980 chunk 459 optimal weight: 0.6980 chunk 333 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 530 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 GLN ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 144 GLN S 200 ASN S 224 GLN ** S 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 199 GLN ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.8199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 66480 Z= 0.185 Angle : 0.551 10.084 92360 Z= 0.292 Chirality : 0.041 0.368 10160 Planarity : 0.005 0.047 10360 Dihedral : 22.214 78.097 13020 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.17 % Allowed : 20.78 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.10), residues: 6720 helix: -0.38 (0.10), residues: 2840 sheet: -1.20 (0.18), residues: 500 loop : -1.55 (0.11), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP U 156 HIS 0.002 0.001 HIS S 278 PHE 0.013 0.001 PHE M 326 TYR 0.025 0.001 TYR A 297 ARG 0.006 0.000 ARG I 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 438 time to evaluate : 4.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 SER cc_start: 0.8547 (m) cc_final: 0.8328 (p) REVERT: A 144 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: A 177 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8565 (mtmt) REVERT: A 255 TYR cc_start: 0.8185 (t80) cc_final: 0.7765 (t80) REVERT: A 334 MET cc_start: 0.7610 (mmp) cc_final: 0.7314 (mmp) REVERT: B 142 ARG cc_start: 0.7884 (ptt180) cc_final: 0.7489 (mtm110) REVERT: B 203 MET cc_start: 0.8721 (ptm) cc_final: 0.8269 (ptm) REVERT: B 291 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: E 200 ASN cc_start: 0.8174 (t0) cc_final: 0.7429 (t0) REVERT: E 219 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8567 (mp) REVERT: G 200 ASN cc_start: 0.8138 (p0) cc_final: 0.7932 (p0) REVERT: G 267 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7915 (mmmm) REVERT: I 121 MET cc_start: 0.8309 (mmp) cc_final: 0.8035 (mmm) REVERT: I 194 LEU cc_start: 0.8272 (tp) cc_final: 0.8018 (tp) REVERT: I 255 TYR cc_start: 0.8453 (t80) cc_final: 0.8038 (t80) REVERT: K 172 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8371 (mtp85) REVERT: M 42 MET cc_start: 0.8173 (ttm) cc_final: 0.7855 (ttp) REVERT: M 86 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7597 (m-30) REVERT: O 193 VAL cc_start: 0.7110 (OUTLIER) cc_final: 0.6742 (m) REVERT: O 194 LEU cc_start: 0.8367 (tp) cc_final: 0.8020 (tp) REVERT: Q 177 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8701 (mtmt) REVERT: Q 255 TYR cc_start: 0.8234 (t80) cc_final: 0.7840 (t80) REVERT: S 5 TYR cc_start: 0.8533 (t80) cc_final: 0.8103 (t80) REVERT: S 177 LYS cc_start: 0.9092 (mmmt) cc_final: 0.8808 (mmmt) REVERT: U 172 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8368 (mtp85) REVERT: U 291 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: W 86 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: W 159 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7463 (pp) REVERT: W 297 TYR cc_start: 0.6933 (t80) cc_final: 0.6588 (t80) REVERT: Y 138 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8298 (p) REVERT: Y 255 TYR cc_start: 0.8580 (t80) cc_final: 0.7854 (t80) REVERT: 0 28 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.8071 (m) REVERT: 0 194 LEU cc_start: 0.8311 (tp) cc_final: 0.8095 (tp) REVERT: 0 297 TYR cc_start: 0.6800 (t80) cc_final: 0.6174 (t80) REVERT: 2 132 TYR cc_start: 0.7832 (m-10) cc_final: 0.6799 (m-10) REVERT: 4 28 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7946 (t) REVERT: 4 116 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7803 (ttm170) REVERT: 4 260 MET cc_start: 0.8267 (mmm) cc_final: 0.7989 (mmm) REVERT: 6 132 TYR cc_start: 0.8157 (m-10) cc_final: 0.7893 (m-10) REVERT: 6 203 MET cc_start: 0.8782 (ptm) cc_final: 0.8409 (ttp) REVERT: 6 264 LEU cc_start: 0.8889 (tt) cc_final: 0.8659 (mt) REVERT: 6 334 MET cc_start: 0.6682 (mmp) cc_final: 0.6337 (mmp) REVERT: 8 203 MET cc_start: 0.8233 (ptp) cc_final: 0.7833 (ttp) REVERT: 8 321 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: 8 334 MET cc_start: 0.7401 (mmp) cc_final: 0.7192 (mmm) REVERT: a 172 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8316 (mtp85) REVERT: a 260 MET cc_start: 0.8296 (tpt) cc_final: 0.8074 (tpt) REVERT: a 321 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7660 (t70) REVERT: c 219 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8145 (mp) REVERT: c 260 MET cc_start: 0.8551 (mmm) cc_final: 0.8139 (mmm) outliers start: 179 outliers final: 141 residues processed: 579 average time/residue: 0.5508 time to fit residues: 560.2193 Evaluate side-chains 581 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 423 time to evaluate : 4.