Starting phenix.real_space_refine (version: dev) on Mon Dec 19 03:45:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cbl_30335/12_2022/7cbl_30335_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cbl_30335/12_2022/7cbl_30335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cbl_30335/12_2022/7cbl_30335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cbl_30335/12_2022/7cbl_30335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cbl_30335/12_2022/7cbl_30335_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cbl_30335/12_2022/7cbl_30335_updated_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.092 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 76": "OD1" <-> "OD2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "E ASP 76": "OD1" <-> "OD2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ARG 204": "NH1" <-> "NH2" Residue "F ASP 76": "OD1" <-> "OD2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "G ASP 76": "OD1" <-> "OD2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "I ASP 76": "OD1" <-> "OD2" Residue "I GLU 166": "OE1" <-> "OE2" Residue "I ARG 204": "NH1" <-> "NH2" Residue "J ASP 76": "OD1" <-> "OD2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "J ARG 204": "NH1" <-> "NH2" Residue "K ASP 76": "OD1" <-> "OD2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "L ASP 76": "OD1" <-> "OD2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "L ARG 204": "NH1" <-> "NH2" Residue "M ASP 76": "OD1" <-> "OD2" Residue "M GLU 166": "OE1" <-> "OE2" Residue "M ARG 204": "NH1" <-> "NH2" Residue "N ASP 76": "OD1" <-> "OD2" Residue "N GLU 166": "OE1" <-> "OE2" Residue "N ARG 204": "NH1" <-> "NH2" Residue "O ASP 76": "OD1" <-> "OD2" Residue "O GLU 166": "OE1" <-> "OE2" Residue "O ARG 204": "NH1" <-> "NH2" Residue "P ASP 76": "OD1" <-> "OD2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P ARG 204": "NH1" <-> "NH2" Residue "Q ASP 76": "OD1" <-> "OD2" Residue "Q GLU 166": "OE1" <-> "OE2" Residue "Q ARG 204": "NH1" <-> "NH2" Residue "R ASP 76": "OD1" <-> "OD2" Residue "R GLU 166": "OE1" <-> "OE2" Residue "R ARG 204": "NH1" <-> "NH2" Residue "S ASP 76": "OD1" <-> "OD2" Residue "S GLU 166": "OE1" <-> "OE2" Residue "S ARG 204": "NH1" <-> "NH2" Residue "T ASP 76": "OD1" <-> "OD2" Residue "T GLU 166": "OE1" <-> "OE2" Residue "T ARG 204": "NH1" <-> "NH2" Residue "U ASP 76": "OD1" <-> "OD2" Residue "U GLU 166": "OE1" <-> "OE2" Residue "U ARG 204": "NH1" <-> "NH2" Residue "V ASP 76": "OD1" <-> "OD2" Residue "V GLU 166": "OE1" <-> "OE2" Residue "V ARG 204": "NH1" <-> "NH2" Residue "W ASP 76": "OD1" <-> "OD2" Residue "W GLU 166": "OE1" <-> "OE2" Residue "W ARG 204": "NH1" <-> "NH2" Residue "X ASP 76": "OD1" <-> "OD2" Residue "X GLU 166": "OE1" <-> "OE2" Residue "X ARG 204": "NH1" <-> "NH2" Residue "Y ASP 76": "OD1" <-> "OD2" Residue "Y GLU 166": "OE1" <-> "OE2" Residue "Y ARG 204": "NH1" <-> "NH2" Residue "Z ASP 76": "OD1" <-> "OD2" Residue "Z GLU 166": "OE1" <-> "OE2" Residue "Z ARG 204": "NH1" <-> "NH2" Residue "a ASP 24": "OD1" <-> "OD2" Residue "a ARG 32": "NH1" <-> "NH2" Residue "a PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 117": "NH1" <-> "NH2" Residue "a ARG 164": "NH1" <-> "NH2" Residue "a ARG 173": "NH1" <-> "NH2" Residue "a GLU 192": "OE1" <-> "OE2" Residue "a ARG 234": "NH1" <-> "NH2" Residue "b ASP 24": "OD1" <-> "OD2" Residue "b ARG 32": "NH1" <-> "NH2" Residue "b PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 117": "NH1" <-> "NH2" Residue "b ARG 164": "NH1" <-> "NH2" Residue "b ARG 173": "NH1" <-> "NH2" Residue "b GLU 192": "OE1" <-> "OE2" Residue "b ARG 234": "NH1" <-> "NH2" Residue "c ASP 24": "OD1" <-> "OD2" Residue "c ARG 32": "NH1" <-> "NH2" Residue "c PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 117": "NH1" <-> "NH2" Residue "c ARG 164": "NH1" <-> "NH2" Residue "c ARG 173": "NH1" <-> "NH2" Residue "c GLU 192": "OE1" <-> "OE2" Residue "c ARG 234": "NH1" <-> "NH2" Residue "d ASP 24": "OD1" <-> "OD2" Residue "d ARG 32": "NH1" <-> "NH2" Residue "d PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 117": "NH1" <-> "NH2" Residue "d ARG 164": "NH1" <-> "NH2" Residue "d ARG 173": "NH1" <-> "NH2" Residue "d GLU 192": "OE1" <-> "OE2" Residue "d ARG 234": "NH1" <-> "NH2" Residue "e ASP 24": "OD1" <-> "OD2" Residue "e ARG 32": "NH1" <-> "NH2" Residue "e PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 117": "NH1" <-> "NH2" Residue "e ARG 164": "NH1" <-> "NH2" Residue "e ARG 173": "NH1" <-> "NH2" Residue "e GLU 192": "OE1" <-> "OE2" Residue "e ARG 234": "NH1" <-> "NH2" Residue "f ASP 24": "OD1" <-> "OD2" Residue "f ARG 32": "NH1" <-> "NH2" Residue "f PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 117": "NH1" <-> "NH2" Residue "f ARG 164": "NH1" <-> "NH2" Residue "f ARG 173": "NH1" <-> "NH2" Residue "f GLU 192": "OE1" <-> "OE2" Residue "f ARG 234": "NH1" <-> "NH2" Residue "g ASP 24": "OD1" <-> "OD2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "g PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 117": "NH1" <-> "NH2" Residue "g ARG 164": "NH1" <-> "NH2" Residue "g ARG 173": "NH1" <-> "NH2" Residue "g GLU 192": "OE1" <-> "OE2" Residue "g ARG 234": "NH1" <-> "NH2" Residue "h ASP 24": "OD1" <-> "OD2" Residue "h ARG 32": "NH1" <-> "NH2" Residue "h PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 117": "NH1" <-> "NH2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "h ARG 173": "NH1" <-> "NH2" Residue "h GLU 192": "OE1" <-> "OE2" Residue "h ARG 234": "NH1" <-> "NH2" Residue "i ASP 24": "OD1" <-> "OD2" Residue "i ARG 32": "NH1" <-> "NH2" Residue "i PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 117": "NH1" <-> "NH2" Residue "i ARG 164": "NH1" <-> "NH2" Residue "i ARG 173": "NH1" <-> "NH2" Residue "i GLU 192": "OE1" <-> "OE2" Residue "i ARG 234": "NH1" <-> "NH2" Residue "j ASP 24": "OD1" <-> "OD2" Residue "j ARG 32": "NH1" <-> "NH2" Residue "j PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 117": "NH1" <-> "NH2" Residue "j ARG 164": "NH1" <-> "NH2" Residue "j ARG 173": "NH1" <-> "NH2" Residue "j GLU 192": "OE1" <-> "OE2" Residue "j ARG 234": "NH1" <-> "NH2" Residue "k ASP 24": "OD1" <-> "OD2" Residue "k ARG 32": "NH1" <-> "NH2" Residue "k PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 117": "NH1" <-> "NH2" Residue "k ARG 164": "NH1" <-> "NH2" Residue "k ARG 173": "NH1" <-> "NH2" Residue "k GLU 192": "OE1" <-> "OE2" Residue "k ARG 234": "NH1" <-> "NH2" Residue "l ASP 24": "OD1" <-> "OD2" Residue "l ARG 32": "NH1" <-> "NH2" Residue "l PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 117": "NH1" <-> "NH2" Residue "l ARG 164": "NH1" <-> "NH2" Residue "l ARG 173": "NH1" <-> "NH2" Residue "l GLU 192": "OE1" <-> "OE2" Residue "l ARG 234": "NH1" <-> "NH2" Residue "m ASP 24": "OD1" <-> "OD2" Residue "m ARG 32": "NH1" <-> "NH2" Residue "m PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 117": "NH1" <-> "NH2" Residue "m ARG 164": "NH1" <-> "NH2" Residue "m ARG 173": "NH1" <-> "NH2" Residue "m GLU 192": "OE1" <-> "OE2" Residue "m ARG 234": "NH1" <-> "NH2" Residue "n ASP 24": "OD1" <-> "OD2" Residue "n ARG 32": "NH1" <-> "NH2" Residue "n PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 117": "NH1" <-> "NH2" Residue "n ARG 164": "NH1" <-> "NH2" Residue "n ARG 173": "NH1" <-> "NH2" Residue "n GLU 192": "OE1" <-> "OE2" Residue "n ARG 234": "NH1" <-> "NH2" Residue "o ASP 24": "OD1" <-> "OD2" Residue "o ARG 32": "NH1" <-> "NH2" Residue "o PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 117": "NH1" <-> "NH2" Residue "o ARG 164": "NH1" <-> "NH2" Residue "o ARG 173": "NH1" <-> "NH2" Residue "o GLU 192": "OE1" <-> "OE2" Residue "o ARG 234": "NH1" <-> "NH2" Residue "p ASP 24": "OD1" <-> "OD2" Residue "p ARG 32": "NH1" <-> "NH2" Residue "p PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 117": "NH1" <-> "NH2" Residue "p ARG 164": "NH1" <-> "NH2" Residue "p ARG 173": "NH1" <-> "NH2" Residue "p GLU 192": "OE1" <-> "OE2" Residue "p ARG 234": "NH1" <-> "NH2" Residue "q ASP 24": "OD1" <-> "OD2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 117": "NH1" <-> "NH2" Residue "q ARG 164": "NH1" <-> "NH2" Residue "q ARG 173": "NH1" <-> "NH2" Residue "q GLU 192": "OE1" <-> "OE2" Residue "q ARG 234": "NH1" <-> "NH2" Residue "r ASP 24": "OD1" <-> "OD2" Residue "r ARG 32": "NH1" <-> "NH2" Residue "r PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 117": "NH1" <-> "NH2" Residue "r ARG 164": "NH1" <-> "NH2" Residue "r ARG 173": "NH1" <-> "NH2" Residue "r GLU 192": "OE1" <-> "OE2" Residue "r ARG 234": "NH1" <-> "NH2" Residue "s ASP 24": "OD1" <-> "OD2" Residue "s ARG 32": "NH1" <-> "NH2" Residue "s PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "s ARG 164": "NH1" <-> "NH2" Residue "s ARG 173": "NH1" <-> "NH2" Residue "s GLU 192": "OE1" <-> "OE2" Residue "s ARG 234": "NH1" <-> "NH2" Residue "t ASP 24": "OD1" <-> "OD2" Residue "t ARG 32": "NH1" <-> "NH2" Residue "t PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 117": "NH1" <-> "NH2" Residue "t ARG 164": "NH1" <-> "NH2" Residue "t ARG 173": "NH1" <-> "NH2" Residue "t GLU 192": "OE1" <-> "OE2" Residue "t ARG 234": "NH1" <-> "NH2" Residue "u ASP 24": "OD1" <-> "OD2" Residue "u ARG 32": "NH1" <-> "NH2" Residue "u PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 117": "NH1" <-> "NH2" Residue "u ARG 164": "NH1" <-> "NH2" Residue "u ARG 173": "NH1" <-> "NH2" Residue "u GLU 192": "OE1" <-> "OE2" Residue "u ARG 234": "NH1" <-> "NH2" Residue "v ASP 24": "OD1" <-> "OD2" Residue "v ARG 32": "NH1" <-> "NH2" Residue "v PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 117": "NH1" <-> "NH2" Residue "v ARG 164": "NH1" <-> "NH2" Residue "v ARG 173": "NH1" <-> "NH2" Residue "v GLU 192": "OE1" <-> "OE2" Residue "v ARG 234": "NH1" <-> "NH2" Residue "w ASP 24": "OD1" <-> "OD2" Residue "w ARG 32": "NH1" <-> "NH2" Residue "w PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 117": "NH1" <-> "NH2" Residue "w ARG 164": "NH1" <-> "NH2" Residue "w ARG 173": "NH1" <-> "NH2" Residue "w GLU 192": "OE1" <-> "OE2" Residue "w ARG 234": "NH1" <-> "NH2" Residue "x ASP 24": "OD1" <-> "OD2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "x PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 117": "NH1" <-> "NH2" Residue "x ARG 164": "NH1" <-> "NH2" Residue "x ARG 173": "NH1" <-> "NH2" Residue "x GLU 192": "OE1" <-> "OE2" Residue "x ARG 234": "NH1" <-> "NH2" Residue "y ASP 24": "OD1" <-> "OD2" Residue "y ARG 32": "NH1" <-> "NH2" Residue "y PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 117": "NH1" <-> "NH2" Residue "y ARG 164": "NH1" <-> "NH2" Residue "y ARG 173": "NH1" <-> "NH2" Residue "y GLU 192": "OE1" <-> "OE2" Residue "y ARG 234": "NH1" <-> "NH2" Residue "z ASP 24": "OD1" <-> "OD2" Residue "z ARG 32": "NH1" <-> "NH2" Residue "z PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 117": "NH1" <-> "NH2" Residue "z ARG 164": "NH1" <-> "NH2" Residue "z ARG 173": "NH1" <-> "NH2" Residue "z GLU 192": "OE1" <-> "OE2" Residue "z ARG 234": "NH1" <-> "NH2" Time to flip residues: 0.29s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 99242 Number of models: 1 Model: "" Number of chains: 78 Chain: "A" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "B" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "C" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "D" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "E" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "F" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "G" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "H" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "I" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "J" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "K" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "L" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "M" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "N" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "O" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "P" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "Q" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "R" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "S" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "T" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "U" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "V" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "W" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "X" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "Y" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "Z" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "a" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "b" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "c" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "d" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "e" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "f" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "g" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "h" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "i" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "j" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "k" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "l" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "m" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "n" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "o" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "p" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "q" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "r" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "s" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "t" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "u" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "v" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "w" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "x" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "y" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "z" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2228 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 40.15, per 1000 atoms: 0.40 Number of scatterers: 99242 At special positions: 0 Unit cell: (267.935, 269.242, 147.691, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 442 16.00 O 19656 8.00 N 17862 7.00 C 61282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS a 273 " - pdb=" SG CYS a 357 " distance=2.04 Simple disulfide: pdb=" SG CYS b 273 " - pdb=" SG CYS b 357 " distance=2.04 Simple disulfide: pdb=" SG CYS c 273 " - pdb=" SG CYS c 357 " distance=2.04 Simple disulfide: pdb=" SG CYS d 273 " - pdb=" SG CYS d 357 " distance=2.04 Simple disulfide: pdb=" SG CYS e 273 " - pdb=" SG CYS e 357 " distance=2.04 Simple disulfide: pdb=" SG CYS f 273 " - pdb=" SG CYS f 357 " distance=2.04 Simple disulfide: pdb=" SG CYS g 273 " - pdb=" SG CYS g 357 " distance=2.03 Simple disulfide: pdb=" SG CYS h 273 " - pdb=" SG CYS h 357 " distance=2.04 Simple disulfide: pdb=" SG CYS i 273 " - pdb=" SG CYS i 357 " distance=2.04 Simple disulfide: pdb=" SG CYS j 273 " - pdb=" SG CYS j 357 " distance=2.04 Simple disulfide: pdb=" SG CYS k 273 " - pdb=" SG CYS k 357 " distance=2.04 Simple disulfide: pdb=" SG CYS l 273 " - pdb=" SG CYS l 357 " distance=2.04 Simple disulfide: pdb=" SG CYS m 273 " - pdb=" SG CYS m 357 " distance=2.04 Simple disulfide: pdb=" SG CYS n 273 " - pdb=" SG CYS n 357 " distance=2.04 Simple disulfide: pdb=" SG CYS o 273 " - pdb=" SG CYS o 357 " distance=2.04 Simple disulfide: pdb=" SG CYS p 273 " - pdb=" SG CYS p 357 " distance=2.04 Simple disulfide: pdb=" SG CYS q 273 " - pdb=" SG CYS q 357 " distance=2.04 Simple disulfide: pdb=" SG CYS r 273 " - pdb=" SG CYS r 357 " distance=2.04 Simple disulfide: pdb=" SG CYS s 273 " - pdb=" SG CYS s 357 " distance=2.04 Simple disulfide: pdb=" SG CYS t 273 " - pdb=" SG CYS t 357 " distance=2.04 Simple disulfide: pdb=" SG CYS u 273 " - pdb=" SG CYS u 357 " distance=2.04 Simple disulfide: pdb=" SG CYS v 273 " - pdb=" SG CYS v 357 " distance=2.04 Simple disulfide: pdb=" SG CYS w 273 " - pdb=" SG CYS w 357 " distance=2.04 Simple disulfide: pdb=" SG CYS x 273 " - pdb=" SG CYS x 357 " distance=2.04 Simple disulfide: pdb=" SG CYS y 273 " - pdb=" SG CYS y 357 " distance=2.04 Simple disulfide: pdb=" SG CYS z 273 " - pdb=" SG CYS z 357 " distance=2.04 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=26, symmetry=0 Number of additional bonds: simple=26, symmetry=0 Coordination: Other bonds: Time building additional restraints: 28.91 Conformation dependent library (CDL) restraints added in 12.1 seconds 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 286 helices and 156 sheets defined 19.1% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.58 Creating SS restraints... Processing helix chain 'A' and resid 111 through 120 removed outlier: 5.073A pdb=" N GLY A 115 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE A 117 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A 120 " --> pdb=" O PHE A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 212 through 217 removed outlier: 4.198A pdb=" N GLN A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE B 117 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY B 118 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN B 119 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER B 120 " --> pdb=" O PHE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN B 217 " --> pdb=" O ILE B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 removed outlier: 3.519A pdb=" N ASN B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY C 115 " --> pdb=" O TYR C 112 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE C 117 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY C 118 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN C 119 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER C 120 " --> pdb=" O PHE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 212 through 217 removed outlier: 4.198A pdb=" N GLN C 217 " --> pdb=" O ILE C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 120 removed outlier: 5.075A pdb=" N GLY D 115 " --> pdb=" O TYR D 112 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE D 117 " --> pdb=" O GLN D 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY D 118 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASN D 119 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER D 120 " --> pdb=" O PHE D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN D 217 " --> pdb=" O ILE D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY E 115 " --> pdb=" O TYR E 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE E 117 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY E 118 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN E 119 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER E 120 " --> pdb=" O PHE E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN E 217 " --> pdb=" O ILE E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY F 115 " --> pdb=" O TYR F 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE F 117 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY F 118 " --> pdb=" O GLY F 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN F 119 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER F 120 " --> pdb=" O PHE F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 188 No H-bonds generated for 'chain 'F' and resid 186 through 188' Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 212 through 217 removed outlier: 4.198A pdb=" N GLN F 217 " --> pdb=" O ILE F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 120 removed outlier: 5.073A pdb=" N GLY G 115 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE G 117 " --> pdb=" O GLN G 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY G 118 " --> pdb=" O GLY G 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN G 119 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER G 120 " --> pdb=" O PHE G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 188 No H-bonds generated for 'chain 'G' and resid 186 through 188' Processing helix chain 'G' and resid 197 through 199 No H-bonds generated for 'chain 'G' and resid 197 through 199' Processing helix chain 'G' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN G 217 " --> pdb=" O ILE G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 229 removed outlier: 3.519A pdb=" N ASN G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 120 removed outlier: 5.073A pdb=" N GLY H 115 " --> pdb=" O TYR H 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE H 117 " --> pdb=" O GLN H 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY H 118 " --> pdb=" O GLY H 115 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN H 119 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER H 120 " --> pdb=" O PHE H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 188 No H-bonds generated for 'chain 'H' and resid 186 through 188' Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 212 through 217 removed outlier: 4.198A pdb=" N GLN H 217 " --> pdb=" O ILE H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 229 removed outlier: 3.519A pdb=" N ASN H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY I 115 " --> pdb=" O TYR I 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE I 117 " --> pdb=" O GLN I 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY I 118 " --> pdb=" O GLY I 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN I 119 " --> pdb=" O LEU I 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER I 120 " --> pdb=" O PHE I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 188 No H-bonds generated for 'chain 'I' and resid 186 through 188' Processing helix chain 'I' and resid 197 through 199 No H-bonds generated for 'chain 'I' and resid 197 through 199' Processing helix chain 'I' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN I 217 " --> pdb=" O ILE I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN I 228 " --> pdb=" O ARG I 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY J 115 " --> pdb=" O TYR J 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE J 117 " --> pdb=" O GLN J 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY J 118 " --> pdb=" O GLY J 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN J 119 " --> pdb=" O LEU J 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER J 120 " --> pdb=" O PHE J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 188 No H-bonds generated for 'chain 'J' and resid 186 through 188' Processing helix chain 'J' and resid 197 through 199 No H-bonds generated for 'chain 'J' and resid 197 through 199' Processing helix chain 'J' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN J 217 " --> pdb=" O ILE J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 229 removed outlier: 3.521A pdb=" N ASN J 228 " --> pdb=" O ARG J 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY K 115 " --> pdb=" O TYR K 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE K 117 " --> pdb=" O GLN K 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY K 118 " --> pdb=" O GLY K 115 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN K 119 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER K 120 " --> pdb=" O PHE K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 188 No H-bonds generated for 'chain 'K' and resid 186 through 188' Processing helix chain 'K' and resid 197 through 199 No H-bonds generated for 'chain 'K' and resid 197 through 199' Processing helix chain 'K' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN K 217 " --> pdb=" O ILE K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 229 removed outlier: 3.519A pdb=" N ASN K 228 " --> pdb=" O ARG K 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY L 115 " --> pdb=" O TYR L 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE L 117 " --> pdb=" O GLN L 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY L 118 " --> pdb=" O GLY L 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN L 119 " --> pdb=" O LEU L 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER L 120 " --> pdb=" O PHE L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 188 No H-bonds generated for 'chain 'L' and resid 186 through 188' Processing helix chain 'L' and resid 197 through 199 No H-bonds generated for 'chain 'L' and resid 197 through 199' Processing helix chain 'L' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN L 217 " --> pdb=" O ILE L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN L 228 " --> pdb=" O ARG L 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY M 115 " --> pdb=" O TYR M 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE M 117 " --> pdb=" O GLN M 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY M 118 " --> pdb=" O GLY M 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN M 119 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER M 120 " --> pdb=" O PHE M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 188 No H-bonds generated for 'chain 'M' and resid 186 through 188' Processing helix chain 'M' and resid 197 through 199 No H-bonds generated for 'chain 'M' and resid 197 through 199' Processing helix chain 'M' and resid 212 through 217 removed outlier: 4.198A pdb=" N GLN M 217 " --> pdb=" O ILE M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN M 228 " --> pdb=" O ARG M 224 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 120 removed outlier: 5.073A pdb=" N GLY N 115 " --> pdb=" O TYR N 112 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE N 117 " --> pdb=" O GLN N 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY N 118 " --> pdb=" O GLY N 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN N 119 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER N 120 " --> pdb=" O PHE N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 197 through 199 No H-bonds generated for 'chain 'N' and resid 197 through 199' Processing helix chain 'N' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN N 217 " --> pdb=" O ILE N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN N 228 " --> pdb=" O ARG N 224 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY O 115 " --> pdb=" O TYR O 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE O 117 " --> pdb=" O GLN O 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY O 118 " --> pdb=" O GLY O 115 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN O 119 " --> pdb=" O LEU O 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER O 120 " --> pdb=" O PHE O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 188 No H-bonds generated for 'chain 'O' and resid 186 through 188' Processing helix chain 'O' and resid 197 through 199 No H-bonds generated for 'chain 'O' and resid 197 through 199' Processing helix chain 'O' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN O 217 " --> pdb=" O ILE O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN O 228 " --> pdb=" O ARG O 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY P 115 " --> pdb=" O TYR P 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE P 117 " --> pdb=" O GLN P 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY P 118 " --> pdb=" O GLY P 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN P 119 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER P 120 " --> pdb=" O PHE P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 186 through 188 No H-bonds generated for 'chain 'P' and resid 186 through 188' Processing helix chain 'P' and resid 197 through 199 No H-bonds generated for 'chain 'P' and resid 197 through 199' Processing helix chain 'P' and resid 212 through 217 removed outlier: 4.198A pdb=" N GLN P 217 " --> pdb=" O ILE P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN P 228 " --> pdb=" O ARG P 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY Q 115 " --> pdb=" O TYR Q 112 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE Q 117 " --> pdb=" O GLN Q 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY Q 118 " --> pdb=" O GLY Q 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN Q 119 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER Q 120 " --> pdb=" O PHE Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 186 through 188 No H-bonds generated for 'chain 'Q' and resid 186 through 188' Processing helix chain 'Q' and resid 197 through 199 No H-bonds generated for 'chain 'Q' and resid 197 through 199' Processing helix chain 'Q' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN Q 217 " --> pdb=" O ILE Q 213 " (cutoff:3.500A) Processing helix chain 'Q' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN Q 228 " --> pdb=" O ARG Q 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY R 115 " --> pdb=" O TYR R 112 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE R 117 " --> pdb=" O GLN R 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY R 118 " --> pdb=" O GLY R 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN R 119 " --> pdb=" O LEU R 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER R 120 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 188 No H-bonds generated for 'chain 'R' and resid 186 through 188' Processing helix chain 'R' and resid 197 through 199 No H-bonds generated for 'chain 'R' and resid 197 through 199' Processing helix chain 'R' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN R 217 " --> pdb=" O ILE R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN R 228 " --> pdb=" O ARG R 224 " (cutoff:3.500A) Processing helix chain 'S' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY S 115 " --> pdb=" O TYR S 112 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE S 117 " --> pdb=" O GLN S 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY S 118 " --> pdb=" O GLY S 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN S 119 " --> pdb=" O LEU S 116 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER S 120 " --> pdb=" O PHE S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 186 through 188 No H-bonds generated for 'chain 'S' and resid 186 through 188' Processing helix chain 'S' and resid 197 through 199 No H-bonds generated for 'chain 'S' and resid 197 through 199' Processing helix chain 'S' and resid 212 through 217 removed outlier: 4.198A pdb=" N GLN S 217 " --> pdb=" O ILE S 213 " (cutoff:3.500A) Processing helix chain 'S' and resid 221 through 229 removed outlier: 3.521A pdb=" N ASN S 228 " --> pdb=" O ARG S 224 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 120 removed outlier: 5.075A pdb=" N GLY T 115 " --> pdb=" O TYR T 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE T 117 " --> pdb=" O GLN T 114 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY T 118 " --> pdb=" O GLY T 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN T 119 " --> pdb=" O LEU T 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER T 120 " --> pdb=" O PHE T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 188 No H-bonds generated for 'chain 'T' and resid 186 through 188' Processing helix chain 'T' and resid 197 through 199 No H-bonds generated for 'chain 'T' and resid 197 through 199' Processing helix chain 'T' and resid 212 through 217 removed outlier: 4.198A pdb=" N GLN T 217 " --> pdb=" O ILE T 213 " (cutoff:3.500A) Processing helix chain 'T' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN T 228 " --> pdb=" O ARG T 224 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY U 115 " --> pdb=" O TYR U 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE U 117 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY U 118 " --> pdb=" O GLY U 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN U 119 " --> pdb=" O LEU U 116 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER U 120 " --> pdb=" O PHE U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 186 through 188 No H-bonds generated for 'chain 'U' and resid 186 through 188' Processing helix chain 'U' and resid 197 through 199 No H-bonds generated for 'chain 'U' and resid 197 through 199' Processing helix chain 'U' and resid 212 through 217 removed outlier: 4.198A pdb=" N GLN U 217 " --> pdb=" O ILE U 213 " (cutoff:3.500A) Processing helix chain 'U' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN U 228 " --> pdb=" O ARG U 224 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY V 115 " --> pdb=" O TYR V 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE V 117 " --> pdb=" O GLN V 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY V 118 " --> pdb=" O GLY V 115 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASN V 119 " --> pdb=" O LEU V 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER V 120 " --> pdb=" O PHE V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 186 through 188 No H-bonds generated for 'chain 'V' and resid 186 through 188' Processing helix chain 'V' and resid 197 through 199 No H-bonds generated for 'chain 'V' and resid 197 through 199' Processing helix chain 'V' and resid 212 through 217 removed outlier: 4.198A pdb=" N GLN V 217 " --> pdb=" O ILE V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN V 228 " --> pdb=" O ARG V 224 " (cutoff:3.500A) Processing helix chain 'W' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY W 115 " --> pdb=" O TYR W 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE W 117 " --> pdb=" O GLN W 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY W 118 " --> pdb=" O GLY W 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN W 119 " --> pdb=" O LEU W 116 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER W 120 " --> pdb=" O PHE W 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 186 through 188 No H-bonds generated for 'chain 'W' and resid 186 through 188' Processing helix chain 'W' and resid 197 through 199 No H-bonds generated for 'chain 'W' and resid 197 through 199' Processing helix chain 'W' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN W 217 " --> pdb=" O ILE W 213 " (cutoff:3.500A) Processing helix chain 'W' and resid 221 through 229 removed outlier: 3.519A pdb=" N ASN W 228 " --> pdb=" O ARG W 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY X 115 " --> pdb=" O TYR X 112 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE X 117 " --> pdb=" O GLN X 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY X 118 " --> pdb=" O GLY X 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN X 119 " --> pdb=" O LEU X 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER X 120 " --> pdb=" O PHE X 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 188 No H-bonds generated for 'chain 'X' and resid 186 through 188' Processing helix chain 'X' and resid 197 through 199 No H-bonds generated for 'chain 'X' and resid 197 through 199' Processing helix chain 'X' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN X 217 " --> pdb=" O ILE X 213 " (cutoff:3.500A) Processing helix chain 'X' and resid 221 through 229 removed outlier: 3.519A pdb=" N ASN X 228 " --> pdb=" O ARG X 224 " (cutoff:3.500A) Processing helix chain 'Y' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY Y 115 " --> pdb=" O TYR Y 112 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE Y 117 " --> pdb=" O GLN Y 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY Y 118 " --> pdb=" O GLY Y 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN Y 119 " --> pdb=" O LEU Y 116 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER Y 120 " --> pdb=" O PHE Y 117 " (cutoff:3.500A) Processing helix chain 'Y' and resid 186 through 188 No H-bonds generated for 'chain 'Y' and resid 186 through 188' Processing helix chain 'Y' and resid 197 through 199 No H-bonds generated for 'chain 'Y' and resid 197 through 199' Processing helix chain 'Y' and resid 212 through 217 removed outlier: 4.198A pdb=" N GLN Y 217 " --> pdb=" O ILE Y 213 " (cutoff:3.500A) Processing helix chain 'Y' and resid 221 through 229 removed outlier: 3.520A pdb=" N ASN Y 228 " --> pdb=" O ARG Y 224 " (cutoff:3.500A) Processing helix chain 'Z' and resid 111 through 120 removed outlier: 5.074A pdb=" N GLY Z 115 " --> pdb=" O TYR Z 112 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE Z 117 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY Z 118 " --> pdb=" O GLY Z 115 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN Z 119 " --> pdb=" O LEU Z 116 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER Z 120 " --> pdb=" O PHE Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 188 No H-bonds generated for 'chain 'Z' and resid 186 through 188' Processing helix chain 'Z' and resid 197 through 199 No H-bonds generated for 'chain 'Z' and resid 197 through 199' Processing helix chain 'Z' and resid 212 through 217 removed outlier: 4.197A pdb=" N GLN Z 217 " --> pdb=" O ILE Z 213 " (cutoff:3.500A) Processing helix chain 'Z' and resid 221 through 229 removed outlier: 3.519A pdb=" N ASN Z 228 " --> pdb=" O ARG Z 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 25 No H-bonds generated for 'chain 'a' and resid 22 through 25' Processing helix chain 'a' and resid 56 through 69 Processing helix chain 'a' and resid 194 through 207 Processing helix chain 'a' and resid 230 through 239 Processing helix chain 'a' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU a 338 " --> pdb=" O ALA a 334 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 355 removed outlier: 4.076A pdb=" N SER a 347 " --> pdb=" O MET a 343 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 25 No H-bonds generated for 'chain 'b' and resid 22 through 25' Processing helix chain 'b' and resid 56 through 69 Processing helix chain 'b' and resid 194 through 207 Processing helix chain 'b' and resid 230 through 239 Processing helix chain 'b' and resid 328 through 338 removed outlier: 3.953A pdb=" N LEU b 338 " --> pdb=" O ALA b 334 " (cutoff:3.500A) Processing helix chain 'b' and resid 342 through 355 removed outlier: 4.076A pdb=" N SER b 347 " --> pdb=" O MET b 343 " (cutoff:3.500A) Processing helix chain 'c' and resid 22 through 25 No H-bonds generated for 'chain 'c' and resid 22 through 25' Processing helix chain 'c' and resid 56 through 69 Processing helix chain 'c' and resid 194 through 207 Processing helix chain 'c' and resid 230 through 239 Processing helix chain 'c' and resid 328 through 338 removed outlier: 3.953A pdb=" N LEU c 338 " --> pdb=" O ALA c 334 " (cutoff:3.500A) Processing helix chain 'c' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER c 347 " --> pdb=" O MET c 343 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 25 No H-bonds generated for 'chain 'd' and resid 22 through 25' Processing helix chain 'd' and resid 56 through 69 Processing helix chain 'd' and resid 194 through 207 Processing helix chain 'd' and resid 230 through 239 Processing helix chain 'd' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU d 338 " --> pdb=" O ALA d 334 " (cutoff:3.500A) Processing helix chain 'd' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER d 347 " --> pdb=" O MET d 343 " (cutoff:3.500A) Processing helix chain 'e' and resid 22 through 25 No H-bonds generated for 'chain 'e' and resid 22 through 25' Processing helix chain 'e' and resid 56 through 69 Processing helix chain 'e' and resid 194 through 207 Processing helix chain 'e' and resid 230 through 239 Processing helix chain 'e' and resid 328 through 338 removed outlier: 3.953A pdb=" N LEU e 338 " --> pdb=" O ALA e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER e 347 " --> pdb=" O MET e 343 " (cutoff:3.500A) Processing helix chain 'f' and resid 22 through 25 No H-bonds generated for 'chain 'f' and resid 22 through 25' Processing helix chain 'f' and resid 56 through 69 Processing helix chain 'f' and resid 194 through 207 Processing helix chain 'f' and resid 230 through 239 Processing helix chain 'f' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU f 338 " --> pdb=" O ALA f 334 " (cutoff:3.500A) Processing helix chain 'f' and resid 342 through 355 removed outlier: 4.076A pdb=" N SER f 347 " --> pdb=" O MET f 343 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 25 No H-bonds generated for 'chain 'g' and resid 22 through 25' Processing helix chain 'g' and resid 56 through 69 Processing helix chain 'g' and resid 194 through 207 Processing helix chain 'g' and resid 230 through 239 Processing helix chain 'g' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU g 338 " --> pdb=" O ALA g 334 " (cutoff:3.500A) Processing helix chain 'g' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER g 347 " --> pdb=" O MET g 343 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 25 No H-bonds generated for 'chain 'h' and resid 22 through 25' Processing helix chain 'h' and resid 56 through 69 Processing helix chain 'h' and resid 194 through 207 Processing helix chain 'h' and resid 230 through 239 Processing helix chain 'h' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU h 338 " --> pdb=" O ALA h 334 " (cutoff:3.500A) Processing helix chain 'h' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER h 347 " --> pdb=" O MET h 343 " (cutoff:3.500A) Processing helix chain 'i' and resid 22 through 25 No H-bonds generated for 'chain 'i' and resid 22 through 25' Processing helix chain 'i' and resid 56 through 69 Processing helix chain 'i' and resid 194 through 207 Processing helix chain 'i' and resid 230 through 239 Processing helix chain 'i' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU i 338 " --> pdb=" O ALA i 334 " (cutoff:3.500A) Processing helix chain 'i' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER i 347 " --> pdb=" O MET i 343 " (cutoff:3.500A) Processing helix chain 'j' and resid 22 through 25 No H-bonds generated for 'chain 'j' and resid 22 through 25' Processing helix chain 'j' and resid 56 through 69 Processing helix chain 'j' and resid 194 through 207 Processing helix chain 'j' and resid 230 through 239 Processing helix chain 'j' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU j 338 " --> pdb=" O ALA j 334 " (cutoff:3.500A) Processing helix chain 'j' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER j 347 " --> pdb=" O MET j 343 " (cutoff:3.500A) Processing helix chain 'k' and resid 22 through 25 No H-bonds generated for 'chain 'k' and resid 22 through 25' Processing helix chain 'k' and resid 56 through 69 Processing helix chain 'k' and resid 194 through 207 Processing helix chain 'k' and resid 230 through 239 Processing helix chain 'k' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU k 338 " --> pdb=" O ALA k 334 " (cutoff:3.500A) Processing helix chain 'k' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER k 347 " --> pdb=" O MET k 343 " (cutoff:3.500A) Processing helix chain 'l' and resid 22 through 25 No H-bonds generated for 'chain 'l' and resid 22 through 25' Processing helix chain 'l' and resid 56 through 69 Processing helix chain 'l' and resid 194 through 207 Processing helix chain 'l' and resid 230 through 239 Processing helix chain 'l' and resid 328 through 338 removed outlier: 3.953A pdb=" N LEU l 338 " --> pdb=" O ALA l 334 " (cutoff:3.500A) Processing helix chain 'l' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER l 347 " --> pdb=" O MET l 343 " (cutoff:3.500A) Processing helix chain 'm' and resid 22 through 25 No H-bonds generated for 'chain 'm' and resid 22 through 25' Processing helix chain 'm' and resid 56 through 69 Processing helix chain 'm' and resid 194 through 207 Processing helix chain 'm' and resid 230 through 239 Processing helix chain 'm' and resid 328 through 338 removed outlier: 3.953A pdb=" N LEU m 338 " --> pdb=" O ALA m 334 " (cutoff:3.500A) Processing helix chain 'm' and resid 342 through 355 removed outlier: 4.076A pdb=" N SER m 347 " --> pdb=" O MET m 343 " (cutoff:3.500A) Processing helix chain 'n' and resid 22 through 25 No H-bonds generated for 'chain 'n' and resid 22 through 25' Processing helix chain 'n' and resid 56 through 69 Processing helix chain 'n' and resid 194 through 207 Processing helix chain 'n' and resid 230 through 239 Processing helix chain 'n' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU n 338 " --> pdb=" O ALA n 334 " (cutoff:3.500A) Processing helix chain 'n' and resid 342 through 355 removed outlier: 4.076A pdb=" N SER n 347 " --> pdb=" O MET n 343 " (cutoff:3.500A) Processing helix chain 'o' and resid 22 through 25 No H-bonds generated for 'chain 'o' and resid 22 through 25' Processing helix chain 'o' and resid 56 through 69 Processing helix chain 'o' and resid 194 through 207 Processing helix chain 'o' and resid 230 through 239 Processing helix chain 'o' and resid 328 through 338 removed outlier: 3.953A pdb=" N LEU o 338 " --> pdb=" O ALA o 334 " (cutoff:3.500A) Processing helix chain 'o' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER o 347 " --> pdb=" O MET o 343 " (cutoff:3.500A) Processing helix chain 'p' and resid 22 through 25 No H-bonds generated for 'chain 'p' and resid 22 through 25' Processing helix chain 'p' and resid 56 through 69 Processing helix chain 'p' and resid 194 through 207 Processing helix chain 'p' and resid 230 through 239 Processing helix chain 'p' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU p 338 " --> pdb=" O ALA p 334 " (cutoff:3.500A) Processing helix chain 'p' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER p 347 " --> pdb=" O MET p 343 " (cutoff:3.500A) Processing helix chain 'q' and resid 22 through 25 No H-bonds generated for 'chain 'q' and resid 22 through 25' Processing helix chain 'q' and resid 56 through 69 Processing helix chain 'q' and resid 194 through 207 Processing helix chain 'q' and resid 230 through 239 Processing helix chain 'q' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU q 338 " --> pdb=" O ALA q 334 " (cutoff:3.500A) Processing helix chain 'q' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER q 347 " --> pdb=" O MET q 343 " (cutoff:3.500A) Processing helix chain 'r' and resid 22 through 25 No H-bonds generated for 'chain 'r' and resid 22 through 25' Processing helix chain 'r' and resid 56 through 69 Processing helix chain 'r' and resid 194 through 207 Processing helix chain 'r' and resid 230 through 239 Processing helix chain 'r' and resid 328 through 338 removed outlier: 3.953A pdb=" N LEU r 338 " --> pdb=" O ALA r 334 " (cutoff:3.500A) Processing helix chain 'r' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER r 347 " --> pdb=" O MET r 343 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 25 No H-bonds generated for 'chain 's' and resid 22 through 25' Processing helix chain 's' and resid 56 through 69 Processing helix chain 's' and resid 194 through 207 Processing helix chain 's' and resid 230 through 239 Processing helix chain 's' and resid 328 through 338 removed outlier: 3.953A pdb=" N LEU s 338 " --> pdb=" O ALA s 334 " (cutoff:3.500A) Processing helix chain 's' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER s 347 " --> pdb=" O MET s 343 " (cutoff:3.500A) Processing helix chain 't' and resid 22 through 25 No H-bonds generated for 'chain 't' and resid 22 through 25' Processing helix chain 't' and resid 56 through 69 Processing helix chain 't' and resid 194 through 207 Processing helix chain 't' and resid 230 through 239 Processing helix chain 't' and resid 328 through 338 removed outlier: 3.953A pdb=" N LEU t 338 " --> pdb=" O ALA t 334 " (cutoff:3.500A) Processing helix chain 't' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER t 347 " --> pdb=" O MET t 343 " (cutoff:3.500A) Processing helix chain 'u' and resid 22 through 25 No H-bonds generated for 'chain 'u' and resid 22 through 25' Processing helix chain 'u' and resid 56 through 69 Processing helix chain 'u' and resid 194 through 207 Processing helix chain 'u' and resid 230 through 239 Processing helix chain 'u' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU u 338 " --> pdb=" O ALA u 334 " (cutoff:3.500A) Processing helix chain 'u' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER u 347 " --> pdb=" O MET u 343 " (cutoff:3.500A) Processing helix chain 'v' and resid 22 through 25 No H-bonds generated for 'chain 'v' and resid 22 through 25' Processing helix chain 'v' and resid 56 through 69 Processing helix chain 'v' and resid 194 through 207 Processing helix chain 'v' and resid 230 through 239 Processing helix chain 'v' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU v 338 " --> pdb=" O ALA v 334 " (cutoff:3.500A) Processing helix chain 'v' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER v 347 " --> pdb=" O MET v 343 " (cutoff:3.500A) Processing helix chain 'w' and resid 22 through 25 No H-bonds generated for 'chain 'w' and resid 22 through 25' Processing helix chain 'w' and resid 56 through 69 Processing helix chain 'w' and resid 194 through 207 Processing helix chain 'w' and resid 230 through 239 Processing helix chain 'w' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU w 338 " --> pdb=" O ALA w 334 " (cutoff:3.500A) Processing helix chain 'w' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER w 347 " --> pdb=" O MET w 343 " (cutoff:3.500A) Processing helix chain 'x' and resid 22 through 25 No H-bonds generated for 'chain 'x' and resid 22 through 25' Processing helix chain 'x' and resid 56 through 69 Processing helix chain 'x' and resid 194 through 207 Processing helix chain 'x' and resid 230 through 239 Processing helix chain 'x' and resid 328 through 338 removed outlier: 3.953A pdb=" N LEU x 338 " --> pdb=" O ALA x 334 " (cutoff:3.500A) Processing helix chain 'x' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER x 347 " --> pdb=" O MET x 343 " (cutoff:3.500A) Processing helix chain 'y' and resid 22 through 25 No H-bonds generated for 'chain 'y' and resid 22 through 25' Processing helix chain 'y' and resid 56 through 69 Processing helix chain 'y' and resid 194 through 207 Processing helix chain 'y' and resid 230 through 239 Processing helix chain 'y' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU y 338 " --> pdb=" O ALA y 334 " (cutoff:3.500A) Processing helix chain 'y' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER y 347 " --> pdb=" O MET y 343 " (cutoff:3.500A) Processing helix chain 'z' and resid 22 through 25 No H-bonds generated for 'chain 'z' and resid 22 through 25' Processing helix chain 'z' and resid 56 through 69 Processing helix chain 'z' and resid 194 through 207 Processing helix chain 'z' and resid 230 through 239 Processing helix chain 'z' and resid 328 through 338 removed outlier: 3.954A pdb=" N LEU z 338 " --> pdb=" O ALA z 334 " (cutoff:3.500A) Processing helix chain 'z' and resid 342 through 355 removed outlier: 4.077A pdb=" N SER z 347 " --> pdb=" O MET z 343 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 194 through 196 removed outlier: 9.102A pdb=" N VAL A 195 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 79 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR A 147 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N GLN A 168 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR A 149 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU A 166 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS A 162 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR A 175 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 194 through 196 removed outlier: 9.102A pdb=" N VAL B 195 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 79 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR B 147 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN B 168 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR B 149 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU B 166 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS B 162 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 175 " --> pdb=" O ASN B 210 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL C 195 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR C 79 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR C 147 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN C 168 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR C 149 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU C 166 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS C 162 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 175 " --> pdb=" O ASN C 210 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL D 195 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR D 79 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR D 147 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN D 168 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR D 149 " --> pdb=" O GLU D 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU D 166 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS D 162 " --> pdb=" O ASP D 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR D 175 " --> pdb=" O ASN D 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL E 195 " --> pdb=" O THR E 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR E 79 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR E 147 " --> pdb=" O GLN E 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN E 168 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR E 149 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU E 166 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS E 162 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR E 175 " --> pdb=" O ASN E 210 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 194 through 196 removed outlier: 9.100A pdb=" N VAL F 195 " --> pdb=" O THR F 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR F 79 " --> pdb=" O VAL F 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR F 147 " --> pdb=" O GLN F 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN F 168 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR F 149 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU F 166 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS F 162 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR F 175 " --> pdb=" O ASN F 210 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL G 195 " --> pdb=" O THR G 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR G 79 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N THR G 147 " --> pdb=" O GLN G 168 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N GLN G 168 " --> pdb=" O THR G 147 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR G 149 " --> pdb=" O GLU G 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU G 166 " --> pdb=" O THR G 149 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N HIS G 162 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR G 175 " --> pdb=" O ASN G 210 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL H 195 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR H 79 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR H 147 " --> pdb=" O GLN H 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN H 168 " --> pdb=" O THR H 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR H 149 " --> pdb=" O GLU H 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU H 166 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS H 162 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR H 175 " --> pdb=" O ASN H 210 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL I 195 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR I 79 " --> pdb=" O VAL I 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR I 147 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN I 168 " --> pdb=" O THR I 147 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR I 149 " --> pdb=" O GLU I 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU I 166 " --> pdb=" O THR I 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS I 162 " --> pdb=" O ASP I 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR I 175 " --> pdb=" O ASN I 210 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 194 through 196 removed outlier: 9.102A pdb=" N VAL J 195 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR J 79 " --> pdb=" O VAL J 195 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N THR J 147 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN J 168 " --> pdb=" O THR J 147 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR J 149 " --> pdb=" O GLU J 166 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU J 166 " --> pdb=" O THR J 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS J 162 " --> pdb=" O ASP J 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR J 175 " --> pdb=" O ASN J 210 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 194 through 196 removed outlier: 9.102A pdb=" N VAL K 195 " --> pdb=" O THR K 77 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR K 79 " --> pdb=" O VAL K 195 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N THR K 147 " --> pdb=" O GLN K 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN K 168 " --> pdb=" O THR K 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR K 149 " --> pdb=" O GLU K 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU K 166 " --> pdb=" O THR K 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS K 162 " --> pdb=" O ASP K 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR K 175 " --> pdb=" O ASN K 210 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL L 195 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR L 79 " --> pdb=" O VAL L 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR L 147 " --> pdb=" O GLN L 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN L 168 " --> pdb=" O THR L 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR L 149 " --> pdb=" O GLU L 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU L 166 " --> pdb=" O THR L 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS L 162 " --> pdb=" O ASP L 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR L 175 " --> pdb=" O ASN L 210 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL M 195 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR M 79 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR M 147 " --> pdb=" O GLN M 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN M 168 " --> pdb=" O THR M 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR M 149 " --> pdb=" O GLU M 166 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU M 166 " --> pdb=" O THR M 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS M 162 " --> pdb=" O ASP M 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR M 175 " --> pdb=" O ASN M 210 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL N 195 " --> pdb=" O THR N 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR N 79 " --> pdb=" O VAL N 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR N 147 " --> pdb=" O GLN N 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN N 168 " --> pdb=" O THR N 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR N 149 " --> pdb=" O GLU N 166 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU N 166 " --> pdb=" O THR N 149 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS N 162 " --> pdb=" O ASP N 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR N 175 " --> pdb=" O ASN N 210 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'O' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL O 195 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR O 79 " --> pdb=" O VAL O 195 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N THR O 147 " --> pdb=" O GLN O 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN O 168 " --> pdb=" O THR O 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR O 149 " --> pdb=" O GLU O 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU O 166 " --> pdb=" O THR O 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS O 162 " --> pdb=" O ASP O 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR O 175 " --> pdb=" O ASN O 210 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'P' and resid 194 through 196 removed outlier: 9.102A pdb=" N VAL P 195 " --> pdb=" O THR P 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR P 79 " --> pdb=" O VAL P 195 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N THR P 147 " --> pdb=" O GLN P 168 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N GLN P 168 " --> pdb=" O THR P 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR P 149 " --> pdb=" O GLU P 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU P 166 " --> pdb=" O THR P 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS P 162 " --> pdb=" O ASP P 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR P 175 " --> pdb=" O ASN P 210 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'Q' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL Q 195 " --> pdb=" O THR Q 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR Q 79 " --> pdb=" O VAL Q 195 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N THR Q 147 " --> pdb=" O GLN Q 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN Q 168 " --> pdb=" O THR Q 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR Q 149 " --> pdb=" O GLU Q 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU Q 166 " --> pdb=" O THR Q 