Starting phenix.real_space_refine on Sat Dec 9 15:55:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6obj_20015/12_2023/6obj_20015.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6obj_20015/12_2023/6obj_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_20015/12_2023/6obj_20015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6obj_20015/12_2023/6obj_20015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6obj_20015/12_2023/6obj_20015.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6obj_20015/12_2023/6obj_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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 26.44, per 1000 atoms: 0.41 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: 19.98 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: 17.45 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: 21.40 Time building geometry restraints manager: 21.92 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: 0.990 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: 0.040 Extract box with map and model: 6.280 Check model and map are aligned: 0.740 Set scattering table: 0.460 Process input model: 137.720 Find NCS groups from input model: 3.130 Set up NCS constraints: 0.620 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:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.130 ------------------------------------------------------------------------------- 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 : 4.995 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 outliers start: 80 outliers final: 12 residues processed: 1279 average time/residue: 0.6639 time to fit residues: 1373.1779 Evaluate side-chains 639 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 627 time to evaluate : 5.382 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4299 time to fit residues: 16.3549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 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 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 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 331 ASN M 21 GLN M 30 ASN ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 ASN M 278 HIS 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 200 ASN Q 331 ASN S 21 GLN S 25 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 0 200 ASN 0 258 ASN 0 278 HIS 2 21 GLN 2 30 ASN ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 258 ASN 4 21 GLN 4 30 ASN ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 258 ASN 4 278 HIS 4 331 ASN 6 21 GLN 6 30 ASN 6 40 GLN ** 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 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 258 ASN c 331 ASN Total number of N/Q/H flips: 92 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 66480 Z= 0.309 Angle : 0.704 11.184 92360 Z= 0.376 Chirality : 0.045 0.167 10160 Planarity : 0.007 0.065 10360 Dihedral : 22.514 73.673 13020 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.31 % Favored : 92.53 % Rotamer: Outliers : 2.71 % Allowed : 14.40 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.09), residues: 6720 helix: -2.41 (0.08), residues: 2680 sheet: -1.96 (0.16), residues: 600 loop : -2.13 (0.10), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP I 156 HIS 0.006 0.001 HIS U 278 PHE 0.025 0.002 PHE M 326 TYR 0.025 0.002 TYR 8 45 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 723 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 570 time to evaluate : 5.074 Fit side-chains 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 outliers start: 153 outliers final: 76 residues processed: 672 average time/residue: 0.5732 time to fit residues: 668.3698 Evaluate side-chains 552 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 476 time to evaluate : 5.025 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 0.4534 time to fit residues: 72.0275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 353 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 529 optimal weight: 8.9990 chunk 432 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 636 optimal weight: 5.9990 chunk 687 optimal weight: 8.9990 chunk 567 optimal weight: 0.7980 chunk 631 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 510 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN 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** K 258 ASN ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 331 ASN S 25 ASN ** S 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 278 HIS ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 224 GLN ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 ASN ** 8 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 278 HIS ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 149 ASN ** c 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.7235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 66480 Z= 0.328 Angle : 0.656 9.744 92360 Z= 0.350 Chirality : 0.044 0.190 10160 Planarity : 0.006 0.057 10360 Dihedral : 22.676 81.466 13020 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 2.39 % Allowed : 16.88 % Favored : 80.73 % 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: -3.01 (0.09), residues: 6720 helix: -1.78 (0.09), residues: 2960 sheet: -1.96 (0.15), residues: 600 loop : -2.14 (0.10), residues: 3160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP O 156 HIS 0.003 0.001 HIS a 278 PHE 0.028 0.002 PHE 8 87 TYR 0.029 0.002 TYR I 5 ARG 0.007 0.001 ARG 0 29 *********************** 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 635 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 500 time to evaluate : 5.200 Fit side-chains revert: symmetry clash outliers start: 135 outliers final: 65 residues processed: 612 average time/residue: 0.6341 time to fit residues: 669.3102 Evaluate side-chains 471 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 406 time to evaluate : 5.125 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.4794 time to fit residues: 66.6327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 330 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 chunk 427 optimal weight: 3.9990 chunk 639 optimal weight: 5.9990 chunk 676 optimal weight: 9.9990 chunk 333 optimal weight: 0.0030 chunk 605 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 278 HIS I 258 ASN ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 224 GLN Q 258 ASN Q 307 HIS S 25 ASN ** S 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 41 ASN 6 224 GLN 6 261 GLN 6 307 HIS 8 25 ASN ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 149 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.7422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 66480 Z= 0.201 Angle : 0.557 8.604 92360 Z= 0.295 Chirality : 0.041 0.146 10160 Planarity : 0.005 0.049 10360 Dihedral : 22.245 76.985 13020 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.74 % Allowed : 18.19 % Favored : 80.07 % 