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 64 TYR Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 172 ARG Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 291 TYR Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 144 GLN Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 186 THR Chi-restraints excluded: chain O residue 193 VAL Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain Q residue 4 THR Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 186 THR Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 219 LEU Chi-restraints excluded: chain Q residue 321 ASP Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 144 GLN Chi-restraints excluded: chain S residue 186 THR Chi-restraints excluded: chain S residue 200 ASN Chi-restraints excluded: chain S residue 208 ILE Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain S residue 264 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain S residue 318 THR Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 62 MET Chi-restraints excluded: chain U residue 64 TYR Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 172 ARG Chi-restraints excluded: chain U residue 186 THR Chi-restraints excluded: chain U residue 291 TYR Chi-restraints excluded: chain U residue 318 THR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 159 LEU Chi-restraints excluded: chain W residue 186 THR Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 73 GLU Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 186 THR Chi-restraints excluded: chain Y residue 315 VAL Chi-restraints excluded: chain Y residue 321 ASP Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 136 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 138 SER Chi-restraints excluded: chain 2 residue 144 GLN Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 2 residue 191 VAL Chi-restraints excluded: chain 2 residue 291 TYR Chi-restraints excluded: chain 2 residue 315 VAL Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 73 GLU Chi-restraints excluded: chain 4 residue 136 THR Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 161 VAL Chi-restraints excluded: chain 4 residue 186 THR Chi-restraints excluded: chain 4 residue 191 VAL Chi-restraints excluded: chain 4 residue 230 VAL Chi-restraints excluded: chain 4 residue 318 THR Chi-restraints excluded: chain 6 residue 64 TYR Chi-restraints excluded: chain 6 residue 136 THR Chi-restraints excluded: chain 6 residue 186 THR Chi-restraints excluded: chain 6 residue 191 VAL Chi-restraints excluded: chain 6 residue 279 THR Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 23 ILE Chi-restraints excluded: chain 8 residue 138 SER Chi-restraints excluded: chain 8 residue 186 THR Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 230 VAL Chi-restraints excluded: chain 8 residue 275 PHE Chi-restraints excluded: chain 8 residue 318 THR Chi-restraints excluded: chain 8 residue 321 ASP Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 62 MET Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 144 GLN Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 172 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 321 ASP Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 136 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 219 LEU Chi-restraints excluded: chain c residue 264 LEU Chi-restraints excluded: chain c residue 297 TYR Chi-restraints excluded: chain c residue 318 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 613 optimal weight: 10.0000 chunk 646 optimal weight: 6.9990 chunk 589 optimal weight: 5.9990 chunk 628 optimal weight: 10.0000 chunk 378 optimal weight: 0.9990 chunk 273 optimal weight: 10.0000 chunk 493 optimal weight: 8.9990 chunk 192 optimal weight: 4.9990 chunk 568 optimal weight: 10.0000 chunk 594 optimal weight: 10.0000 chunk 626 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 GLN ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN S 200 ASN S 224 GLN ** U 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 252 GLN 8 144 GLN 8 199 GLN ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.8276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 66480 Z= 0.332 Angle : 0.619 11.672 92360 Z= 0.326 Chirality : 0.044 0.379 10160 Planarity : 0.005 0.054 10360 Dihedral : 22.422 79.083 13020 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 3.58 % Allowed : 20.74 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.10), residues: 6720 helix: -0.60 (0.10), residues: 2940 sheet: -1.23 (0.18), residues: 500 loop : -1.75 (0.11), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 156 HIS 0.004 0.001 HIS S 278 PHE 0.016 0.001 PHE 8 87 TYR 0.029 0.002 TYR Q 297 ARG 0.008 0.000 ARG 6 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 413 time to evaluate : 4.