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS Q 162 " --> pdb=" O ASP Q 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR Q 175 " --> pdb=" O ASN Q 210 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL R 195 " --> pdb=" O THR R 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR R 79 " --> pdb=" O VAL R 195 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N THR R 147 " --> pdb=" O GLN R 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN R 168 " --> pdb=" O THR R 147 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR R 149 " --> pdb=" O GLU R 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU R 166 " --> pdb=" O THR R 149 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS R 162 " --> pdb=" O ASP R 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR R 175 " --> pdb=" O ASN R 210 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S' and resid 194 through 196 removed outlier: 9.102A pdb=" N VAL S 195 " --> pdb=" O THR S 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR S 79 " --> pdb=" O VAL S 195 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N THR S 147 " --> pdb=" O GLN S 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN S 168 " --> pdb=" O THR S 147 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR S 149 " --> pdb=" O GLU S 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU S 166 " --> pdb=" O THR S 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS S 162 " --> pdb=" O ASP S 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR S 175 " --> pdb=" O ASN S 210 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'T' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL T 195 " --> pdb=" O THR T 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR T 79 " --> pdb=" O VAL T 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR T 147 " --> pdb=" O GLN T 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN T 168 " --> pdb=" O THR T 147 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR T 149 " --> pdb=" O GLU T 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU T 166 " --> pdb=" O THR T 149 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS T 162 " --> pdb=" O ASP T 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR T 175 " --> pdb=" O ASN T 210 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'U' and resid 194 through 196 removed outlier: 9.102A pdb=" N VAL U 195 " --> pdb=" O THR U 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR U 79 " --> pdb=" O VAL U 195 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N THR U 147 " --> pdb=" O GLN U 168 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N GLN U 168 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR U 149 " --> pdb=" O GLU U 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU U 166 " --> pdb=" O THR U 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS U 162 " --> pdb=" O ASP U 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR U 175 " --> pdb=" O ASN U 210 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'V' and resid 194 through 196 removed outlier: 9.100A pdb=" N VAL V 195 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR V 79 " --> pdb=" O VAL V 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR V 147 " --> pdb=" O GLN V 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN V 168 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR V 149 " --> pdb=" O GLU V 166 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU V 166 " --> pdb=" O THR V 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS V 162 " --> pdb=" O ASP V 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR V 175 " --> pdb=" O ASN V 210 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'W' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL W 195 " --> pdb=" O THR W 77 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR W 79 " --> pdb=" O VAL W 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR W 147 " --> pdb=" O GLN W 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN W 168 " --> pdb=" O THR W 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR W 149 " --> pdb=" O GLU W 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU W 166 " --> pdb=" O THR W 149 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N HIS W 162 " --> pdb=" O ASP W 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR W 175 " --> pdb=" O ASN W 210 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL X 195 " --> pdb=" O THR X 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR X 79 " --> pdb=" O VAL X 195 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N THR X 147 " --> pdb=" O GLN X 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN X 168 " --> pdb=" O THR X 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR X 149 " --> pdb=" O GLU X 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU X 166 " --> pdb=" O THR X 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS X 162 " --> pdb=" O ASP X 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR X 175 " --> pdb=" O ASN X 210 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Y' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL Y 195 " --> pdb=" O THR Y 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR Y 79 " --> pdb=" O VAL Y 195 " (cutoff:3.500A) removed outlier: 13.178A pdb=" N THR Y 147 " --> pdb=" O GLN Y 168 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N GLN Y 168 " --> pdb=" O THR Y 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR Y 149 " --> pdb=" O GLU Y 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU Y 166 " --> pdb=" O THR Y 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS Y 162 " --> pdb=" O ASP Y 153 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR Y 175 " --> pdb=" O ASN Y 210 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 194 through 196 removed outlier: 9.101A pdb=" N VAL Z 195 " --> pdb=" O THR Z 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR Z 79 " --> pdb=" O VAL Z 195 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N THR Z 147 " --> pdb=" O GLN Z 168 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN Z 168 " --> pdb=" O THR Z 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR Z 149 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU Z 166 " --> pdb=" O THR Z 149 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS Z 162 " --> pdb=" O ASP Z 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR Z 175 " --> pdb=" O ASN Z 210 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'a' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR a 220 " --> pdb=" O ASP a 217 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP a 217 " --> pdb=" O THR a 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN a 222 " --> pdb=" O ALA a 215 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA a 215 " --> pdb=" O GLN a 222 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'a' and resid 34 through 43 Processing sheet with id= AC, first strand: chain 'a' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU a 126 " --> pdb=" O TYR a 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU a 136 " --> pdb=" O THR a 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR a 124 " --> pdb=" O LEU a 136 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'a' and resid 261 through 264 Processing sheet with id= AE, first strand: chain 'a' and resid 273 through 276 Processing sheet with id= AF, first strand: chain 'b' and resid 26 through 28 removed outlier: 3.596A pdb=" N THR b 220 " --> pdb=" O ASP b 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP b 217 " --> pdb=" O THR b 220 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN b 222 " --> pdb=" O ALA b 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA b 215 " --> pdb=" O GLN b 222 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'b' and resid 34 through 43 Processing sheet with id= AH, first strand: chain 'b' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU b 126 " --> pdb=" O TYR b 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU b 136 " --> pdb=" O THR b 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR b 124 " --> pdb=" O LEU b 136 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'b' and resid 261 through 264 Processing sheet with id= AJ, first strand: chain 'b' and resid 273 through 276 Processing sheet with id= AK, first strand: chain 'c' and resid 26 through 28 removed outlier: 3.596A pdb=" N THR c 220 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP c 217 " --> pdb=" O THR c 220 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN c 222 " --> pdb=" O ALA c 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA c 215 " --> pdb=" O GLN c 222 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'c' and resid 34 through 43 Processing sheet with id= AM, first strand: chain 'c' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU c 126 " --> pdb=" O TYR c 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU c 136 " --> pdb=" O THR c 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR c 124 " --> pdb=" O LEU c 136 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'c' and resid 261 through 264 Processing sheet with id= AO, first strand: chain 'c' and resid 273 through 276 Processing sheet with id= AP, first strand: chain 'd' and resid 26 through 28 removed outlier: 3.596A pdb=" N THR d 220 " --> pdb=" O ASP d 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP d 217 " --> pdb=" O THR d 220 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN d 222 " --> pdb=" O ALA d 215 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA d 215 " --> pdb=" O GLN d 222 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'd' and resid 34 through 43 Processing sheet with id= AR, first strand: chain 'd' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU d 126 " --> pdb=" O TYR d 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU d 136 " --> pdb=" O THR d 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR d 124 " --> pdb=" O LEU d 136 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'd' and resid 261 through 264 Processing sheet with id= AT, first strand: chain 'd' and resid 273 through 276 Processing sheet with id= AU, first strand: chain 'e' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR e 220 " --> pdb=" O ASP e 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP e 217 " --> pdb=" O THR e 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN e 222 " --> pdb=" O ALA e 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA e 215 " --> pdb=" O GLN e 222 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'e' and resid 34 through 43 Processing sheet with id= AW, first strand: chain 'e' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU e 126 " --> pdb=" O TYR e 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU e 136 " --> pdb=" O THR e 124 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR e 124 " --> pdb=" O LEU e 136 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'e' and resid 261 through 264 Processing sheet with id= AY, first strand: chain 'e' and resid 273 through 276 Processing sheet with id= AZ, first strand: chain 'f' and resid 26 through 28 removed outlier: 3.596A pdb=" N THR f 220 " --> pdb=" O ASP f 217 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP f 217 " --> pdb=" O THR f 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN f 222 " --> pdb=" O ALA f 215 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA f 215 " --> pdb=" O GLN f 222 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'f' and resid 34 through 43 Processing sheet with id= BB, first strand: chain 'f' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU f 126 " --> pdb=" O TYR f 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU f 136 " --> pdb=" O THR f 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR f 124 " --> pdb=" O LEU f 136 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'f' and resid 261 through 264 Processing sheet with id= BD, first strand: chain 'f' and resid 273 through 276 Processing sheet with id= BE, first strand: chain 'g' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR g 220 " --> pdb=" O ASP g 217 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP g 217 " --> pdb=" O THR g 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN g 222 " --> pdb=" O ALA g 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA g 215 " --> pdb=" O GLN g 222 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'g' and resid 34 through 43 Processing sheet with id= BG, first strand: chain 'g' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU g 126 " --> pdb=" O TYR g 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU g 136 " --> pdb=" O THR g 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR g 124 " --> pdb=" O LEU g 136 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'g' and resid 261 through 264 Processing sheet with id= BI, first strand: chain 'g' and resid 273 through 276 Processing sheet with id= BJ, first strand: chain 'h' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR h 220 " --> pdb=" O ASP h 217 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP h 217 " --> pdb=" O THR h 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN h 222 " --> pdb=" O ALA h 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA h 215 " --> pdb=" O GLN h 222 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'h' and resid 34 through 43 Processing sheet with id= BL, first strand: chain 'h' and resid 169 through 171 removed outlier: 6.790A pdb=" N LEU h 126 " --> pdb=" O TYR h 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU h 136 " --> pdb=" O THR h 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR h 124 " --> pdb=" O LEU h 136 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'h' and resid 261 through 264 Processing sheet with id= BN, first strand: chain 'h' and resid 273 through 276 Processing sheet with id= BO, first strand: chain 'i' and resid 26 through 28 removed outlier: 3.596A pdb=" N THR i 220 " --> pdb=" O ASP i 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP i 217 " --> pdb=" O THR i 220 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN i 222 " --> pdb=" O ALA i 215 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA i 215 " --> pdb=" O GLN i 222 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'i' and resid 34 through 43 Processing sheet with id= BQ, first strand: chain 'i' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU i 126 " --> pdb=" O TYR i 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU i 136 " --> pdb=" O THR i 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR i 124 " --> pdb=" O LEU i 136 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'i' and resid 261 through 264 Processing sheet with id= BS, first strand: chain 'i' and resid 273 through 276 Processing sheet with id= BT, first strand: chain 'j' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR j 220 " --> pdb=" O ASP j 217 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP j 217 " --> pdb=" O THR j 220 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN j 222 " --> pdb=" O ALA j 215 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA j 215 " --> pdb=" O