Starting phenix.real_space_refine on Thu Feb 15 14:10:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khw_22881/02_2024/7khw_22881_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khw_22881/02_2024/7khw_22881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khw_22881/02_2024/7khw_22881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khw_22881/02_2024/7khw_22881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khw_22881/02_2024/7khw_22881_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khw_22881/02_2024/7khw_22881_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 400 5.16 5 C 40400 2.51 5 N 11050 2.21 5 O 13700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 58": "OD1" <-> "OD2" Residue "A ASP 66": "OD1" <-> "OD2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ASP 105": "OD1" <-> "OD2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E ASP 105": "OD1" <-> "OD2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 183": "NH1" <-> "NH2" Residue "F ASP 58": "OD1" <-> "OD2" Residue "F ASP 66": "OD1" <-> "OD2" Residue "F ASP 105": "OD1" <-> "OD2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 183": "NH1" <-> "NH2" Residue "G ASP 58": "OD1" <-> "OD2" Residue "G ASP 66": "OD1" <-> "OD2" Residue "G ASP 105": "OD1" <-> "OD2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G ARG 183": "NH1" <-> "NH2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H ASP 66": "OD1" <-> "OD2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H ARG 183": "NH1" <-> "NH2" Residue "I ASP 58": "OD1" <-> "OD2" Residue "I ASP 66": "OD1" <-> "OD2" Residue "I ASP 105": "OD1" <-> "OD2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "I ARG 183": "NH1" <-> "NH2" Residue "J ASP 58": "OD1" <-> "OD2" Residue "J ASP 66": "OD1" <-> "OD2" Residue "J ASP 105": "OD1" <-> "OD2" Residue "J ARG 115": "NH1" <-> "NH2" Residue "J ARG 183": "NH1" <-> "NH2" Residue "K ASP 58": "OD1" <-> "OD2" Residue "K ASP 66": "OD1" <-> "OD2" Residue "K ASP 105": "OD1" <-> "OD2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "K ARG 183": "NH1" <-> "NH2" Residue "L ASP 58": "OD1" <-> "OD2" Residue "L ASP 66": "OD1" <-> "OD2" Residue "L ASP 105": "OD1" <-> "OD2" Residue "L ARG 115": "NH1" <-> "NH2" Residue "L ARG 183": "NH1" <-> "NH2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M ASP 66": "OD1" <-> "OD2" Residue "M ASP 105": "OD1" <-> "OD2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ARG 183": "NH1" <-> "NH2" Residue "N ASP 58": "OD1" <-> "OD2" Residue "N ASP 66": "OD1" <-> "OD2" Residue "N ASP 105": "OD1" <-> "OD2" Residue "N ARG 115": "NH1" <-> "NH2" Residue "N ARG 183": "NH1" <-> "NH2" Residue "O ASP 58": "OD1" <-> "OD2" Residue "O ASP 66": "OD1" <-> "OD2" Residue "O ASP 105": "OD1" <-> "OD2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 183": "NH1" <-> "NH2" Residue "P ASP 58": "OD1" <-> "OD2" Residue "P ASP 66": "OD1" <-> "OD2" Residue "P ASP 105": "OD1" <-> "OD2" Residue "P ARG 115": "NH1" <-> "NH2" Residue "P ARG 183": "NH1" <-> "NH2" Residue "Q ASP 58": "OD1" <-> "OD2" Residue "Q ASP 66": "OD1" <-> "OD2" Residue "Q ASP 105": "OD1" <-> "OD2" Residue "Q ARG 115": "NH1" <-> "NH2" Residue "Q ARG 183": "NH1" <-> "NH2" Residue "R ASP 58": "OD1" <-> "OD2" Residue "R ASP 66": "OD1" <-> "OD2" Residue "R ASP 105": "OD1" <-> "OD2" Residue "R ARG 115": "NH1" <-> "NH2" Residue "R ARG 183": "NH1" <-> "NH2" Residue "S ASP 58": "OD1" <-> "OD2" Residue "S ASP 66": "OD1" <-> "OD2" Residue "S ASP 105": "OD1" <-> "OD2" Residue "S ARG 115": "NH1" <-> "NH2" Residue "S ARG 183": "NH1" <-> "NH2" Residue "T ASP 58": "OD1" <-> "OD2" Residue "T ASP 66": "OD1" <-> "OD2" Residue "T ASP 105": "OD1" <-> "OD2" Residue "T ARG 115": "NH1" <-> "NH2" Residue "T ARG 183": "NH1" <-> "NH2" Residue "U ASP 58": "OD1" <-> "OD2" Residue "U ASP 66": "OD1" <-> "OD2" Residue "U ASP 105": "OD1" <-> "OD2" Residue "U ARG 115": "NH1" <-> "NH2" Residue "U ARG 183": "NH1" <-> "NH2" Residue "V ASP 58": "OD1" <-> "OD2" Residue "V ASP 66": "OD1" <-> "OD2" Residue "V ASP 105": "OD1" <-> "OD2" Residue "V ARG 115": "NH1" <-> "NH2" Residue "V ARG 183": "NH1" <-> "NH2" Residue "W ASP 58": "OD1" <-> "OD2" Residue "W ASP 66": "OD1" <-> "OD2" Residue "W ASP 105": "OD1" <-> "OD2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "W ARG 183": "NH1" <-> "NH2" Residue "X ASP 58": "OD1" <-> "OD2" Residue "X ASP 66": "OD1" <-> "OD2" Residue "X ASP 105": "OD1" <-> "OD2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 183": "NH1" <-> "NH2" Residue "Y ASP 58": "OD1" <-> "OD2" Residue "Y ASP 66": "OD1" <-> "OD2" Residue "Y ASP 105": "OD1" <-> "OD2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 183": "NH1" <-> "NH2" Residue "Z ASP 58": "OD1" <-> "OD2" Residue "Z ASP 66": "OD1" <-> "OD2" Residue "Z ASP 105": "OD1" <-> "OD2" Residue "Z ARG 115": "NH1" <-> "NH2" Residue "Z ARG 183": "NH1" <-> "NH2" Residue "a ASP 58": "OD1" <-> "OD2" Residue "a ASP 66": "OD1" <-> "OD2" Residue "a ASP 105": "OD1" <-> "OD2" Residue "a ARG 115": "NH1" <-> "NH2" Residue "a ARG 183": "NH1" <-> "NH2" Residue "b ASP 58": "OD1" <-> "OD2" Residue "b ASP 66": "OD1" <-> "OD2" Residue "b ASP 105": "OD1" <-> "OD2" Residue "b ARG 115": "NH1" <-> "NH2" Residue "b ARG 183": "NH1" <-> "NH2" Residue "c ASP 58": "OD1" <-> "OD2" Residue "c ASP 66": "OD1" <-> "OD2" Residue "c ASP 105": "OD1" <-> "OD2" Residue "c ARG 115": "NH1" <-> "NH2" Residue "c ARG 183": "NH1" <-> "NH2" Residue "d ASP 58": "OD1" <-> "OD2" Residue "d ASP 66": "OD1" <-> "OD2" Residue "d ASP 105": "OD1" <-> "OD2" Residue "d ARG 115": "NH1" <-> "NH2" Residue "d ARG 183": "NH1" <-> "NH2" Residue "e ASP 58": "OD1" <-> "OD2" Residue "e ASP 66": "OD1" <-> "OD2" Residue "e ASP 105": "OD1" <-> "OD2" Residue "e ARG 115": "NH1" <-> "NH2" Residue "e ARG 183": "NH1" <-> "NH2" Residue "f ASP 58": "OD1" <-> "OD2" Residue "f ASP 66": "OD1" <-> "OD2" Residue "f ASP 105": "OD1" <-> "OD2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 183": "NH1" <-> "NH2" Residue "g ASP 58": "OD1" <-> "OD2" Residue "g ASP 66": "OD1" <-> "OD2" Residue "g ASP 105": "OD1" <-> "OD2" Residue "g ARG 115": "NH1" <-> "NH2" Residue "g ARG 183": "NH1" <-> "NH2" Residue "h ASP 58": "OD1" <-> "OD2" Residue "h ASP 66": "OD1" <-> "OD2" Residue "h ASP 105": "OD1" <-> "OD2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "h ARG 183": "NH1" <-> "NH2" Residue "i ASP 58": "OD1" <-> "OD2" Residue "i ASP 66": "OD1" <-> "OD2" Residue "i ASP 105": "OD1" <-> "OD2" Residue "i ARG 115": "NH1" <-> "NH2" Residue "i ARG 183": "NH1" <-> "NH2" Residue "j ASP 58": "OD1" <-> "OD2" Residue "j ASP 66": "OD1" <-> "OD2" Residue "j ASP 105": "OD1" <-> "OD2" Residue "j ARG 115": "NH1" <-> "NH2" Residue "j ARG 183": "NH1" <-> "NH2" Residue "k ASP 58": "OD1" <-> "OD2" Residue "k ASP 66": "OD1" <-> "OD2" Residue "k ASP 105": "OD1" <-> "OD2" Residue "k ARG 115": "NH1" <-> "NH2" Residue "k ARG 183": "NH1" <-> "NH2" Residue "l ASP 58": "OD1" <-> "OD2" Residue "l ASP 66": "OD1" <-> "OD2" Residue "l ASP 105": "OD1" <-> "OD2" Residue "l ARG 115": "NH1" <-> "NH2" Residue "l ARG 183": "NH1" <-> "NH2" Residue "m ASP 58": "OD1" <-> "OD2" Residue "m ASP 66": "OD1" <-> "OD2" Residue "m ASP 105": "OD1" <-> "OD2" Residue "m ARG 115": "NH1" <-> "NH2" Residue "m ARG 183": "NH1" <-> "NH2" Residue "n ASP 58": "OD1" <-> "OD2" Residue "n ASP 66": "OD1" <-> "OD2" Residue "n ASP 105": "OD1" <-> "OD2" Residue "n ARG 115": "NH1" <-> "NH2" Residue "n ARG 183": "NH1" <-> "NH2" Residue "o ASP 58": "OD1" <-> "OD2" Residue "o ASP 66": "OD1" <-> "OD2" Residue "o ASP 105": "OD1" <-> "OD2" Residue "o ARG 115": "NH1" <-> "NH2" Residue "o ARG 183": "NH1" <-> "NH2" Residue "p ASP 58": "OD1" <-> "OD2" Residue "p ASP 66": "OD1" <-> "OD2" Residue "p ASP 105": "OD1" <-> "OD2" Residue "p ARG 115": "NH1" <-> "NH2" Residue "p ARG 183": "NH1" <-> "NH2" Residue "q ASP 58": "OD1" <-> "OD2" Residue "q ASP 66": "OD1" <-> "OD2" Residue "q ASP 105": "OD1" <-> "OD2" Residue "q ARG 115": "NH1" <-> "NH2" Residue "q ARG 183": "NH1" <-> "NH2" Residue "r ASP 58": "OD1" <-> "OD2" Residue "r ASP 66": "OD1" <-> "OD2" Residue "r ASP 105": "OD1" <-> "OD2" Residue "r ARG 115": "NH1" <-> "NH2" Residue "r ARG 183": "NH1" <-> "NH2" Residue "s ASP 58": "OD1" <-> "OD2" Residue "s ASP 66": "OD1" <-> "OD2" Residue "s ASP 105": "OD1" <-> "OD2" Residue "s ARG 115": "NH1" <-> "NH2" Residue "s ARG 183": "NH1" <-> "NH2" Residue "t ASP 58": "OD1" <-> "OD2" Residue "t ASP 66": "OD1" <-> "OD2" Residue "t ASP 105": "OD1" <-> "OD2" Residue "t ARG 115": "NH1" <-> "NH2" Residue "t ARG 183": "NH1" <-> "NH2" Residue "u ASP 58": "OD1" <-> "OD2" Residue "u ASP 66": "OD1" <-> "OD2" Residue "u ASP 105": "OD1" <-> "OD2" Residue "u ARG 115": "NH1" <-> "NH2" Residue "u ARG 183": "NH1" <-> "NH2" Residue "v ASP 58": "OD1" <-> "OD2" Residue "v ASP 66": "OD1" <-> "OD2" Residue "v ASP 105": "OD1" <-> "OD2" Residue "v ARG 115": "NH1" <-> "NH2" Residue "v ARG 183": "NH1" <-> "NH2" Residue "w ASP 58": "OD1" <-> "OD2" Residue "w ASP 66": "OD1" <-> "OD2" Residue "w ASP 105": "OD1" <-> "OD2" Residue "w ARG 115": "NH1" <-> "NH2" Residue "w ARG 183": "NH1" <-> "NH2" Residue "x ASP 58": "OD1" <-> "OD2" Residue "x ASP 66": "OD1" <-> "OD2" Residue "x ASP 105": "OD1" <-> "OD2" Residue "x ARG 115": "NH1" <-> "NH2" Residue "x ARG 183": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 65550 