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 SER cc_start: 0.8465 (m) cc_final: 0.8254 (p) REVERT: A 177 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8512 (mtmt) REVERT: A 255 TYR cc_start: 0.8264 (t80) cc_final: 0.7791 (t80) REVERT: A 297 TYR cc_start: 0.5828 (t80) cc_final: 0.5572 (t80) REVERT: B 203 MET cc_start: 0.8733 (ptm) cc_final: 0.8278 (ptm) REVERT: B 291 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.8652 (m-80) REVERT: E 177 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8690 (mtmt) REVERT: E 200 ASN cc_start: 0.8189 (t0) cc_final: 0.7482 (t0) REVERT: E 219 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8643 (mp) REVERT: G 200 ASN cc_start: 0.8130 (p0) cc_final: 0.7903 (p0) REVERT: I 121 MET cc_start: 0.8350 (mmp) cc_final: 0.8074 (mmm) REVERT: I 194 LEU cc_start: 0.8367 (tp) cc_final: 0.8048 (tp) REVERT: I 255 TYR cc_start: 0.8470 (t80) cc_final: 0.8019 (t80) REVERT: K 172 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8395 (mtp85) REVERT: K 237 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8292 (tt) REVERT: M 86 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7747 (m-30) REVERT: M 260 MET cc_start: 0.8108 (mmm) cc_final: 0.7836 (mmm) REVERT: M 297 TYR cc_start: 0.6254 (t80) cc_final: 0.6019 (t80) REVERT: O 193 VAL cc_start: 0.7187 (OUTLIER) cc_final: 0.6849 (m) REVERT: O 194 LEU cc_start: 0.8417 (tp) cc_final: 0.8090 (tp) REVERT: O 252 GLN cc_start: 0.8655 (tp40) cc_final: 0.8354 (tm-30) REVERT: O 336 LEU cc_start: 0.8141 (pp) cc_final: 0.7801 (mt) REVERT: Q 255 TYR cc_start: 0.8332 (t80) cc_final: 0.7868 (t80) REVERT: S 5 TYR cc_start: 0.8779 (t80) cc_final: 0.8361 (t80) REVERT: S 177 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8781 (mmmt) REVERT: U 172 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8433 (mtp85) REVERT: U 177 LYS cc_start: 0.9037 (mmmt) cc_final: 0.8722 (mmmt) REVERT: U 291 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.8491 (m-80) REVERT: W 86 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: W 159 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7423 (pp) REVERT: W 260 MET cc_start: 0.8643 (mmm) cc_final: 0.8011 (mmm) REVERT: W 297 TYR cc_start: 0.6995 (t80) cc_final: 0.6658 (t80) REVERT: Y 138 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8306 (p) REVERT: Y 177 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8498 (mtmt) REVERT: Y 255 TYR cc_start: 0.8590 (t80) cc_final: 0.7829 (t80) REVERT: 0 28 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8145 (m) REVERT: 0 297 TYR cc_start: 0.7016 (t80) cc_final: 0.6418 (t80) REVERT: 2 138 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.8000 (p) REVERT: 4 28 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7867 (t) REVERT: 4 252 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: 4 260 MET cc_start: 0.8298 (mmm) cc_final: 0.7942 (mmm) REVERT: 6 132 TYR cc_start: 0.8241 (m-10) cc_final: 0.7964 (m-10) REVERT: 6 203 MET cc_start: 0.8759 (ptm) cc_final: 0.8426 (ttp) REVERT: 6 334 MET cc_start: 0.6993 (mmp) cc_final: 0.6661 (mmp) REVERT: 8 203 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7845 (ttp) REVERT: 8 321 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8276 (m-30) REVERT: 8 334 MET cc_start: 0.7574 (mmp) cc_final: 0.7092 (mmm) REVERT: a 172 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8363 (mtp85) REVERT: c 219 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8263 (mp) REVERT: c 260 MET cc_start: 0.8512 (mmm) cc_final: 0.8068 (mmm) outliers start: 202 outliers final: 167 residues processed: 577 average time/residue: 0.5482 time to fit residues: 557.7418 Evaluate side-chains 591 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 405 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 64 TYR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 172 ARG Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 104 ILE Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 144 GLN Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 186 THR Chi-restraints excluded: chain O residue 193 VAL Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain Q residue 4 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 