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: -2.24 (0.10), residues: 6720 helix: -1.05 (0.10), residues: 2840 sheet: -1.69 (0.17), residues: 500 loop : -1.81 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 156 HIS 0.003 0.001 HIS 8 278 PHE 0.013 0.001 PHE M 326 TYR 0.021 0.001 TYR M 297 ARG 0.009 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 573 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 475 time to evaluate : 5.217 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 34 residues processed: 556 average time/residue: 0.5863 time to fit residues: 564.5420 Evaluate side-chains 458 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 424 time to evaluate : 5.133 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4790 time to fit residues: 36.8510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 563 optimal weight: 9.9990 chunk 384 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 503 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 577 optimal weight: 20.0000 chunk 467 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 345 optimal weight: 20.0000 chunk 607 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 overall best weight: 7.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 ASN G 224 GLN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 224 GLN S 199 GLN S 224 GLN ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 252 GLN ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 224 GLN 6 258 ASN 8 224 GLN ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 278 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.7885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 66480 Z= 0.449 Angle : 0.694 10.618 92360 Z= 0.364 Chirality : 0.046 0.170 10160 Planarity : 0.006 0.060 10360 Dihedral : 22.560 78.642 13020 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 1.91 % Allowed : 19.52 % Favored : 78.56 % 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: -2.40 (0.10), residues: 6720 helix: -1.12 (0.10), residues: 2940 sheet: -1.56 (0.17), residues: 500 loop : -2.02 (0.10), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP 6 111 HIS 0.005 0.002 HIS 8 278 PHE 0.023 0.002 PHE Q 35 TYR 0.030 0.002 TYR 0 297 ARG 0.007 0.001 ARG E 249 *********************** 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 534 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 426 time to evaluate : 5.236 Fit side-chains outliers start: 108 outliers final: 71 residues processed: 505 average time/residue: 0.6158 time to fit residues: 541.5965 Evaluate side-chains 464 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 393 time to evaluate : 5.160 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.4939 time to fit residues: 73.4361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 227 optimal weight: 7.9990 chunk 609 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 397 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 677 optimal weight: 20.0000 chunk 562 optimal weight: 2.9990 chunk 313 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 355 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** E 41 ASN ** 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 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 GLN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 224 GLN ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 331 ASN ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 224 GLN ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.8077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 66480 Z= 0.359 Angle : 0.639 10.654 92360 Z= 0.336 Chirality : 0.044 0.171 10160 Planarity : 0.005 0.054 10360 Dihedral : 22.444 78.299 13020 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 1.29 % Allowed : 20.43 % Favored : 78.28 % 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: -2.22 (0.10), residues: 6720 helix: -0.95 (0.10), residues: 2940 sheet: -1.44 (0.17), residues: 500 loop : -1.94 (0.10), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 156 HIS 0.003 0.001 HIS A 307 PHE 0.018 0.002 PHE Q 35 TYR 0.027 0.002 TYR a 297 ARG 0.006 0.000 ARG E 249 *********************** 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 494 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 421 time to evaluate : 5.115 Fit side-chains outliers start: 73 outliers final: 46 residues processed: 471 average time/residue: 0.5851 time to fit residues: 478.6075 Evaluate side-chains 448 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 402 time to evaluate : 5.108 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.4588 time to fit residues: 46.3612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 652 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 385 optimal weight: 9.9990 chunk 494 optimal weight: 5.9990 chunk 383 optimal weight: 10.0000 chunk 570 optimal weight: 2.9990 chunk 378 optimal weight: 9.9990 chunk 674 optimal weight: 1.9990 chunk 422 optimal weight: 7.9990 chunk 411 optimal weight: 10.0000 chunk 311 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 GLN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 GLN ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN S 224 GLN S 231 GLN ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 40 GLN ** a 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.8198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 66480 Z= 0.301 Angle : 0.612 11.185 92360 Z= 0.321 Chirality : 0.043 0.170 10160 Planarity : 0.005 0.053 10360 Dihedral : 22.383 78.388 13020 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.19 % Favored : 89.79 % Rotamer: Outliers : 0.92 % Allowed : 21.45 % Favored : 77.62 % 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: -2.07 (0.10), residues: 6720 helix: -0.81 (0.10), residues: 2940 sheet: -1.31 (0.17), residues: 500 loop : -1.89 (0.11), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP U 156 HIS 0.003 0.001 HIS 8 278 PHE 0.014 0.001 PHE Q 35 TYR 0.023 0.002 TYR M 297 ARG 0.006 0.000 ARG G 134 *********************** 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 479 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 427 time to evaluate : 5.102 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 33 residues processed: 462 average time/residue: 0.6309 time to fit residues: 509.1937 Evaluate side-chains 438 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 405 time to evaluate : 5.080 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4949 time to fit residues: 37.4744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 417 optimal weight: 2.9990 chunk 269 optimal weight: 8.9990 chunk 402 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 428 optimal weight: 7.9990 chunk 459 optimal weight: 2.9990 chunk 333 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 530 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 GLN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 