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "B" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "C" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "D" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "E" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "F" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "G" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "H" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "I" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "J" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "K" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "L" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "M" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "N" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "O" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "P" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "Q" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "R" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "S" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "T" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "U" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "V" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "W" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "X" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "Y" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "Z" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "a" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "b" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "c" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "d" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "e" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "f" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "g" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "h" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "i" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "j" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "k" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "l" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "m" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "n" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "o" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "p" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "q" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "r" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "s" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "t" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "u" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "v" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "w" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "x" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Time building chain proxies: 24.57, per 1000 atoms: 0.37 Number of scatterers: 65550 At special positions: 0 Unit cell: (128.52, 128.52, 320.76, 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 400 16.00 O 13700 8.00 N 11050 7.00 C 40400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.36 Conformation dependent library (CDL) restraints added in 9.6 seconds 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16700 Finding SS restraints... Secondary structure from input PDB file: 400 helices and 0 sheets defined 69.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 89 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP A 117 " --> pdb=" O PRO A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 89 Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP B 117 " --> pdb=" O PRO B 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 114 through 117' Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 89 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP C 117 " --> pdb=" O PRO C 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 114 through 117' Processing helix chain 'C' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 186 removed outlier: 3.508A pdb=" N GLN C 161 " --> pdb=" O GLN C 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 89 Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP D 117 " --> pdb=" O PRO D 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 114 through 117' Processing helix chain 'D' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 186 removed outlier: 3.508A pdb=" N GLN D 161 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D 185 " --> pdb=" O GLN D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 89 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP E 117 " --> pdb=" O PRO E 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 114 through 117' Processing helix chain 'E' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE E 185 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 89 Processing helix chain 'F' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP F 117 " --> pdb=" O PRO F 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 114 through 117' Processing helix chain 'F' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN F 155 " --> pdb=" O THR F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN F 161 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN F 162 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE F 185 " --> pdb=" O GLN F 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 89 Processing helix chain 'G' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER G 109 " --> pdb=" O ASP G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP G 117 " --> pdb=" O PRO G 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 114 through 117' Processing helix chain 'G' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL G 138 " --> pdb=" O ASP G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN G 155 " --> pdb=" O THR G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN G 161 " --> pdb=" O GLN G 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN G 162 " --> pdb=" O LEU G 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA G 173 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE G 185 " --> pdb=" O GLN G 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 89 Processing helix chain 'H' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER H 109 " --> pdb=" O ASP H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP H 117 " --> pdb=" O PRO H 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 114 through 117' Processing helix chain 'H' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL H 138 " --> pdb=" O ASP H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN H 155 " --> pdb=" O THR H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN H 161 " --> pdb=" O GLN H 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN H 162 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA H 173 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE H 185 " --> pdb=" O GLN H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP I 34 " --> pdb=" O ASP I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 89 Processing helix chain 'I' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER I 109 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP I 117 " --> pdb=" O PRO I 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 114 through 117' Processing helix chain 'I' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL I 138 " --> pdb=" O ASP I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN I 161 " --> pdb=" O GLN I 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 89 Processing helix chain 'J' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER J 109 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP J 117 " --> pdb=" O PRO J 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'J' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN J 155 " --> pdb=" O THR J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN J 161 " --> pdb=" O GLN J 157 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN J 162 " --> pdb=" O LEU J 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA J 173 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP J 176 " --> pdb=" O SER J 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET J 177 " --> pdb=" O ALA J 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE J 185 " --> pdb=" O GLN J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP K 34 " --> pdb=" O ASP K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 89 Processing helix chain 'K' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER K 109 " --> pdb=" O ASP K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP K 117 " --> pdb=" O PRO K 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 114 through 117' Processing helix chain 'K' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL K 138 " --> pdb=" O ASP K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN K 155 " --> pdb=" O THR K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN K 161 " --> pdb=" O GLN K 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN K 162 " --> pdb=" O LEU K 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA K 173 " --> pdb=" O LEU K 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET K 177 " --> pdb=" O ALA K 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE K 185 " --> pdb=" O GLN K 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP L 34 " --> pdb=" O ASP L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 89 Processing helix chain 'L' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER L 109 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP L 117 " --> pdb=" O PRO L 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 114 through 117' Processing helix chain 'L' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL L 138 " --> pdb=" O ASP L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN L 155 " --> pdb=" O THR L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN L 161 " --> pdb=" O GLN L 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN L 162 " --> pdb=" O LEU L 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA L 173 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP L 176 " --> pdb=" O SER L 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 185 " --> pdb=" O GLN L 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP M 34 " --> pdb=" O ASP M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA M 45 " --> pdb=" O VAL M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 89 Processing helix chain 'M' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER M 109 " --> pdb=" O ASP M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP M 117 " --> pdb=" O PRO M 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 114 through 117' Processing helix chain 'M' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL M 138 " --> pdb=" O ASP M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN M 155 " --> pdb=" O THR M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN M 161 " --> pdb=" O GLN M 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA M 173 " --> pdb=" O LEU M 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP M 176 " --> pdb=" O SER M 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET M 177 " --> pdb=" O ALA M 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE M 185 " --> pdb=" O GLN M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP N 34 " --> pdb=" O ASP N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA N 45 " --> pdb=" O VAL N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 89 Processing helix chain 'N' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER N 109 " --> pdb=" O ASP N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP N 117 " --> pdb=" O PRO N 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 114 through 117' Processing helix chain 'N' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL N 138 " --> pdb=" O ASP N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN N 155 " --> pdb=" O THR N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN N 161 " --> pdb=" O GLN N 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN N 162 " --> pdb=" O LEU N 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA N 173 " --> pdb=" O LEU N 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP N 176 " --> pdb=" O SER N 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE N 185 " --> pdb=" O GLN N 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP O 34 " --> pdb=" O ASP O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA O 45 " --> pdb=" O VAL O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 89 Processing helix chain 'O' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER O 109 " --> pdb=" O ASP O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 117 removed outlier: 3.971A pdb=" N ASP O 117 " --> pdb=" O PRO O 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 114 through 117' Processing helix chain 'O' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL O 138 " --> pdb=" O ASP O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN O 155 " --> pdb=" O THR O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN O 161 " --> pdb=" O GLN O 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN O 162 " --> pdb=" O LEU O 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA O 173 " --> pdb=" O LEU O 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP O 176 " --> pdb=" O SER O 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE O 185 " --> pdb=" O GLN O 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP P 34 " --> pdb=" O ASP P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA P 45 " --> pdb=" O VAL P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 89 Processing helix chain 'P' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER P 109 " --> pdb=" O ASP P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP P 117 " --> pdb=" O PRO P 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 114 through 117' Processing helix chain 'P' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL P 138 " --> pdb=" O ASP P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN P 155 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN P 161 " --> pdb=" O GLN P 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN P 162 " --> pdb=" O LEU P 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA P 173 " --> pdb=" O LEU P 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP P 176 " --> pdb=" O SER P 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET P 177 " --> pdb=" O ALA P 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE P 185 " --> pdb=" O GLN P 181 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP Q 34 " --> pdb=" O ASP Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA Q 45 " --> pdb=" O VAL Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 89 Processing helix chain 'Q' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER Q 109 " --> pdb=" O ASP Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP Q 117 " --> pdb=" O PRO Q 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 114 through 117' Processing helix chain 'Q' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL Q 138 " --> pdb=" O ASP Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN Q 155 " --> pdb=" O THR Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN Q 161 " --> pdb=" O GLN Q 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN Q 162 " --> pdb=" O LEU Q 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA Q 173 " --> pdb=" O LEU Q 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP Q 176 " --> pdb=" O SER Q 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET Q 177 " --> pdb=" O ALA Q 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE Q 185 " --> pdb=" O GLN Q 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP R 34 " --> pdb=" O ASP R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA R 45 " --> pdb=" O VAL R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 89 Processing helix chain 'R' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER R 109 " --> pdb=" O ASP R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP R 117 " --> pdb=" O PRO R 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 114 through 117' Processing helix chain 'R' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL R 138 " --> pdb=" O ASP R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN R 155 " --> pdb=" O THR R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN R 161 " --> pdb=" O GLN R 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP R 176 " --> pdb=" O SER R 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET R 177 " --> pdb=" O ALA R 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE R 185 " --> pdb=" O GLN R 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP S 34 " --> pdb=" O ASP S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA S 45 " --> pdb=" O VAL S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 89 Processing helix chain 'S' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER S 109 " --> pdb=" O ASP S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP S 117 " --> pdb=" O PRO S 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 114 through 117' Processing helix chain 'S' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL S 138 " --> pdb=" O ASP S 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN S 155 " --> pdb=" O THR S 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN S 161 " --> pdb=" O GLN S 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN S 162 " --> pdb=" O LEU S 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA S 173 " --> pdb=" O LEU S 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP S 176 " --> pdb=" O SER S 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET S 177 " --> pdb=" O ALA S 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE S 185 " --> pdb=" O GLN S 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP T 34 " --> pdb=" O ASP T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA T 45 " --> pdb=" O VAL T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 89 Processing helix chain 'T' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER T 109 " --> pdb=" O ASP T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP T 117 " --> pdb=" O PRO T 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 114 through 117' Processing helix chain 'T' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL T 138 " --> pdb=" O ASP T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN T 155 " --> pdb=" O THR T 151 " (cutoff:3.500A) Processing helix chain 'T' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN T 161 " --> pdb=" O GLN T 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA T 173 " --> pdb=" O LEU T 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP T 176 " --> pdb=" O SER T 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET T 177 " --> pdb=" O ALA T 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE T 185 " --> pdb=" O GLN T 181 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP U 34 " --> pdb=" O ASP U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA U 45 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 89 Processing helix chain 'U' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER U 109 " --> pdb=" O ASP U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP U 117 " --> pdb=" O PRO U 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 114 through 117' Processing helix chain 'U' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL U 138 " --> pdb=" O ASP U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN U 155 " --> pdb=" O THR U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN U 161 " --> pdb=" O GLN U 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN U 162 " --> pdb=" O LEU U 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA U 173 " --> pdb=" O LEU U 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP U 176 " --> pdb=" O SER U 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET U 177 " --> pdb=" O ALA U 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE U 185 " --> pdb=" O GLN U 181 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP V 34 " --> pdb=" O ASP V 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA V 45 " --> pdb=" O VAL V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 89 Processing helix chain 'V' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER V 109 " --> pdb=" O ASP V 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP V 117 " --> pdb=" O PRO V 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 114 through 117' Processing helix chain 'V' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL V 138 " --> pdb=" O ASP V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN V 155 " --> pdb=" O THR V 151 " (cutoff:3.500A) Processing helix chain 'V' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN V 161 " --> pdb=" O GLN V 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN V 162 " --> pdb=" O LEU V 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA V 173 " --> pdb=" O LEU V 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP V 176 " --> pdb=" O SER V 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET V 177 " --> pdb=" O ALA V 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE V 185 " --> pdb=" O GLN V 181 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP W 34 " --> pdb=" O ASP W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA W 45 " --> pdb=" O VAL W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 89 Processing helix chain 'W' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER W 109 " --> pdb=" O ASP W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP W 117 " --> pdb=" O PRO W 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 114 through 117' Processing helix chain 'W' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL W 138 " --> pdb=" O ASP W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN W 161 " --> pdb=" O GLN W 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN W 162 " --> pdb=" O LEU W 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP W 176 " --> pdb=" O SER W 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET W 177 " --> pdb=" O ALA W 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE W 185 " --> pdb=" O GLN W 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP X 34 " --> pdb=" O ASP X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA X 45 " --> pdb=" O VAL X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 67 through 89 Processing helix chain 'X' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER X 109 " --> pdb=" O ASP X 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP X 117 " --> pdb=" O PRO X 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 114 through 117' Processing helix chain 'X' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL X 138 " --> pdb=" O ASP X 134 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN X 155 " --> pdb=" O THR X 151 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN X 161 " --> pdb=" O GLN X 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN X 162 " --> pdb=" O LEU X 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA X 173 " --> pdb=" O LEU X 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP X 176 " --> pdb=" O SER X 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET X 177 " --> pdb=" O ALA X 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE X 185 " --> pdb=" O GLN X 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP Y 34 " --> pdb=" O ASP Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA Y 45 " --> pdb=" O VAL Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 89 Processing helix chain 'Y' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER Y 109 " --> pdb=" O ASP Y 105 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP Y 117 " --> pdb=" O PRO Y 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 114 through 117' Processing helix chain 'Y' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL Y 138 " --> pdb=" O ASP Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN Y 155 " --> pdb=" O THR Y 151 " (cutoff:3.500A) Processing helix chain 'Y' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN Y 161 " --> pdb=" O GLN Y 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN Y 162 " --> pdb=" O LEU Y 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA Y 173 " --> pdb=" O LEU Y 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP Y 176 " --> pdb=" O SER Y 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET Y 177 " --> pdb=" O ALA Y 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE Y 185 " --> pdb=" O GLN Y 181 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP Z 34 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA Z 45 " --> pdb=" O VAL Z 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 67 through 89 Processing helix chain 'Z' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER Z 109 " --> pdb=" O ASP Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP Z 117 " --> pdb=" O PRO Z 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 114 through 117' Processing helix chain 'Z' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL Z 138 " --> pdb=" O ASP Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN Z 155 " --> pdb=" O THR Z 151 " (cutoff:3.500A) Processing helix chain 'Z' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN Z 161 " --> pdb=" O GLN Z 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN Z 162 " --> pdb=" O LEU Z 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA Z 173 " --> pdb=" O LEU Z 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP Z 176 " --> pdb=" O SER Z 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET Z 177 " --> pdb=" O ALA Z 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE Z 185 " --> pdb=" O GLN Z 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP a 34 " --> pdb=" O ASP a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA a 45 " --> pdb=" O VAL a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 67 through 89 Processing helix chain 'a' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER a 109 " --> pdb=" O ASP a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP a 117 " --> pdb=" O PRO a 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 114 through 117' Processing helix chain 'a' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL a 138 " --> pdb=" O ASP a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN a 155 " --> pdb=" O THR a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN a 161 " --> pdb=" O GLN a 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN a 162 " --> pdb=" O LEU a 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA a 173 " --> pdb=" O LEU a 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP a 176 " --> pdb=" O SER a 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET a 177 " --> pdb=" O ALA a 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE a 185 " --> pdb=" O GLN a 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP b 34 " --> pdb=" O ASP b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA b 45 " --> pdb=" O VAL b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 89 Processing helix chain 'b' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER b 109 " --> pdb=" O ASP b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 114 through 117 removed outlier: 3.971A pdb=" N ASP b 117 " --> pdb=" O PRO b 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 114 through 117' Processing helix chain 'b' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL b 138 " --> pdb=" O ASP b 134 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN b 155 " --> pdb=" O THR b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN b 161 " --> pdb=" O GLN b 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN b 162 " --> pdb=" O LEU b 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA b 173 " --> pdb=" O LEU b 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP b 176 " --> pdb=" O SER b 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET b 177 " --> pdb=" O ALA b 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE b 185 " --> pdb=" O GLN b 181 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP c 34 " --> pdb=" O ASP c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA c 45 " --> pdb=" O VAL c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 89 Processing helix chain 'c' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER c 109 " --> pdb=" O ASP c 105 " (cutoff:3.500A) Processing helix chain 'c' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP c 117 " --> pdb=" O PRO c 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 114 through 117' Processing helix chain 'c' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL c 138 " --> pdb=" O ASP c 134 " (cutoff:3.500A) Processing helix chain 'c' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN c 155 " --> pdb=" O THR c 151 " (cutoff:3.500A) Processing helix chain 'c' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN c 161 " --> pdb=" O GLN c 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN c 162 " --> pdb=" O LEU c 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA c 173 " --> pdb=" O LEU c 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP c 176 " --> pdb=" O SER c 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET c 177 " --> pdb=" O ALA c 173 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE c 185 " --> pdb=" O GLN c 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP d 34 " --> pdb=" O ASP d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA d 45 " --> pdb=" O VAL d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 89 Processing helix chain 'd' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER d 109 " --> pdb=" O ASP d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP d 117 " --> pdb=" O PRO d 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 114 through 117' Processing helix chain 'd' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL d 138 " --> pdb=" O ASP d 134 " (cutoff:3.500A) Processing helix chain 'd' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN d 155 " --> pdb=" O THR d 151 " (cutoff:3.500A) Processing helix chain 'd' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN d 161 " --> pdb=" O GLN d 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA d 173 " --> pdb=" O LEU d 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP d 176 " --> pdb=" O SER d 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET d 177 " --> pdb=" O ALA d 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE d 185 " --> pdb=" O GLN d 181 " (cutoff:3.500A) Processing helix chain 'e' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP e 34 " --> pdb=" O ASP e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA e 45 " --> pdb=" O VAL e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 