186 THR Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 219 LEU Chi-restraints excluded: chain Q residue 321 ASP Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 104 ILE Chi-restraints excluded: chain S residue 144 GLN Chi-restraints excluded: chain S residue 186 THR Chi-restraints excluded: chain S residue 200 ASN Chi-restraints excluded: chain S residue 208 ILE Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain S residue 264 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain S residue 318 THR Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 62 MET Chi-restraints excluded: chain U residue 64 TYR Chi-restraints excluded: chain U residue 104 ILE Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 172 ARG Chi-restraints excluded: chain U residue 186 THR Chi-restraints excluded: chain U residue 203 MET Chi-restraints excluded: chain U residue 291 TYR Chi-restraints excluded: chain U residue 318 THR Chi-restraints excluded: chain U residue 336 LEU Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 73 GLU Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 159 LEU Chi-restraints excluded: chain W residue 186 THR Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain W residue 230 VAL Chi-restraints excluded: chain W residue 290 THR Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 73 GLU Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 186 THR Chi-restraints excluded: chain Y residue 315 VAL Chi-restraints excluded: chain Y residue 321 ASP Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 136 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 138 SER Chi-restraints excluded: chain 2 residue 144 GLN Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 2 residue 191 VAL Chi-restraints excluded: chain 2 residue 291 TYR Chi-restraints excluded: chain 2 residue 315 VAL Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 73 GLU Chi-restraints excluded: chain 4 residue 104 ILE Chi-restraints excluded: chain 4 residue 136 THR Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 161 VAL Chi-restraints excluded: chain 4 residue 186 THR Chi-restraints excluded: chain 4 residue 191 VAL Chi-restraints excluded: chain 4 residue 230 VAL Chi-restraints excluded: chain 4 residue 252 GLN Chi-restraints excluded: chain 4 residue 318 THR Chi-restraints excluded: chain 6 residue 64 TYR Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 6 residue 136 THR Chi-restraints excluded: chain 6 residue 186 THR Chi-restraints excluded: chain 6 residue 191 VAL Chi-restraints excluded: chain 6 residue 279 THR Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 23 ILE Chi-restraints excluded: chain 8 residue 136 THR Chi-restraints excluded: chain 8 residue 138 SER Chi-restraints excluded: chain 8 residue 186 THR Chi-restraints excluded: chain 8 residue 191 VAL Chi-restraints excluded: chain 8 residue 203 MET Chi-restraints excluded: chain 8 residue 230 VAL Chi-restraints excluded: chain 8 residue 242 LYS Chi-restraints excluded: chain 8 residue 275 PHE Chi-restraints excluded: chain 8 residue 318 THR Chi-restraints excluded: chain 8 residue 321 ASP Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 62 MET Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 144 GLN Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 172 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 321 ASP Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 64 TYR Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 136 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 203 MET Chi-restraints excluded: chain c residue 219 LEU Chi-restraints excluded: chain c residue 264 LEU Chi-restraints excluded: chain c residue 297 TYR Chi-restraints excluded: chain c residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 412 optimal weight: 10.0000 chunk 664 optimal weight: 8.9990 chunk 405 optimal weight: 20.0000 chunk 315 optimal weight: 8.9990 chunk 462 optimal weight: 2.9990 chunk 697 optimal weight: 3.9990 chunk 641 optimal weight: 9.9990 chunk 555 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 428 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 GLN ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN S 200 ASN S 224 GLN ** U 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 144 GLN 8 199 GLN ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.8321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 66480 Z= 0.216 Angle : 0.567 10.760 92360 Z= 0.300 Chirality : 0.041 0.336 10160 Planarity : 0.005 0.048 10360 Dihedral : 22.266 79.114 13020 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.12 % Allowed : 21.22 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.10), residues: 6720 helix: -0.35 (0.10), residues: 2840 sheet: -1.13 (0.18), residues: 500 loop : -1.50 (0.11), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP U 156 HIS 0.002 0.001 HIS S 278 PHE 0.014 0.001 PHE M 326 TYR 0.025 0.001 TYR Q 297 ARG 0.005 0.000 ARG I 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13440 Ramachandran restraints generated. 