GLN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN S 224 GLN ** 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** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.8292 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= 0.323 Angle : 0.625 12.125 92360 Z= 0.328 Chirality : 0.044 0.173 10160 Planarity : 0.005 0.053 10360 Dihedral : 22.413 78.933 13020 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 0.83 % Allowed : 22.30 % Favored : 76.86 % 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: -2.01 (0.10), residues: 6720 helix: -0.76 (0.10), residues: 2940 sheet: -1.23 (0.17), residues: 500 loop : -1.87 (0.11), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 8 204 HIS 0.003 0.001 HIS a 278 PHE 0.015 0.001 PHE M 326 TYR 0.025 0.002 TYR U 297 ARG 0.006 0.000 ARG E 249 *********************** 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 463 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 416 time to evaluate : 5.207 Fit side-chains outliers start: 47 outliers final: 20 residues processed: 453 average time/residue: 0.5950 time to fit residues: 471.2328 Evaluate side-chains 426 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 406 time to evaluate : 5.123 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4632 time to fit residues: 24.0641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 613 optimal weight: 0.6980 chunk 646 optimal weight: 0.9980 chunk 589 optimal weight: 7.9990 chunk 628 optimal weight: 10.0000 chunk 378 optimal weight: 9.9990 chunk 273 optimal weight: 0.5980 chunk 493 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 568 optimal weight: 5.9990 chunk 594 optimal weight: 8.9990 chunk 626 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 278 HIS ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 199 GLN ** 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 224 GLN ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 144 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** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 231 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.8364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 66480 Z= 0.201 Angle : 0.572 10.881 92360 Z= 0.301 Chirality : 0.041 0.171 10160 Planarity : 0.005 0.048 10360 Dihedral : 22.219 78.314 13020 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.34 % Allowed : 23.26 % Favored : 76.40 % 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: -1.60 (0.10), residues: 6720 helix: -0.40 (0.10), residues: 2840 sheet: -1.11 (0.18), residues: 500 loop : -1.61 (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 8 278 PHE 0.013 0.001 PHE M 326 TYR 0.026 0.001 TYR 0 297 ARG 0.007 0.000 ARG I 29 *********************** 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 473 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 454 time to evaluate : 5.214 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 466 average time/residue: 0.6063 time to fit residues: 496.2497 Evaluate side-chains 426 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 420 time to evaluate : 5.083 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5176 time to fit residues: 12.1950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 412 optimal weight: 9.9990 chunk 664 optimal weight: 10.0000 chunk 405 optimal weight: 7.9990 chunk 315 optimal weight: 0.0170 chunk 462 optimal weight: 0.8980 chunk 697 optimal weight: 10.0000 chunk 641 optimal weight: 10.0000 chunk 555 optimal weight: 10.0000 chunk 57 optimal weight: 0.0000 chunk 428 optimal weight: 0.6980 chunk 340 optimal weight: 0.8980 overall best weight: 0.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 331 ASN ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 GLN ** 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** ** U 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 199 GLN ** 2 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 39 GLN 6 41 ASN ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.8499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 66480 Z= 0.160 Angle : 0.553 9.961 92360 Z= 0.292 Chirality : 0.040 0.169 10160 Planarity : 0.005 0.046 10360 Dihedral : 22.112 79.559 13020 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.23 % Allowed : 23.58 % Favored : 76.19 % 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: -1.31 (0.10), residues: 6720 helix: -0.14 (0.10), residues: 2820 sheet: -0.93 (0.19), residues: 500 loop : -1.47 (0.11), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 156 HIS 0.001 0.000 HIS W 81 PHE 0.014 0.001 PHE K 54 TYR 0.025 0.001 TYR W 297 ARG 0.008 0.000 ARG G 229 ********************** 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 504 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 491 time to evaluate : 5.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 497 average time/residue: 0.5917 time to fit residues: 515.7590 Evaluate side-chains 451 residues out of total 5640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 445 time to evaluate : 5.081 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4865 time to fit residues: 11.9301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 441 optimal weight: 10.0000 chunk 591 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 512 optimal weight: 0.5980 chunk 81 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 556 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 571 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 199 GLN ** 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** ** U 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 199 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** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 331 ASN ** c 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.113326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095373 restraints weight = 151316.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097510 restraints weight = 75369.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098830 restraints weight = 50068.714| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.8524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 66480 Z= 0.199 Angle : 0.567 8.958 92360 Z= 0.297 Chirality : 0.041 0.170 10160 Planarity : 0.005 0.045 10360 Dihedral : 22.247 81.655 13020 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.30 % Allowed : 23.87 % Favored : 75.83 % 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: -1.23 (0.10), residues: 6720 helix: -0.10 (0.10), residues: 2820 sheet: -0.89 (0.19), residues: 500 loop : -1.41 (0.11), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP a 156 HIS 0.003 0.001 HIS Q 307 PHE 0.013 0.001 PHE W 54 TYR 0.024 0.001 TYR 0 297 ARG 0.006 0.000 ARG I 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10934.11 seconds wall clock time: 193 minutes 58.63 seconds (11638.63 seconds total)