GLN j 222 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'j' and resid 34 through 43 Processing sheet with id= BV, first strand: chain 'j' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU j 126 " --> pdb=" O TYR j 134 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU j 136 " --> pdb=" O THR j 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR j 124 " --> pdb=" O LEU j 136 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'j' and resid 261 through 264 Processing sheet with id= BX, first strand: chain 'j' and resid 273 through 276 Processing sheet with id= BY, first strand: chain 'k' and resid 26 through 28 removed outlier: 3.596A pdb=" N THR k 220 " --> pdb=" O ASP k 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP k 217 " --> pdb=" O THR k 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN k 222 " --> pdb=" O ALA k 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA k 215 " --> pdb=" O GLN k 222 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'k' and resid 34 through 43 Processing sheet with id= CA, first strand: chain 'k' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU k 126 " --> pdb=" O TYR k 134 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU k 136 " --> pdb=" O THR k 124 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR k 124 " --> pdb=" O LEU k 136 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'k' and resid 261 through 264 Processing sheet with id= CC, first strand: chain 'k' and resid 273 through 276 Processing sheet with id= CD, first strand: chain 'l' and resid 26 through 28 removed outlier: 3.596A pdb=" N THR l 220 " --> pdb=" O ASP l 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP l 217 " --> pdb=" O THR l 220 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN l 222 " --> pdb=" O ALA l 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA l 215 " --> pdb=" O GLN l 222 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'l' and resid 34 through 43 Processing sheet with id= CF, first strand: chain 'l' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU l 126 " --> pdb=" O TYR l 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU l 136 " --> pdb=" O THR l 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR l 124 " --> pdb=" O LEU l 136 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'l' and resid 261 through 264 Processing sheet with id= CH, first strand: chain 'l' and resid 273 through 276 Processing sheet with id= CI, first strand: chain 'm' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR m 220 " --> pdb=" O ASP m 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP m 217 " --> pdb=" O THR m 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN m 222 " --> pdb=" O ALA m 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA m 215 " --> pdb=" O GLN m 222 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'm' and resid 34 through 43 Processing sheet with id= CK, first strand: chain 'm' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU m 126 " --> pdb=" O TYR m 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU m 136 " --> pdb=" O THR m 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR m 124 " --> pdb=" O LEU m 136 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'm' and resid 261 through 264 Processing sheet with id= CM, first strand: chain 'm' and resid 273 through 276 Processing sheet with id= CN, first strand: chain 'n' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR n 220 " --> pdb=" O ASP n 217 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP n 217 " --> pdb=" O THR n 220 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN n 222 " --> pdb=" O ALA n 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA n 215 " --> pdb=" O GLN n 222 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'n' and resid 34 through 43 Processing sheet with id= CP, first strand: chain 'n' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU n 126 " --> pdb=" O TYR n 134 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU n 136 " --> pdb=" O THR n 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR n 124 " --> pdb=" O LEU n 136 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'n' and resid 261 through 264 Processing sheet with id= CR, first strand: chain 'n' and resid 273 through 276 Processing sheet with id= CS, first strand: chain 'o' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR o 220 " --> pdb=" O ASP o 217 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP o 217 " --> pdb=" O THR o 220 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN o 222 " --> pdb=" O ALA o 215 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA o 215 " --> pdb=" O GLN o 222 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'o' and resid 34 through 43 Processing sheet with id= CU, first strand: chain 'o' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU o 126 " --> pdb=" O TYR o 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU o 136 " --> pdb=" O THR o 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR o 124 " --> pdb=" O LEU o 136 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'o' and resid 261 through 264 Processing sheet with id= CW, first strand: chain 'o' and resid 273 through 276 Processing sheet with id= CX, first strand: chain 'p' and resid 26 through 28 removed outlier: 3.596A pdb=" N THR p 220 " --> pdb=" O ASP p 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP p 217 " --> pdb=" O THR p 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN p 222 " --> pdb=" O ALA p 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA p 215 " --> pdb=" O GLN p 222 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'p' and resid 34 through 43 Processing sheet with id= CZ, first strand: chain 'p' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU p 126 " --> pdb=" O TYR p 134 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU p 136 " --> pdb=" O THR p 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR p 124 " --> pdb=" O LEU p 136 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'p' and resid 261 through 264 Processing sheet with id= DB, first strand: chain 'p' and resid 273 through 276 Processing sheet with id= DC, first strand: chain 'q' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR q 220 " --> pdb=" O ASP q 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP q 217 " --> pdb=" O THR q 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN q 222 " --> pdb=" O ALA q 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA q 215 " --> pdb=" O GLN q 222 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'q' and resid 34 through 43 Processing sheet with id= DE, first strand: chain 'q' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU q 126 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU q 136 " --> pdb=" O THR q 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR q 124 " --> pdb=" O LEU q 136 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'q' and resid 261 through 264 Processing sheet with id= DG, first strand: chain 'q' and resid 273 through 276 Processing sheet with id= DH, first strand: chain 'r' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR r 220 " --> pdb=" O ASP r 217 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP r 217 " --> pdb=" O THR r 220 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN r 222 " --> pdb=" O ALA r 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA r 215 " --> pdb=" O GLN r 222 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'r' and resid 34 through 43 Processing sheet with id= DJ, first strand: chain 'r' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU r 126 " --> pdb=" O TYR r 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU r 136 " --> pdb=" O THR r 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR r 124 " --> pdb=" O LEU r 136 " (cutoff:3.500A) Processing sheet with id= DK, first strand: chain 'r' and resid 261 through 264 Processing sheet with id= DL, first strand: chain 'r' and resid 273 through 276 Processing sheet with id= DM, first strand: chain 's' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR s 220 " --> pdb=" O ASP s 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP s 217 " --> pdb=" O THR s 220 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN s 222 " --> pdb=" O ALA s 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA s 215 " --> pdb=" O GLN s 222 " (cutoff:3.500A) Processing sheet with id= DN, first strand: chain 's' and resid 34 through 43 Processing sheet with id= DO, first strand: chain 's' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU s 126 " --> pdb=" O TYR s 134 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU s 136 " --> pdb=" O THR s 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR s 124 " --> pdb=" O LEU s 136 " (cutoff:3.500A) Processing sheet with id= DP, first strand: chain 's' and resid 261 through 264 Processing sheet with id= DQ, first strand: chain 's' and resid 273 through 276 Processing sheet with id= DR, first strand: chain 't' and resid 26 through 28 removed outlier: 3.596A pdb=" N THR t 220 " --> pdb=" O ASP t 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP t 217 " --> pdb=" O THR t 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN t 222 " --> pdb=" O ALA t 215 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA t 215 " --> pdb=" O GLN t 222 " (cutoff:3.500A) Processing sheet with id= DS, first strand: chain 't' and resid 34 through 43 Processing sheet with id= DT, first strand: chain 't' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU t 126 " --> pdb=" O TYR t 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU t 136 " --> pdb=" O THR t 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR t 124 " --> pdb=" O LEU t 136 " (cutoff:3.500A) Processing sheet with id= DU, first strand: chain 't' and resid 261 through 264 Processing sheet with id= DV, first strand: chain 't' and resid 273 through 276 Processing sheet with id= DW, first strand: chain 'u' and resid 26 through 28 removed outlier: 3.596A pdb=" N THR u 220 " --> pdb=" O ASP u 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP u 217 " --> pdb=" O THR u 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN u 222 " --> pdb=" O ALA u 215 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA u 215 " --> pdb=" O GLN u 222 " (cutoff:3.500A) Processing sheet with id= DX, first strand: chain 'u' and resid 34 through 43 Processing sheet with id= DY, first strand: chain 'u' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU u 126 " --> pdb=" O TYR u 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU u 136 " --> pdb=" O THR u 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR u 124 " --> pdb=" O LEU u 136 " (cutoff:3.500A) Processing sheet with id= DZ, first strand: chain 'u' and resid 261 through 264 Processing sheet with id= EA, first strand: chain 'u' and resid 273 through 276 Processing sheet with id= ,, first strand: chain 'v' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR v 220 " --> pdb=" O ASP v 217 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP v 217 " --> pdb=" O THR v 220 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN v 222 " --> pdb=" O ALA v 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA v 215 " --> pdb=" O GLN v 222 " (cutoff:3.500A) Processing sheet with id= -, first strand: chain 'v' and resid 34 through 43 Processing sheet with id= ., first strand: chain 'v' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU v 126 " --> pdb=" O TYR v 134 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU v 136 " --> pdb=" O THR v 124 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR v 124 " --> pdb=" O LEU v 136 " (cutoff:3.500A) Processing sheet with id= /, first strand: chain 'v' and resid 261 through 264 Processing sheet with id= 0, first strand: chain 'v' and resid 273 through 276 Processing sheet with id= 1, first strand: chain 'w' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR w 220 " --> pdb=" O ASP w 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP w 217 " --> pdb=" O THR w 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN w 222 " --> pdb=" O ALA w 215 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA w 215 " --> pdb=" O GLN w 222 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'w' and resid 34 through 43 Processing sheet with id= 3, first strand: chain 'w' and resid 169 through 171 removed outlier: 6.788A pdb=" N LEU w 126 " --> pdb=" O TYR w 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU w 136 " --> pdb=" O THR w 124 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR w 124 " --> pdb=" O LEU w 136 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'w' and resid 261 through 264 Processing sheet with id= 5, first strand: chain 'w' and resid 273 through 276 Processing sheet with id= 6, first strand: chain 'x' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR x 220 " --> pdb=" O ASP x 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP x 217 " --> pdb=" O THR x 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN x 222 " --> pdb=" O ALA x 215 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA x 215 " --> pdb=" O GLN x 222 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'x' and resid 34 through 43 Processing sheet with id= 8, first strand: chain 'x' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU x 126 " --> pdb=" O TYR x 134 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU x 136 " --> pdb=" O THR x 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR x 124 " --> pdb=" O LEU x 136 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'x' and resid 261 through 264 Processing sheet with id= :, first strand: chain 'x' and resid 273 through 276 Processing sheet with id= ;, first strand: chain 'y' and resid 26 through 28 removed outlier: 3.597A pdb=" N THR y 220 " --> pdb=" O ASP y 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP y 217 " --> pdb=" O THR y 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN y 222 " --> pdb=" O ALA y 215 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA y 215 " --> pdb=" O GLN y 222 " (cutoff:3.500A) Processing sheet with id= <, first strand: chain 'y' and resid 34 through 43 Processing sheet with id= =, first strand: chain 'y' and resid 169 through 171 removed outlier: 6.789A pdb=" N LEU y 126 " --> pdb=" O TYR y 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU y 136 " --> pdb=" O THR y 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR y 124 " --> pdb=" O LEU y 136 " (cutoff:3.500A) Processing sheet with id= >, first strand: chain 'y' and resid 261 through 264 Processing sheet with id= ?, first strand: chain 'y' and resid 273 through 276 Processing sheet with id= @, first strand: chain 'z' and resid 26 through 28 removed outlier: 3.598A pdb=" N THR z 220 " --> pdb=" O ASP z 217 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP z 217 " --> pdb=" O THR z 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN z 222 " --> pdb=" O ALA z 215 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA z 215 " --> pdb=" O GLN z 222 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'z' and resid 34 through 43 Processing sheet with id= (, first strand: chain 'z' and resid 169 through 171 removed outlier: 6.788A pdb=" N LEU z 126 " --> pdb=" O TYR z 134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU z 136 " --> pdb=" O THR z 124 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR z 124 " --> pdb=" O LEU z 136 " (cutoff:3.500A) Processing sheet with id= ), first strand: chain 'z' and resid 261 through 264 Processing sheet with id= *, first strand: chain 'z' and resid 273 through 276 3458 hydrogen bonds defined for protein. 