6720 Oldfield, 0 Emsley, 6720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 421 time to evaluate : 5.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 SER cc_start: 0.8574 (m) cc_final: 0.8365 (p) REVERT: A 177 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8518 (mtmt) REVERT: A 255 TYR cc_start: 0.8185 (t80) cc_final: 0.7776 (t80) REVERT: A 334 MET cc_start: 0.7593 (mmp) cc_final: 0.7330 (mmp) REVERT: B 203 MET cc_start: 0.8719 (ptm) cc_final: 0.8267 (ptm) REVERT: B 291 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8699 (m-80) REVERT: E 177 LYS cc_start: 0.9085 (mmmt) cc_final: 0.8665 (mtmt) REVERT: E 200 ASN cc_start: 0.8307 (t0) cc_final: 0.7835 (t0) REVERT: E 219 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8537 (mp) REVERT: G 200 ASN cc_start: 0.8079 (p0) cc_final: 0.7836 (p0) REVERT: G 267 LYS cc_start: 0.8418 (mmmm) cc_final: 0.7841 (mmmm) REVERT: I 121 MET cc_start: 0.8315 (mmp) cc_final: 0.8015 (mmm) REVERT: I 194 LEU cc_start: 0.8308 (tp) cc_final: 0.7980 (tp) REVERT: I 255 TYR cc_start: 0.8430 (t80) cc_final: 0.7998 (t80) REVERT: K 172 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8391 (mtp85) REVERT: M 86 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: O 193 VAL cc_start: 0.7215 (OUTLIER) cc_final: 0.6807 (m) REVERT: O 194 LEU cc_start: 0.8399 (tp) cc_final: 0.8053 (tp) REVERT: O 252 GLN cc_start: 0.8630 (tp40) cc_final: 0.8218 (tm-30) REVERT: Q 255 TYR cc_start: 0.8271 (t80) cc_final: 0.7826 (t80) REVERT: S 5 TYR cc_start: 0.8585 (t80) cc_final: 0.8163 (t80) REVERT: S 177 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8774 (mmmt) REVERT: U 172 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8397 (mtp85) REVERT: U 291 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.8535 (m-80) REVERT: W 86 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7747 (m-30) REVERT: W 159 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7391 (pp) REVERT: W 297 TYR cc_start: 0.6941 (t80) cc_final: 0.6573 (t80) REVERT: Y 138 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8287 (p) REVERT: Y 255 TYR cc_start: 0.8612 (t80) cc_final: 0.7863 (t80) REVERT: 0 28 VAL cc_start: 0.8330 (OUTLIER) cc_final: 0.8095 (m) REVERT: 0 194 LEU cc_start: 0.8296 (tp) cc_final: 0.8074 (tp) REVERT: 0 297 TYR cc_start: 0.6845 (t80) cc_final: 0.6211 (t80) REVERT: 4 28 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7903 (t) REVERT: 4 260 MET cc_start: 0.8296 (mmm) cc_final: 0.8012 (mmm) REVERT: 6 132 TYR cc_start: 0.8176 (m-10) cc_final: 0.7883 (m-10) REVERT: 6 203 MET cc_start: 0.8710 (ptm) cc_final: 0.8380 (ttp) REVERT: 6 334 MET cc_start: 0.6935 (mmp) cc_final: 0.6662 (mmp) REVERT: 8 203 MET cc_start: 0.8202 (ptp) cc_final: 0.7840 (ttp) REVERT: 8 321 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8214 (m-30) REVERT: a 172 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8347 (mtp85) REVERT: c 219 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8174 (mp) REVERT: c 260 MET cc_start: 0.8522 (mmm) cc_final: 0.8100 (mmm) outliers start: 176 outliers final: 149 residues processed: 564 average time/residue: 0.5495 time to fit residues: 547.0749 Evaluate side-chains 578 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 414 time to evaluate : 4.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 64 TYR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 172 ARG Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 144 GLN Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 186 THR Chi-restraints excluded: chain O residue 193 VAL Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain Q residue 4 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 186 THR Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 219 LEU Chi-restraints excluded: chain Q residue 321 ASP Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 104 ILE Chi-restraints excluded: chain S residue 186 THR Chi-restraints excluded: chain S residue 208 ILE Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain S residue 264 