67 through 89 Processing helix chain 'e' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER e 109 " --> pdb=" O ASP e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP e 117 " --> pdb=" O PRO e 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 114 through 117' Processing helix chain 'e' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL e 138 " --> pdb=" O ASP e 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN e 155 " --> pdb=" O THR e 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN e 161 " --> pdb=" O GLN e 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN e 162 " --> pdb=" O LEU e 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP e 176 " --> pdb=" O SER e 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET e 177 " --> pdb=" O ALA e 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE e 185 " --> pdb=" O GLN e 181 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP f 34 " --> pdb=" O ASP f 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA f 45 " --> pdb=" O VAL f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 89 Processing helix chain 'f' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER f 109 " --> pdb=" O ASP f 105 " (cutoff:3.500A) Processing helix chain 'f' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP f 117 " --> pdb=" O PRO f 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 114 through 117' Processing helix chain 'f' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL f 138 " --> pdb=" O ASP f 134 " (cutoff:3.500A) Processing helix chain 'f' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN f 155 " --> pdb=" O THR f 151 " (cutoff:3.500A) Processing helix chain 'f' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN f 161 " --> pdb=" O GLN f 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN f 162 " --> pdb=" O LEU f 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP f 176 " --> pdb=" O SER f 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET f 177 " --> pdb=" O ALA f 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE f 185 " --> pdb=" O GLN f 181 " (cutoff:3.500A) Processing helix chain 'g' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP g 34 " --> pdb=" O ASP g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA g 45 " --> pdb=" O VAL g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 67 through 89 Processing helix chain 'g' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER g 109 " --> pdb=" O ASP g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP g 117 " --> pdb=" O PRO g 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 114 through 117' Processing helix chain 'g' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL g 138 " --> pdb=" O ASP g 134 " (cutoff:3.500A) Processing helix chain 'g' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN g 155 " --> pdb=" O THR g 151 " (cutoff:3.500A) Processing helix chain 'g' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN g 161 " --> pdb=" O GLN g 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN g 162 " --> pdb=" O LEU g 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA g 173 " --> pdb=" O LEU g 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP g 176 " --> pdb=" O SER g 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET g 177 " --> pdb=" O ALA g 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE g 185 " --> pdb=" O GLN g 181 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP h 34 " --> pdb=" O ASP h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA h 45 " --> pdb=" O VAL h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 67 through 89 Processing helix chain 'h' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER h 109 " --> pdb=" O ASP h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP h 117 " --> pdb=" O PRO h 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 114 through 117' Processing helix chain 'h' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL h 138 " --> pdb=" O ASP h 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN h 155 " --> pdb=" O THR h 151 " (cutoff:3.500A) Processing helix chain 'h' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN h 161 " --> pdb=" O GLN h 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN h 162 " --> pdb=" O LEU h 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA h 173 " --> pdb=" O LEU h 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP h 176 " --> pdb=" O SER h 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET h 177 " --> pdb=" O ALA h 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE h 185 " --> pdb=" O GLN h 181 " (cutoff:3.500A) Processing helix chain 'i' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP i 34 " --> pdb=" O ASP i 30 " (cutoff:3.500A) Processing helix chain 'i' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA i 45 " --> pdb=" O VAL i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 89 Processing helix chain 'i' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER i 109 " --> pdb=" O ASP i 105 " (cutoff:3.500A) Processing helix chain 'i' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP i 117 " --> pdb=" O PRO i 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 114 through 117' Processing helix chain 'i' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL i 138 " --> pdb=" O ASP i 134 " (cutoff:3.500A) Processing helix chain 'i' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN i 155 " --> pdb=" O THR i 151 " (cutoff:3.500A) Processing helix chain 'i' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN i 161 " --> pdb=" O GLN i 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN i 162 " --> pdb=" O LEU i 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA i 173 " --> pdb=" O LEU i 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP i 176 " --> pdb=" O SER i 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET i 177 " --> pdb=" O ALA i 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE i 185 " --> pdb=" O GLN i 181 " (cutoff:3.500A) Processing helix chain 'j' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP j 34 " --> pdb=" O ASP j 30 " (cutoff:3.500A) Processing helix chain 'j' and resid 41 through 65 removed outlier: 3.563A pdb=" N ALA j 45 " --> pdb=" O VAL j 41 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 89 Processing helix chain 'j' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER j 109 " --> pdb=" O ASP j 105 " (cutoff:3.500A) Processing helix chain 'j' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP j 117 " --> pdb=" O PRO j 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 114 through 117' Processing helix chain 'j' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL j 138 " --> pdb=" O ASP j 134 " (cutoff:3.500A) Processing helix chain 'j' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN j 155 " --> pdb=" O THR j 151 " (cutoff:3.500A) Processing helix chain 'j' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN j 161 " --> pdb=" O GLN j 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN j 162 " --> pdb=" O LEU j 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA j 173 " --> pdb=" O LEU j 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP j 176 " --> pdb=" O SER j 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET j 177 " --> pdb=" O ALA j 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE j 185 " --> pdb=" O GLN j 181 " (cutoff:3.500A) Processing helix chain 'k' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP k 34 " --> pdb=" O ASP k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA k 45 " --> pdb=" O VAL k 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 89 Processing helix chain 'k' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER k 109 " --> pdb=" O ASP k 105 " (cutoff:3.500A) Processing helix chain 'k' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP k 117 " --> pdb=" O PRO k 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 114 through 117' Processing helix chain 'k' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL k 138 " --> pdb=" O ASP k 134 " (cutoff:3.500A) Processing helix chain 'k' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN k 155 " --> pdb=" O THR k 151 " (cutoff:3.500A) Processing helix chain 'k' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN k 161 " --> pdb=" O GLN k 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN k 162 " --> pdb=" O LEU k 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA k 173 " --> pdb=" O LEU k 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP k 176 " --> pdb=" O SER k 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET k 177 " --> pdb=" O ALA k 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE k 185 " --> pdb=" O GLN k 181 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP l 34 " --> pdb=" O ASP l 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA l 45 " --> pdb=" O VAL l 41 " (cutoff:3.500A) Processing helix chain 'l' and resid 67 through 89 Processing helix chain 'l' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER l 109 " --> pdb=" O ASP l 105 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP l 117 " --> pdb=" O PRO l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 114 through 117' Processing helix chain 'l' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL l 138 " --> pdb=" O ASP l 134 " (cutoff:3.500A) Processing helix chain 'l' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN l 155 " --> pdb=" O THR l 151 " (cutoff:3.500A) Processing helix chain 'l' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN l 161 " --> pdb=" O GLN l 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN l 162 " --> pdb=" O LEU l 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA l 173 " --> pdb=" O LEU l 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP l 176 " --> pdb=" O SER l 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET l 177 " --> pdb=" O ALA l 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE l 185 " --> pdb=" O GLN l 181 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP m 34 " --> pdb=" O ASP m 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA m 45 " --> pdb=" O VAL m 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 89 Processing helix chain 'm' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER m 109 " --> pdb=" O ASP m 105 " (cutoff:3.500A) Processing helix chain 'm' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP m 117 " --> pdb=" O PRO m 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 114 through 117' Processing helix chain 'm' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL m 138 " --> pdb=" O ASP m 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN m 155 " --> pdb=" O THR m 151 " (cutoff:3.500A) Processing helix chain 'm' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN m 161 " --> pdb=" O GLN m 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN m 162 " --> pdb=" O LEU m 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA m 173 " --> pdb=" O LEU m 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP m 176 " --> pdb=" O SER m 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET m 177 " --> pdb=" O ALA m 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE m 185 " --> pdb=" O GLN m 181 " (cutoff:3.500A) Processing helix chain 'n' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP n 34 " --> pdb=" O ASP n 30 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA n 45 " --> pdb=" O VAL n 41 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 89 Processing helix chain 'n' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER n 109 " --> pdb=" O ASP n 105 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP n 117 " --> pdb=" O PRO n 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 114 through 117' Processing helix chain 'n' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL n 138 " --> pdb=" O ASP n 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN n 155 " --> pdb=" O THR n 151 " (cutoff:3.500A) Processing helix chain 'n' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN n 161 " --> pdb=" O GLN n 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN n 162 " --> pdb=" O LEU n 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA n 173 " --> pdb=" O LEU n 169 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP n 176 " --> pdb=" O SER n 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET n 177 " --> pdb=" O ALA n 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE n 185 " --> pdb=" O GLN n 181 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP o 34 " --> pdb=" O ASP o 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA o 45 " --> pdb=" O VAL o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 89 Processing helix chain 'o' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER o 109 " --> pdb=" O ASP o 105 " (cutoff:3.500A) Processing helix chain 'o' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP o 117 " --> pdb=" O PRO o 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 114 through 117' Processing helix chain 'o' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL o 138 " --> pdb=" O ASP o 134 " (cutoff:3.500A) Processing helix chain 'o' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN o 155 " --> pdb=" O THR o 151 " (cutoff:3.500A) Processing helix chain 'o' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN o 161 " --> pdb=" O GLN o 157 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN o 162 " --> pdb=" O LEU o 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA o 173 " --> pdb=" O LEU o 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP o 176 " --> pdb=" O SER o 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET o 177 " --> pdb=" O ALA o 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE o 185 " --> pdb=" O GLN o 181 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP p 34 " --> pdb=" O ASP p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA p 45 " --> pdb=" O VAL p 41 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 89 Processing helix chain 'p' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER p 109 " --> pdb=" O ASP p 105 " (cutoff:3.500A) Processing helix chain 'p' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP p 117 " --> pdb=" O PRO p 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 114 through 117' Processing helix chain 'p' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL p 138 " --> pdb=" O ASP p 134 " (cutoff:3.500A) Processing helix chain 'p' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN p 155 " --> pdb=" O THR p 151 " (cutoff:3.500A) Processing helix chain 'p' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN p 161 " --> pdb=" O GLN p 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN p 162 " --> pdb=" O LEU p 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA p 173 " --> pdb=" O LEU p 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP p 176 " --> pdb=" O SER p 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET p 177 " --> pdb=" O ALA p 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE p 185 " --> pdb=" O GLN p 181 " (cutoff:3.500A) Processing helix chain 'q' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP q 34 " --> pdb=" O ASP q 30 " (cutoff:3.500A) Processing helix chain 'q' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA q 45 " --> pdb=" O VAL q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 89 Processing helix chain 'q' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER q 109 " --> pdb=" O ASP q 105 " (cutoff:3.500A) Processing helix chain 'q' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP q 117 " --> pdb=" O PRO q 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 114 through 117' Processing helix chain 'q' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL q 138 " --> pdb=" O ASP q 134 " (cutoff:3.500A) Processing helix chain 'q' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN q 155 " --> pdb=" O THR q 151 " (cutoff:3.500A) Processing helix chain 'q' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN q 161 " --> pdb=" O GLN q 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN q 162 " --> pdb=" O LEU q 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA q 173 " --> pdb=" O LEU q 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP q 176 " --> pdb=" O SER q 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET q 177 " --> pdb=" O ALA q 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE q 185 " --> pdb=" O GLN q 181 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP r 34 " --> pdb=" O ASP r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA r 45 " --> pdb=" O VAL r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 67 through 89 Processing helix chain 'r' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER r 109 " --> pdb=" O ASP r 105 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP r 117 " --> pdb=" O PRO r 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 114 through 117' Processing helix chain 'r' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL r 138 " --> pdb=" O ASP r 134 " (cutoff:3.500A) Processing helix chain 'r' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN r 155 " --> pdb=" O THR r 151 " (cutoff:3.500A) Processing helix chain 'r' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN r 161 " --> pdb=" O GLN r 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN r 162 " --> pdb=" O LEU r 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA r 173 " --> pdb=" O LEU r 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP r 176 " --> pdb=" O SER r 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET r 177 " --> pdb=" O ALA r 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE r 185 " --> pdb=" O GLN r 181 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP s 34 " --> pdb=" O ASP s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA s 45 " --> pdb=" O VAL s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 67 through 89 Processing helix chain 's' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER s 109 " --> pdb=" O ASP s 105 " (cutoff:3.500A) Processing helix chain 's' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP s 117 " --> pdb=" O PRO s 114 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 114 through 117' Processing helix chain 's' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL s 138 " --> pdb=" O ASP s 134 " (cutoff:3.500A) Processing helix chain 's' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN s 155 " --> pdb=" O THR s 151 " (cutoff:3.500A) Processing helix chain 's' and resid 157 through 186 removed outlier: 3.508A pdb=" N GLN s 161 " --> pdb=" O GLN s 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN s 162 " --> pdb=" O LEU s 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA s 173 " --> pdb=" O LEU s 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP s 176 " --> pdb=" O SER s 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET s 177 " --> pdb=" O ALA s 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE s 185 " --> pdb=" O GLN s 181 " (cutoff:3.500A) Processing helix chain 't' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP t 34 " --> pdb=" O ASP t 30 " (cutoff:3.500A) Processing helix chain 't' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA t 45 " --> pdb=" O VAL t 41 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 89 Processing helix chain 't' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER t 109 " --> pdb=" O ASP t 105 " (cutoff:3.500A) Processing helix chain 't' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP t 117 " --> pdb=" O PRO t 114 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 114 through 117' Processing helix chain 't' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL t 138 " --> pdb=" O ASP t 134 " (cutoff:3.500A) Processing helix chain 't' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN t 155 " --> pdb=" O THR t 151 " (cutoff:3.500A) Processing helix chain 't' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN t 161 " --> pdb=" O GLN