9594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 45.84 Time building geometry restraints manager: 31.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 34684 1.34 - 1.46: 15576 1.46 - 1.57: 49398 1.57 - 1.69: 0 1.69 - 1.81: 806 Bond restraints: 100464 Sorted by residual: bond pdb=" C1 OCA G 301 " pdb=" C2 OCA G 301 " ideal model delta sigma weight residual 1.539 1.498 0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C1 OCA A 301 " pdb=" C2 OCA A 301 " ideal model delta sigma weight residual 1.539 1.498 0.041 2.00e-02 2.50e+03 4.16e+00 bond pdb=" C1 OCA Z 301 " pdb=" C2 OCA Z 301 " ideal model delta sigma weight residual 1.539 1.498 0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C1 OCA M 301 " pdb=" C2 OCA M 301 " ideal model delta sigma weight residual 1.539 1.498 0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" C1 OCA R 301 " pdb=" C2 OCA R 301 " ideal model delta sigma weight residual 1.539 1.498 0.041 2.00e-02 2.50e+03 4.11e+00 ... (remaining 100459 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.53: 2626 106.53 - 113.40: 56230 113.40 - 120.26: 34056 120.26 - 127.13: 42678 127.13 - 134.00: 702 Bond angle restraints: 136292 Sorted by residual: angle pdb=" C GLY c 111 " pdb=" N ASN c 112 " pdb=" CA ASN c 112 " ideal model delta sigma weight residual 121.54 126.95 -5.41 1.91e+00 2.74e-01 8.03e+00 angle pdb=" C GLY n 111 " pdb=" N ASN n 112 " pdb=" CA ASN n 112 " ideal model delta sigma weight residual 121.54 126.95 -5.41 1.91e+00 2.74e-01 8.02e+00 angle pdb=" C GLY z 111 " pdb=" N ASN z 112 " pdb=" CA ASN z 112 " ideal model delta sigma weight residual 121.54 126.95 -5.41 1.91e+00 2.74e-01 8.02e+00 angle pdb=" C GLY i 111 " pdb=" N ASN i 112 " pdb=" CA ASN i 112 " ideal model delta sigma weight residual 121.54 126.95 -5.41 1.91e+00 2.74e-01 8.01e+00 angle pdb=" C GLY w 111 " pdb=" N ASN w 112 " pdb=" CA ASN w 112 " ideal model delta sigma weight residual 121.54 126.95 -5.41 1.91e+00 2.74e-01 8.01e+00 ... (remaining 136287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 54651 17.26 - 34.53: 4421 34.53 - 51.79: 1352 51.79 - 69.05: 338 69.05 - 86.32: 78 Dihedral angle restraints: 60840 sinusoidal: 23374 harmonic: 37466 Sorted by residual: dihedral pdb=" CB CYS n 273 " pdb=" SG CYS n 273 " pdb=" SG CYS n 357 " pdb=" CB CYS n 357 " ideal model delta sinusoidal sigma weight residual 93.00 142.48 -49.48 1 1.00e+01 1.00e-02 3.36e+01 dihedral pdb=" CB CYS d 273 " pdb=" SG CYS d 273 " pdb=" SG CYS d 357 " pdb=" CB CYS d 357 " ideal model delta sinusoidal sigma weight residual 93.00 142.47 -49.47 1 1.00e+01 1.00e-02 3.36e+01 dihedral pdb=" CB CYS u 273 " pdb=" SG CYS u 273 " pdb=" SG CYS u 357 " pdb=" CB CYS u 357 " ideal model delta sinusoidal sigma weight residual 93.00 142.46 -49.46 1 1.00e+01 1.00e-02 3.36e+01 ... (remaining 60837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 9969 0.034 - 0.068: 3834 0.068 - 0.103: 1480 0.103 - 0.137: 758 0.137 - 0.171: 27 Chirality restraints: 16068 Sorted by residual: chirality pdb=" CA ASN o 112 " pdb=" N ASN o 112 " pdb=" C ASN o 112 " pdb=" CB ASN o 112 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA ASN l 112 " pdb=" N ASN l 112 " pdb=" C ASN l 112 " pdb=" CB ASN l 112 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA ASN k 112 " pdb=" N ASN k 112 " pdb=" C ASN k 112 " pdb=" CB ASN k 112 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 16065 not shown) Planarity restraints: 18200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 172 " -0.005 2.00e-02 2.50e+03 9.85e-03 9.71e-01 pdb=" C ASN B 172 " 0.017 2.00e-02 2.50e+03 pdb=" O ASN B 172 " -0.006 2.00e-02 2.50e+03 pdb=" N GLN B 173 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 185 " -0.016 5.00e-02 4.00e+02 2.45e-02 9.64e-01 pdb=" N PRO E 186 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO E 186 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 186 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN Q 172 " 0.005 2.00e-02 2.50e+03 9.82e-03 9.63e-01 pdb=" C ASN Q 172 " -0.017 2.00e-02 2.50e+03 pdb=" O ASN Q 172 " 0.006 2.00e-02 2.50e+03 pdb=" N GLN Q 173 " 0.006 2.00e-02 2.50e+03 ... (remaining 18197 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 4099 2.71 - 3.26: 94781 3.26 - 3.80: 152464 3.80 - 4.35: 200336 4.35 - 4.90: 353084 Nonbonded interactions: 804764 Sorted by model distance: nonbonded pdb=" NH2 ARG T 70 " pdb=" OG1 THR v 72 " model vdw 2.161 2.520 nonbonded pdb=" OE2 GLU T 84 " pdb=" OG SER T 197 " model vdw 2.174 2.440 nonbonded pdb=" OE2 GLU G 84 " pdb=" OG SER G 197 " model vdw 2.174 2.440 nonbonded pdb=" OE2 GLU A 84 " pdb=" OG SER A 197 " model vdw 2.174 2.440 nonbonded pdb=" OE2 GLU L 84 " pdb=" OG SER L 197 " model vdw 2.174 2.440 ... (remaining 804759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 442 5.16 5 C 61282 2.51 5 N 17862 2.21 5 O 19656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 30.910 Check model and map are aligned: 1.180 Convert atoms to be neutral: 0.640 Process input model: 205.540 Find NCS groups from input model: 6.450 Set up NCS constraints: 1.670 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:10.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 260.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 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 : 0.006 0.068 100464 Z= 0.414 Angle : 0.589 7.380 136292 Z= 0.328 Chirality : 0.046 0.171 16068 Planarity : 0.003 0.025 18200 Dihedral : 14.820 86.318 36790 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.98 % Favored : 96.82 % Rotamer Outliers : 5.25 % 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: -2.55 (0.06), residues: 13156 helix: -0.81 (0.09), residues: 2522 sheet: -1.53 (0.07), residues: 4368 loop : -2.14 (0.07), residues: 6266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2278 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 571 poor density : 1707 time to evaluate : 8.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 571 outliers final: 265 residues processed: 2211 average time/residue: 1.6812 time to fit residues: 5121.2461 Evaluate side-chains 1664 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1399 time to evaluate : 8.880 Switching outliers to nearest non-outliers outliers start: 265 outliers final: 247 residues processed: 18 average time/residue: 0.6615 time to fit residues: 34.9843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1326 random chunks: chunk 1119 optimal weight: 0.8980 chunk 1005 optimal weight: 3.9990 chunk 557 optimal weight: 0.9990 chunk 343 optimal weight: 2.9990 chunk 677 optimal weight: 1.9990 chunk 536 optimal weight: 3.9990 chunk 1039 optimal weight: 1.9990 chunk 402 optimal weight: 0.7980 chunk 631 optimal weight: 4.9990 chunk 773 optimal weight: 0.9980 chunk 1204 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 114 GLN A 133 ASN A 172 ASN A 217 GLN B 114 GLN B 119 ASN B 172 ASN B 217 GLN B 218 ASN C 83 GLN C 114 GLN C 119 ASN C 172 ASN C 217 GLN D 114 GLN D 119 ASN D 172 ASN D 217 GLN D 218 ASN E 83 GLN E 114 GLN E 119 ASN E 172 ASN E 217 GLN F 32 GLN F 114 GLN F 172 ASN F 217 GLN G 83 GLN G 114 GLN G 119 ASN G 172 ASN G 217 GLN H 114 GLN H 119 ASN H 133 ASN H 172 ASN H 217 GLN I 114 GLN I 119 ASN I 172 ASN I 217 GLN J 114 GLN J 119 ASN J 172 ASN J 217 GLN K 114 GLN K 119 ASN K 133 ASN K 172 ASN K 217 GLN L 83 GLN L 114 GLN L 119 ASN L 133 ASN L 172 ASN L 217 GLN L 218 ASN M 114 GLN M 119 ASN M 133 ASN M 160 ASN M 172 ASN M 217 GLN N 114 GLN N 119 ASN N 172 ASN N 217 GLN N 218 ASN O 83 GLN O 114 GLN O 119 ASN O 172 ASN O 217 GLN P 114 GLN P 119 ASN P 172 ASN P 217 GLN Q 83 GLN Q 114 GLN Q 119 ASN Q 133 ASN Q 172 ASN Q 217 GLN R 114 GLN R 119 ASN R 154 GLN R 217 GLN R 218 ASN S 114 GLN S 119 ASN S 133 ASN S 172 ASN S 217 GLN T 83 GLN T 114 GLN T 119 ASN T 172 ASN T 217 GLN U 114 GLN U 119 ASN U 172 ASN U 217 GLN V 83 GLN V 114 GLN V 119 ASN V 172 ASN V 217 GLN W 83 GLN W 114 GLN W 119 ASN W 172 ASN W 217 GLN X 114 GLN X 119 ASN X 172 ASN X 217 GLN Y 114 GLN Y 119 ASN Y 133 ASN Y 172 ASN Y 217 GLN Z 83 GLN Z 85 ASN Z 114 GLN Z 119 ASN Z 133 ASN Z 172 ASN Z 217 GLN a 159 GLN a 161 ASN a 188 GLN a 198 GLN ** a 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN b 159 GLN b 161 ASN b 188 GLN b 198 GLN ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 159 GLN c 161 ASN c 188 GLN d 68 GLN d 159 GLN d 161 ASN d 188 GLN d 198 GLN ** d 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 68 GLN e 159 GLN e 161 ASN e 188 GLN e 198 GLN ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN f 80 GLN f 159 GLN f 161 ASN f 188 GLN f 198 GLN ** f 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 GLN g 80 GLN g 159 GLN g 161 ASN g 188 GLN g 198 GLN ** g 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 80 GLN h 159 GLN h 161 ASN h 188 GLN h 198 GLN ** h 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 68 GLN i 159 GLN i 161 ASN i 188 GLN i 198 GLN ** i 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 80 GLN j 159 GLN j 161 ASN j 188 GLN j 198 GLN ** j 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 GLN k 80 GLN k 159 GLN k 161 ASN k 188 GLN k 198 GLN l 159 GLN l 161 ASN l 188 GLN l 198 GLN l 241 ASN m 68 GLN m 80 GLN m 159 GLN m 161 ASN m 188 GLN m 198 GLN m 241 ASN n 159 GLN n 161 ASN n 188 GLN n 198 GLN o 68 GLN o 159 GLN o 161 ASN o 188 GLN o 198 GLN o 241 ASN p 159 GLN p 161 ASN p 188 GLN p 198 GLN q 68 GLN q 159 GLN q 161 ASN q 188 GLN q 241 ASN q 245 ASN ** q 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN r 68 GLN r 159 GLN r 161 ASN r 188 GLN r 198 GLN ** r 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 159 GLN s 161 ASN s 188 GLN s 198 GLN s 249 GLN t 68 GLN t 159 GLN t 161 ASN t 183 ASN t 188 GLN t 198 GLN u 68 GLN u 80 GLN u 159 GLN u 161 ASN u 188 GLN u 198 GLN v 68 GLN v 80 GLN v 159 GLN v 161 ASN v 188 GLN v 198 GLN w 68 GLN w 159 GLN w 161 ASN w 188 GLN w 198 GLN x 68 GLN x 159 GLN x 161 ASN x 167 ASN x 188 GLN x 198 GLN y 54 GLN y 68 GLN y 159 GLN y 161 ASN y 188 GLN y 198 GLN ** y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 GLN z 80 GLN z 159 GLN z 161 ASN z 188 GLN z 198 GLN Total number of N/Q/H flips: 269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 100464 Z= 0.255 Angle : 0.506 7.438 136292 Z= 0.262 Chirality : 0.046 0.174 16068 Planarity : 0.003 0.028 18200 Dihedral : 5.268 52.917 14352 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 4.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.07), residues: 13156 helix: 0.12 (0.10), residues: 2548 sheet: -1.19 (0.07), residues: 4264 loop : -1.54 (0.07), residues: 6344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2017 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 506 poor density : 1511 time to evaluate : 9.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 506 outliers final: 354 residues processed: 1916 average time/residue: 1.7686 time to fit residues: 4617.7302 Evaluate side-chains 1765 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 354 poor density : 1411 time to evaluate : 8.649 Switching outliers to nearest non-outliers outliers start: 354 outliers final: 313 residues processed: 41 average time/residue: 1.2071 time to fit residues: 85.7544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1326 random chunks: chunk 669 optimal weight: 1.9990 chunk 373 optimal weight: 1.9990 chunk 1002 optimal weight: 2.9990 chunk 819 optimal weight: 2.9990 chunk 332 optimal weight: 0.9980 chunk 1206 optimal weight: 3.9990 chunk 1303 optimal weight: 1.9990 chunk 1074 optimal weight: 6.9990 chunk 1196 optimal weight: 2.9990 chunk 411 optimal weight: 0.9990 chunk 967 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 217 GLN ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 GLN Q 218 ASN R 133 ASN a 68 GLN ** a 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 GLN ** c 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 80 GLN d 277 GLN e 161 ASN ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 80 GLN ** g 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 80 GLN h 265 ASN h 277 GLN i 80 GLN ** i 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 241 ASN ** j 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 277 GLN l 241 ASN n 241 ASN ** n 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 241 ASN ** q 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN ** r 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN t 245 ASN ** u 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 80 GLN ** v 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 241 ASN ** x 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 54 GLN y 249 GLN ** y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 100464 Z= 0.341 Angle : 0.546 7.589 136292 Z= 0.283 Chirality : 0.047 0.181 16068 Planarity : 0.003 0.033 18200 Dihedral : 5.446 57.826 14352 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 5.41 % 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: -1.37 (0.07), residues: 13156 helix: 0.38 (0.10), residues: 2548 sheet: -1.02 (0.08), residues: 4290 loop : -1.30 (0.07), residues: 6318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2029 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 588 poor density : 1441 time to evaluate : 9.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 588 outliers final: 421 residues processed: 1908 average time/residue: 1.7820 time to fit residues: 4646.3990 Evaluate side-chains 1828 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 421 poor density : 1407 time to evaluate : 8.905 Switching outliers to nearest non-outliers outliers start: 421 outliers final: 369 residues processed: 52 average time/residue: 1.3531 time to fit residues: 115.1058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1326 random chunks: chunk 1191 optimal weight: 4.9990 chunk 906 optimal weight: 0.0270 chunk 626 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 575 optimal weight: 4.9990 chunk 810 optimal weight: 0.0970 chunk 1210 optimal weight: 2.9990 chunk 1281 optimal weight: 4.9990 chunk 632 optimal weight: 4.9990 chunk 1147 optimal weight: 0.7980 chunk 345 optimal weight: 2.9990 overall best weight: 1.3840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 217 GLN ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN X 63 GLN ** a 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 320 GLN g 80 GLN ** g 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 80 GLN i 80 GLN i 277 GLN i 350 GLN j 68 GLN j 277 GLN ** n 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 241 ASN n 279 ASN q 241 ASN ** q 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN ** r 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 279 ASN ** s 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 249 GLN ** u 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 245 ASN ** v 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 167 ASN ** x 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 279 ASN y 54 GLN ** y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 100464 Z= 0.298 Angle : 0.522 6.777 136292 Z= 0.271 Chirality : 0.046 0.176 16068 Planarity : 0.003 0.032 18200 Dihedral : 5.319 58.133 14352 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 5.30 % 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: -1.10 (0.07), residues: 13156 helix: 0.61 (0.10), residues: 2548 sheet: -0.87 (0.08), residues: 4290 loop : -1.11 (0.07), residues: 6318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1996 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 576 poor density : 1420 time to evaluate : 9.