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain S residue 318 THR Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 62 MET Chi-restraints excluded: chain U residue 64 TYR Chi-restraints excluded: chain U residue 104 ILE Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 172 ARG Chi-restraints excluded: chain U residue 186 THR Chi-restraints excluded: chain U residue 291 TYR Chi-restraints excluded: chain U residue 318 THR Chi-restraints excluded: chain U residue 336 LEU Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 159 LEU Chi-restraints excluded: chain W residue 186 THR Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain W residue 318 THR Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 73 GLU Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 186 THR Chi-restraints excluded: chain Y residue 315 VAL Chi-restraints excluded: chain Y residue 321 ASP Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 136 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 138 SER Chi-restraints excluded: chain 2 residue 144 GLN Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 2 residue 191 VAL Chi-restraints excluded: chain 2 residue 291 TYR Chi-restraints excluded: chain 2 residue 315 VAL Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 73 GLU Chi-restraints excluded: chain 4 residue 136 THR Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 161 VAL Chi-restraints excluded: chain 4 residue 186 THR Chi-restraints excluded: chain 4 residue 191 VAL Chi-restraints excluded: chain 4 residue 230 VAL Chi-restraints excluded: chain 4 residue 318 THR Chi-restraints excluded: chain 6 residue 64 TYR Chi-restraints excluded: chain 6 residue 136 THR Chi-restraints excluded: chain 6 residue 186 THR Chi-restraints excluded: chain 6 residue 191 VAL Chi-restraints excluded: chain 6 residue 279 THR Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 23 ILE Chi-restraints excluded: chain 8 residue 136 THR Chi-restraints excluded: chain 8 residue 138 SER Chi-restraints excluded: chain 8 residue 144 GLN Chi-restraints excluded: chain 8 residue 186 THR Chi-restraints excluded: chain 8 residue 230 VAL Chi-restraints excluded: chain 8 residue 275 PHE Chi-restraints excluded: chain 8 residue 318 THR Chi-restraints excluded: chain 8 residue 321 ASP Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 62 MET Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 144 GLN Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 172 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 321 ASP Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 136 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 219 LEU Chi-restraints excluded: chain c residue 264 LEU Chi-restraints excluded: chain c residue 297 TYR Chi-restraints excluded: chain c residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 441 optimal weight: 6.9990 chunk 591 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 512 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 556 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 571 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 231 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 GLN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 GLN ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 200 ASN S 224 GLN ** U 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 252 GLN 8 144 GLN 8 199 GLN ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 165 GLN ** a 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.107238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.089123 restraints weight = 152649.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.091149 restraints weight = 77057.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.092402 restraints weight = 51707.793| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.8376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 66480 Z= 0.443 Angle : 0.690 13.380 92360 Z= 0.361 Chirality : 0.047 0.399 10160 Planarity : 0.006 0.059 10360 Dihedral : 22.550 79.183 13020 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 3.65 % Allowed : 20.78 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.10), residues: 6720 helix: -0.73 (0.10), residues: 2940 sheet: -1.20 (0.18), residues: 500 loop : -1.80 (0.11), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 117 HIS 0.005 0.002 HIS S 278 PHE 0.023 0.002 PHE Q 35 TYR 0.032 0.002 TYR Q 297 ARG 0.009 0.001 ARG E 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11201.21 seconds wall clock time: 198 minutes 26.17 seconds (11906.17 seconds total)