t 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN t 162 " --> pdb=" O LEU t 158 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA t 173 " --> pdb=" O LEU t 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP t 176 " --> pdb=" O SER t 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET t 177 " --> pdb=" O ALA t 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE t 185 " --> pdb=" O GLN t 181 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP u 34 " --> pdb=" O ASP u 30 " (cutoff:3.500A) Processing helix chain 'u' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA u 45 " --> pdb=" O VAL u 41 " (cutoff:3.500A) Processing helix chain 'u' and resid 67 through 89 Processing helix chain 'u' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER u 109 " --> pdb=" O ASP u 105 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP u 117 " --> pdb=" O PRO u 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 114 through 117' Processing helix chain 'u' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL u 138 " --> pdb=" O ASP u 134 " (cutoff:3.500A) Processing helix chain 'u' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN u 155 " --> pdb=" O THR u 151 " (cutoff:3.500A) Processing helix chain 'u' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN u 161 " --> pdb=" O GLN u 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN u 162 " --> pdb=" O LEU u 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA u 173 " --> pdb=" O LEU u 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP u 176 " --> pdb=" O SER u 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET u 177 " --> pdb=" O ALA u 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE u 185 " --> pdb=" O GLN u 181 " (cutoff:3.500A) Processing helix chain 'v' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP v 34 " --> pdb=" O ASP v 30 " (cutoff:3.500A) Processing helix chain 'v' and resid 41 through 65 removed outlier: 3.563A pdb=" N ALA v 45 " --> pdb=" O VAL v 41 " (cutoff:3.500A) Processing helix chain 'v' and resid 67 through 89 Processing helix chain 'v' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER v 109 " --> pdb=" O ASP v 105 " (cutoff:3.500A) Processing helix chain 'v' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP v 117 " --> pdb=" O PRO v 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 114 through 117' Processing helix chain 'v' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL v 138 " --> pdb=" O ASP v 134 " (cutoff:3.500A) Processing helix chain 'v' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN v 155 " --> pdb=" O THR v 151 " (cutoff:3.500A) Processing helix chain 'v' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN v 161 " --> pdb=" O GLN v 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN v 162 " --> pdb=" O LEU v 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA v 173 " --> pdb=" O LEU v 169 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP v 176 " --> pdb=" O SER v 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET v 177 " --> pdb=" O ALA v 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE v 185 " --> pdb=" O GLN v 181 " (cutoff:3.500A) Processing helix chain 'w' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP w 34 " --> pdb=" O ASP w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA w 45 " --> pdb=" O VAL w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 67 through 89 Processing helix chain 'w' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER w 109 " --> pdb=" O ASP w 105 " (cutoff:3.500A) Processing helix chain 'w' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP w 117 " --> pdb=" O PRO w 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 114 through 117' Processing helix chain 'w' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL w 138 " --> pdb=" O ASP w 134 " (cutoff:3.500A) Processing helix chain 'w' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN w 155 " --> pdb=" O THR w 151 " (cutoff:3.500A) Processing helix chain 'w' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN w 161 " --> pdb=" O GLN w 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN w 162 " --> pdb=" O LEU w 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA w 173 " --> pdb=" O LEU w 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP w 176 " --> pdb=" O SER w 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET w 177 " --> pdb=" O ALA w 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE w 185 " --> pdb=" O GLN w 181 " (cutoff:3.500A) Processing helix chain 'x' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP x 34 " --> pdb=" O ASP x 30 " (cutoff:3.500A) Processing helix chain 'x' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA x 45 " --> pdb=" O VAL x 41 " (cutoff:3.500A) Processing helix chain 'x' and resid 67 through 89 Processing helix chain 'x' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER x 109 " --> pdb=" O ASP x 105 " (cutoff:3.500A) Processing helix chain 'x' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP x 117 " --> pdb=" O PRO x 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 114 through 117' Processing helix chain 'x' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL x 138 " --> pdb=" O ASP x 134 " (cutoff:3.500A) Processing helix chain 'x' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN x 155 " --> pdb=" O THR x 151 " (cutoff:3.500A) Processing helix chain 'x' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN x 161 " --> pdb=" O GLN x 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN x 162 " --> pdb=" O LEU x 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA x 173 " --> pdb=" O LEU x 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP x 176 " --> pdb=" O SER x 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET x 177 " --> pdb=" O ALA x 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE x 185 " --> pdb=" O GLN x 181 " (cutoff:3.500A) 3850 hydrogen bonds defined for protein. 11550 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: 22.29 Time building geometry restraints manager: 22.31 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: 21898 1.34 - 1.45: 6190 1.45 - 1.57: 37162 1.57 - 1.69: 0 1.69 - 1.80: 800 Bond restraints: 66050 Sorted by residual: bond pdb=" CG1 ILE u 111 " pdb=" CD1 ILE u 111 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.43e+00 bond pdb=" CG1 ILE G 111 " pdb=" CD1 ILE G 111 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.42e+00 bond pdb=" CG1 ILE R 111 " pdb=" CD1 ILE R 111 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.41e+00 bond pdb=" CG1 ILE Q 111 " pdb=" CD1 ILE Q 111 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.41e+00 bond pdb=" CG1 ILE t 111 " pdb=" CD1 ILE t 111 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.40e+00 ... (remaining 66045 not shown) Histogram of bond angle deviations from ideal: 99.41 - 105.48: 850 105.48 - 111.55: 28302 111.55 - 117.63: 18452 117.63 - 123.70: 40646 123.70 - 129.77: 900 Bond angle restraints: 89150 Sorted by residual: angle pdb=" N VAL J 91 " pdb=" CA VAL J 91 " pdb=" C VAL J 91 " ideal model delta sigma weight residual 113.42 107.69 5.73 1.17e+00 7.31e-01 2.40e+01 angle pdb=" N VAL L 91 " pdb=" CA VAL L 91 " pdb=" C VAL L 91 " ideal model delta sigma weight residual 113.42 107.70 5.72 1.17e+00 7.31e-01 2.39e+01 angle pdb=" N VAL d 91 " pdb=" CA VAL d 91 " pdb=" C VAL d 91 " ideal model delta sigma weight residual 113.42 107.71 5.71 1.17e+00 7.31e-01 2.39e+01 angle pdb=" N VAL W 91 " pdb=" CA VAL W 91 " pdb=" C VAL W 91 " ideal model delta sigma weight residual 113.42 107.71 5.71 1.17e+00 7.31e-01 2.38e+01 angle pdb=" N VAL F 91 " pdb=" CA VAL F 91 " pdb=" C VAL F 91 " ideal model delta sigma weight residual 113.42 107.71 5.71 1.17e+00 7.31e-01 2.38e+01 ... (remaining 89145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 37797 16.84 - 33.69: 2753 33.69 - 50.53: 500 50.53 - 67.38: 50 67.38 - 84.22: 150 Dihedral angle restraints: 41250 sinusoidal: 15650 harmonic: 25600 Sorted by residual: dihedral pdb=" CA LEU I 130 " pdb=" C LEU I 130 " pdb=" N GLY I 131 " pdb=" CA GLY I 131 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA LEU i 130 " pdb=" C LEU i 130 " pdb=" N GLY i 131 " pdb=" CA GLY i 131 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LEU Y 130 " pdb=" C LEU Y 130 " pdb=" N GLY Y 131 " pdb=" CA GLY Y 131 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 41247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 5602 0.037 - 0.074: 3677 0.074 - 0.111: 1028 0.111 - 0.148: 251 0.148 - 0.185: 142 Chirality restraints: 10700 Sorted by residual: chirality pdb=" CB ILE N 118 " pdb=" CA ILE N 118 " pdb=" CG1 ILE N 118 " pdb=" CG2 ILE N 118 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CB ILE b 118 " pdb=" CA ILE b 118 " pdb=" CG1 ILE b 118 " pdb=" CG2 ILE b 118 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CB ILE v 118 " pdb=" CA ILE v 118 " pdb=" CG1 ILE v 118 " pdb=" CG2 ILE v 118 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 10697 not shown) Planarity restraints: 11650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP Y 113 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO Y 114 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO Y 114 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO Y 114 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP w 113 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO w 114 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO w 114 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO w 114 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP L 113 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO L 114 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 114 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 114 " -0.018 5.00e-02 4.00e+02 ... (remaining 11647 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 218 2.30 - 2.95: 31336 2.95 - 3.60: 92475 3.60 - 4.25: 140855 4.25 - 4.90: 249779 Nonbonded interactions: 514663 Sorted by model distance: nonbonded