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 576 outliers final: 451 residues processed: 1882 average time/residue: 1.7641 time to fit residues: 4574.0463 Evaluate side-chains 1870 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 451 poor density : 1419 time to evaluate : 8.838 Switching outliers to nearest non-outliers outliers start: 451 outliers final: 400 residues processed: 51 average time/residue: 1.4166 time to fit residues: 117.4883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1326 random chunks: chunk 1067 optimal weight: 2.9990 chunk 727 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 954 optimal weight: 5.9990 chunk 528 optimal weight: 0.9980 chunk 1093 optimal weight: 3.9990 chunk 885 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 654 optimal weight: 6.9990 chunk 1150 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN F 217 GLN ** a 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 80 GLN ** g 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 80 GLN i 241 ASN ** l 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 241 ASN ** n 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 279 ASN ** o 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 241 ASN ** q 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN ** r 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 277 GLN u 83 ASN ** u 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 80 GLN ** v 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 277 GLN ** x 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 279 ASN y 54 GLN ** y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 100464 Z= 0.359 Angle : 0.554 7.214 136292 Z= 0.288 Chirality : 0.047 0.189 16068 Planarity : 0.003 0.033 18200 Dihedral : 5.423 58.223 14352 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 5.55 % 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: -1.05 (0.07), residues: 13156 helix: 0.60 (0.10), residues: 2548 sheet: -0.85 (0.08), residues: 4290 loop : -1.04 (0.07), residues: 6318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2041 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 603 poor density : 1438 time to evaluate : 11.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 603 outliers final: 494 residues processed: 1929 average time/residue: 1.7382 time to fit residues: 4623.6033 Evaluate side-chains 1905 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 494 poor density : 1411 time to evaluate : 8.841 Switching outliers to nearest non-outliers outliers start: 494 outliers final: 440 residues processed: 55 average time/residue: 1.3739 time to fit residues: 123.0244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1326 random chunks: chunk 431 optimal weight: 3.9990 chunk 1154 optimal weight: 0.8980 chunk 253 optimal weight: 0.8980 chunk 752 optimal weight: 0.0370 chunk 316 optimal weight: 0.3980 chunk 1282 optimal weight: 2.9990 chunk 1065 optimal weight: 1.9990 chunk 594 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 424 optimal weight: 1.9990 chunk 673 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN F 217 GLN J 133 ASN K 218 ASN Q 63 GLN T 133 ASN V 32 GLN ** a 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 68 GLN ** b 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN ** f 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 GLN h 80 GLN i 277 GLN ** n 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 241 ASN n 279 ASN o 241 ASN q 241 ASN ** q 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 GLN ** r 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 277 GLN u 83 ASN x 241 ASN x 279 ASN y 54 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 100464 Z= 0.169 Angle : 0.469 6.861 136292 Z= 0.245 Chirality : 0.044 0.236 16068 Planarity : 0.003 0.040 18200 Dihedral : 4.797 57.945 14352 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 5.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.07), residues: 13156 helix: 1.55 (0.11), residues: 2236 sheet: -0.68 (0.08), residues: 4342 loop : -0.70 (0.08), residues: 6578 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2019 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 553 poor density : 1466 time to evaluate : 8.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 553 outliers final: 458 residues processed: 1939 average time/residue: 1.7643 time to fit residues: 4699.0640 Evaluate side-chains 1855 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 458 poor density : 1397 time to evaluate : 8.917 Switching outliers to nearest non-outliers outliers start: 458 outliers final: 431 residues processed: 28 average time/residue: 1.3027 time to fit residues: 66.0499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1326 random chunks: chunk 1236 optimal weight: 0.0980 chunk 144 optimal weight: 2.9990 chunk 730 optimal weight: 3.9990 chunk 936 optimal weight: 4.9990 chunk 725 optimal weight: 0.5980 chunk 1079 optimal weight: 0.9980 chunk 716 optimal weight: 5.9990 chunk 1278 optimal weight: 0.8980 chunk 799 optimal weight: 4.9990 chunk 779 optimal weight: 4.9990 chunk 590 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 217 GLN E 38 GLN F 217 GLN K 217 GLN U 83 GLN ** a 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN e 54 GLN ** f 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 80 GLN ** g 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 80 GLN i 277 GLN i 279 ASN m 279 ASN n 80 GLN n 241 ASN n 279 ASN q 241 ASN ** q 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 279 ASN r 83 ASN ** r 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 83 ASN ** u 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 GLN x 279 ASN y 54 GLN ** y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 100464 Z= 0.216 Angle : 0.497 8.240 136292 Z= 0.258 Chirality : 0.045 0.235 16068 Planarity : 0.003 0.045 18200 Dihedral : 4.835 59.759 14352 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 5.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.07), residues: 13156 helix: 1.68 (0.11), residues: 2210 sheet: -0.62 (0.08), residues: 4342 loop : -0.64 (0.08), residues: 6604 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1964 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 548 poor density : 1416 time to evaluate : 9.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 548 outliers final: 482 residues processed: 1901 average time/residue: 1.8044 time to fit residues: 4732.5606 Evaluate side-chains 1871 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 482 poor density : 1389 time to evaluate : 8.885 Switching outliers to nearest non-outliers outliers start: 482 outliers final: 451 residues processed: 31 average time/residue: 1.4983 time to fit residues: 79.1201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1326 random chunks: chunk 790 optimal weight: 0.7980 chunk 510 optimal weight: 2.9990 chunk 763 optimal weight: 1.9990 chunk 384 optimal weight: 0.9980 chunk 251 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 812 optimal weight: 0.0050 chunk 870 optimal weight: 0.9980 chunk 631 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 1004 optimal weight: 3.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 217 GLN D 32 GLN E 38 GLN F 217 GLN Q 32 GLN ** a 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN e 54 GLN ** f 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 80 GLN h 80 GLN i 277 GLN j 249 GLN m 279 ASN ** n 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 279 ASN q 198 GLN q 241 ASN ** q 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 279 ASN y 54 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 100464 Z= 0.189 Angle : 0.486 8.251 136292 Z= 0.252 Chirality : 0.045 0.222 16068 Planarity : 0.003 0.050 18200 Dihedral : 4.601 58.412 14352 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 4.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.07), residues: 13156 helix: 1.78 (0.11), residues: 2210 sheet: -0.55 (0.08), residues: 4342 loop : -0.57 (0.08), residues: 6604 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1929 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 523 poor density : 1406 time to evaluate : 9.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 523 outliers final: 477 residues processed: 1883 average time/residue: 1.7695 time to fit residues: 4581.7502 Evaluate side-chains 1863 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 477 poor density : 1386 time to evaluate : 9.638 Switching outliers to nearest non-outliers outliers start: 477 outliers final: 451 residues processed: 26 average time/residue: 1.7460 time to fit residues: 76.4843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1326 random chunks: chunk 1162 optimal weight: 3.9990 chunk 1224 optimal weight: 5.9990 chunk 1117 optimal weight: 2.9990 chunk 1190 optimal weight: 1.9990 chunk 716 optimal weight: 3.9990 chunk 518 optimal weight: 2.9990 chunk 935 optimal weight: 2.9990 chunk 365 optimal weight: 0.9980 chunk 1076 optimal weight: 3.9990 chunk 1126 optimal weight: 0.0670 chunk 1186 optimal weight: 1.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 217 GLN E 38 GLN F 217 GLN K 217 GLN L 217 GLN ** a 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN c 198 GLN ** c 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 80 GLN h 80 GLN i 277 GLN ** l 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 80 GLN n 241 ASN ** n 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 241 ASN ** q 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 277 GLN ** u 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 241 ASN ** x 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 279 ASN y 54 GLN ** y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 100464 Z= 0.345 Angle : 0.564 9.354 136292 Z= 0.292 Chirality : 0.047 0.227 16068 Planarity : 0.003 0.055 18200 Dihedral : 5.010 59.562 14352 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 4.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.07), residues: 13156 helix: 1.25 (0.11), residues: 2366 sheet: -0.59 (0.08), residues: 4290 loop : -0.71 (0.08), residues: 6500 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1929 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 521 poor density : 1408 time to evaluate : 9.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 521 outliers final: 471 residues processed: 1883 average time/residue: 1.8139 time to fit residues: 4708.7083 Evaluate side-chains 1868 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 471 poor density : 1397 time to evaluate : 8.855 Switching outliers to nearest non-outliers outliers start: 471 outliers final: 455 residues processed: 16 average time/residue: 1.4498 time to fit residues: 45.6814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1326 random chunks: chunk 782 optimal weight: 2.9990 chunk 1259 optimal weight: 0.9980 chunk 768 optimal weight: 3.9990 chunk 597 optimal weight: 0.9990 chunk 875 optimal weight: 0.9990 chunk 1321 optimal weight: 4.9990 chunk 1215 optimal weight: 3.9990 chunk 1051 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 812 optimal weight: 2.9990 chunk 645 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN E 38 GLN F 217 GLN L 217 GLN ** a 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN ** c 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 80 GLN h 80 GLN i 277 GLN ** l 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 279 ASN n 80 GLN n 241 ASN ** n 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 279 ASN ** o 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 241 ASN ** q 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN ** r 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 279 ASN y 54 GLN ** y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 100464 Z= 0.381 Angle : 0.583 9.810 136292 Z= 0.302 Chirality : 0.048 0.222 16068 Planarity : 0.003 0.060 18200 Dihedral : 5.066 58.110 14352 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 4.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.07), residues: 13156 helix: 1.15 (0.11), residues: 2366 sheet: -0.67 (0.08), residues: 4290 loop : -0.76 (0.08), residues: 6500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1892 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 498 poor density : 1394 time to evaluate : 9.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 498 outliers final: 469 residues processed: 1865 average time/residue: 1.7939 time to fit residues: 4602.8361 Evaluate side-chains 1858 residues out of total 10868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 469 poor density : 1389 time to evaluate : 8.784 Switching outliers to nearest non-outliers outliers start: 469 outliers final: 458 residues processed: 12 average time/residue: 1.5914 time to fit residues: 38.3302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1326 random chunks: chunk 835 optimal weight: 3.9990 chunk 1120 optimal weight: 0.8980 chunk 322 optimal weight: 3.9990 chunk 969 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 292 optimal weight: 1.9990 chunk 1053 optimal weight: 3.9990 chunk 440 optimal weight: 0.9990 chunk 1081 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN F 217 GLN Q 32 GLN V 32 GLN ** a 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN e 54 GLN ** f 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 80 GLN h 80 GLN i 277 GLN m 279 ASN n 80 GLN n 241 ASN ** n 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 279 ASN q 241 ASN ** q 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN ** r 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 279 ASN y 54 GLN ** y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.085024 restraints weight = 134840.020| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.24 r_work: 0.2830 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 100464 Z= 0.259 Angle : 0.533 9.535 136292 Z= 0.276 Chirality : 0.046 0.217 16068 Planarity : 0.003 0.059 18200 Dihedral : 4.757 59.187 14352 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 4.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.07), residues: 13156 helix: 1.32 (0.11), residues: 2366 sheet: -0.57 (0.08), residues: 4290 loop : -0.68 (0.08), residues: 6500 =============================================================================== Job complete usr+sys time: 55602.27 seconds wall clock time: 956 minutes 35.62 seconds (57395.62 seconds total)