pdb=" CD1 ILE T 185 " pdb=" ND2 ASN b 154 " model vdw 1.645 3.540 nonbonded pdb=" NE2 GLN N 78 " pdb=" CD2 LEU O 59 " model vdw 1.656 3.540 nonbonded pdb=" NE2 GLN X 78 " pdb=" CD2 LEU Y 59 " model vdw 1.656 3.540 nonbonded pdb=" NE2 GLN D 78 " pdb=" CD2 LEU E 59 " model vdw 1.656 3.540 nonbonded pdb=" NE2 GLN h 78 " pdb=" CD2 LEU i 59 " model vdw 1.656 3.540 ... (remaining 514658 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' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 6.610 Check model and map are aligned: 0.720 Set scattering table: 0.480 Process input model: 131.050 Find NCS groups from input model: 3.990 Set up NCS constraints: 0.880 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 : 0.008 0.061 66050 Z= 0.494 Angle : 0.972 9.760 89150 Z= 0.546 Chirality : 0.052 0.185 10700 Planarity : 0.004 0.032 11650 Dihedral : 13.298 84.219 24550 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.09), residues: 8600 helix: -0.57 (0.06), residues: 6400 sheet: None (None), residues: 0 loop : -2.84 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE g 42 TYR 0.010 0.002 TYR o 22 ARG 0.001 0.000 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1386 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1386 time to evaluate : 5.461 Fit side-chains revert: symmetry clash REVERT: A 82 ASN cc_start: 0.7649 (m-40) cc_final: 0.7242 (t0) REVERT: B 34 ASP cc_start: 0.7346 (m-30) cc_final: 0.7058 (m-30) REVERT: B 38 LYS cc_start: 0.8089 (tttp) cc_final: 0.7582 (tttm) REVERT: B 85 ASP cc_start: 0.7479 (m-30) cc_final: 0.7142 (t0) REVERT: C 34 ASP cc_start: 0.7123 (m-30) cc_final: 0.6792 (m-30) REVERT: D 79 LYS cc_start: 0.7947 (ttpp) cc_final: 0.6751 (tptm) REVERT: E 20 MET cc_start: 0.6520 (ptm) cc_final: 0.6150 (ptm) REVERT: E 38 LYS cc_start: 0.8068 (tttp) cc_final: 0.7783 (ttpp) REVERT: F 79 LYS cc_start: 0.7497 (ttpp) cc_final: 0.6900 (mttp) REVERT: G 38 LYS cc_start: 0.8161 (tttp) cc_final: 0.7715 (ttmt) REVERT: H 38 LYS cc_start: 0.7773 (tttp) cc_final: 0.7448 (ttpt) REVERT: I 30 ASP cc_start: 0.7830 (m-30) cc_final: 0.7263 (m-30) REVERT: I 34 ASP cc_start: 0.7564 (m-30) cc_final: 0.6960 (m-30) REVERT: K 148 ASN cc_start: 0.8345 (p0) cc_final: 0.8135 (p0) REVERT: L 34 ASP cc_start: 0.7596 (m-30) cc_final: 0.7114 (m-30) REVERT: L 58 ASP cc_start: 0.8148 (m-30) cc_final: 0.7863 (m-30) REVERT: L 85 ASP cc_start: 0.7485 (m-30) cc_final: 0.7138 (t0) REVERT: M 34 ASP cc_start: 0.7325 (m-30) cc_final: 0.6606 (m-30) REVERT: M 85 ASP cc_start: 0.7498 (m-30) cc_final: 0.7062 (t0) REVERT: P 38 LYS cc_start: 0.7718 (tttp) cc_final: 0.7021 (ttmt) REVERT: Q 38 LYS cc_start: 0.8016 (tttp) cc_final: 0.7736 (tttm) REVERT: U 20 MET cc_start: 0.6103 (ptm) cc_final: 0.5265 (mtm) REVERT: V 79 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7937 (ttmt) REVERT: V 85 ASP cc_start: 0.7450 (m-30) cc_final: 0.7184 (t0) REVERT: W 34 ASP cc_start: 0.7180 (m-30) cc_final: 0.6706 (m-30) REVERT: W 79 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7364 (mttt) REVERT: W 80 MET cc_start: 0.7585 (mmp) cc_final: 0.7266 (mmp) REVERT: W 183 ARG cc_start: 0.8231 (mtm110) cc_final: 0.8013 (mtm110) REVERT: X 79 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7767 (ttpp) REVERT: Y 38 LYS cc_start: 0.7891 (tttp) cc_final: 0.7682 (tttt) REVERT: Y 79 LYS cc_start: 0.8066 (ttpp) cc_final: 0.7676 (ttmm) REVERT: Z 23 ASP cc_start: 0.7654 (p0) cc_final: 0.7384 (p0) REVERT: Z 30 ASP cc_start: 0.7484 (m-30) cc_final: 0.6980 (m-30) REVERT: a 30 ASP cc_start: 0.8179 (m-30) cc_final: 0.7771 (m-30) REVERT: a 31 ASP cc_start: 0.8022 (m-30) cc_final: 0.7818 (m-30) REVERT: a 34 ASP cc_start: 0.7316 (m-30) cc_final: 0.6942 (m-30) REVERT: a 79 LYS cc_start: 0.7447 (ttpp) cc_final: 0.7150 (mttt) REVERT: b 172 SER cc_start: 0.7945 (t) cc_final: 0.7694 (m) REVERT: c 80 MET cc_start: 0.8096 (mmp) cc_final: 0.7794 (mmt) REVERT: c 164 SER cc_start: 0.9141 (m) cc_final: 0.8908 (m) REVERT: d 67 MET cc_start: 0.8479 (mtp) cc_final: 0.8269 (mtm) REVERT: e 79 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7348 (mttt) REVERT: e 113 ASP cc_start: 0.7820 (t70) cc_final: 0.7476 (t0) REVERT: f 34 ASP cc_start: 0.7448 (m-30) cc_final: 0.7204 (m-30) REVERT: f 58 ASP cc_start: 0.8585 (m-30) cc_final: 0.8331 (m-30) REVERT: f 79 LYS cc_start: 0.7764 (ttpp) cc_final: 0.7283 (mttt) REVERT: f 145 LYS cc_start: 0.8336 (ttpp) cc_final: 0.7803 (tttm) REVERT: g 38 LYS cc_start: 0.8289 (tttp) cc_final: 0.8057 (tttt) REVERT: h 79 LYS cc_start: 0.7902 (ttpp) cc_final: 0.7279 (ttmm) REVERT: h 119 THR cc_start: 0.7856 (m) cc_final: 0.7579 (p) REVERT: i 38 LYS cc_start: 0.7803 (tttp) cc_final: 0.7544 (tttm) REVERT: j 79 LYS cc_start: 0.7523 (ttpp) cc_final: 0.6953 (mttt) REVERT: l 88 ILE cc_start: 0.7189 (mt) cc_final: 0.6942 (tt) REVERT: m 145 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8228 (tttp) REVERT: o 52 MET cc_start: 0.8202 (mtp) cc_final: 0.7968 (mtm) REVERT: o 79 LYS cc_start: 0.7864 (ttpp) cc_final: 0.7314 (mttt) REVERT: p 30 ASP cc_start: 0.7637 (m-30) cc_final: 0.7119 (m-30) REVERT: p 34 ASP cc_start: 0.7399 (m-30) cc_final: 0.7037 (m-30) REVERT: p 38 LYS cc_start: 0.8330 (tttp) cc_final: 0.8001 (ttpp) REVERT: p 79 LYS cc_start: 0.7255 (ttpp) cc_final: 0.6712 (mttt) REVERT: q 31 ASP cc_start: 0.8630 (m-30) cc_final: 0.8399 (m-30) REVERT: r 27 MET cc_start: 0.9044 (mtp) cc_final: 0.8694 (mtp) REVERT: s 20 MET cc_start: 0.6668 (ptm) cc_final: 0.6342 (ptm) REVERT: t 30 ASP cc_start: 0.8356 (m-30) cc_final: 0.8027 (m-30) REVERT: t 31 ASP cc_start: 0.8082 (m-30) cc_final: 0.7809 (m-30) REVERT: t 34 ASP cc_start: 0.7134 (m-30) cc_final: 0.6734 (m-30) REVERT: t 38 LYS cc_start: 0.7869 (tttp) cc_final: 0.7303 (ttmt) REVERT: t 63 LYS cc_start: 0.8460 (tptp) cc_final: 0.8167 (tptm) REVERT: u 38 LYS cc_start: 0.7916 (tttp) cc_final: 0.7699 (tttm) REVERT: w 145 LYS cc_start: 0.8527 (ttpp) cc_final: 0.7739 (mtpp) outliers start: 0 outliers final: 0 residues processed: 1386 average time/residue: 0.5873 time to fit residues: 1401.0201 Evaluate side-chains 896 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 896 time to evaluate : 5.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 717 optimal weight: 0.8980 chunk 644 optimal weight: 2.9990 chunk 357 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 434 optimal weight: 7.9990 chunk 344 optimal weight: 0.7980 chunk 666 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 405 optimal weight: 2.9990 chunk 495 optimal weight: 2.9990 chunk 771 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 GLN ** G 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 GLN ** J 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 GLN ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 GLN ** N 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN O 78 GLN ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 GLN P 68 ASN ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 GLN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN R 78 GLN ** R 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 181 GLN ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 78 GLN ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 ASN X 78 GLN ** X 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 78 GLN ** Z 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 ASN a 78 GLN ** a 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 78 GLN ** b 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN c 78 GLN ** c 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 54 GLN ** e 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 78 GLN f 154 ASN ** f 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 181 GLN ** g 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 GLN h 68 ASN h 78 GLN ** h 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 78 GLN ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 54 GLN k 78 GLN ** k 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 78 GLN ** l 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 GLN n 181 GLN o 68 ASN o 154 ASN p 78 GLN p 154 ASN p 162 GLN q 78 GLN ** q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 162 GLN ** q 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 78 GLN ** r 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 78 GLN ** t 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 78 GLN ** u 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 78 GLN ** w 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 181 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 66050 Z= 0.181 Angle : 0.592 7.527 89150 Z= 0.311 Chirality : 0.038 0.206 10700 Planarity : 0.004 0.053 11650 Dihedral : 5.930 24.212 9050 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.37 % Allowed : 7.47 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: -0.74 (0.09), residues: 8600 helix: 0.66 (0.07), residues: 6000 sheet: None (None), residues: 0 loop : -3.31 (0.09), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE J 49 TYR 0.008 0.001 TYR W 22 ARG 0.003 0.000 ARG n 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1048 time to evaluate : 5.515 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.7865 (mtt) cc_final: 0.7555 (mtt) REVERT: B 34 ASP cc_start: 0.7250 (m-30) cc_final: 0.6820 (m-30) REVERT: B 38 LYS cc_start: 0.8139 (tttp) cc_final: 0.7795 (tttm) REVERT: B 85 ASP cc_start: 0.7394 (m-30) cc_final: 0.7037 (t0) REVERT: B 126 ILE cc_start: 0.5494 (OUTLIER) cc_final: 0.5233 (tt) REVERT: B 177 MET cc_start: 0.8586 (mmm) cc_final: 0.8289 (tpt) REVERT: C 30 ASP cc_start: 0.8407 (m-30) cc_final: 0.8091 (m-30) REVERT: C 34 ASP cc_start: 0.7088 (m-30) cc_final: 0.6703 (m-30) REVERT: C 172 SER cc_start: 0.8689 (t) cc_final: 0.8425 (m) REVERT: D 48 MET cc_start: 0.7723 (tmm) cc_final: 0.7235 (tmm) REVERT: E 20 MET cc_start: 0.6043 (ptm) cc_final: 0.5793 (ptm) REVERT: E 177 MET cc_start: 0.8286 (tpt) cc_final: 0.8023 (tpt) REVERT: F 79 LYS cc_start: 0.7543 (ttpp) cc_final: 0.6963 (mttp) REVERT: G 31 ASP cc_start: 0.7783 (m-30) cc_final: 0.7558 (m-30) REVERT: G 38 LYS cc_start: 0.8349 (tttp) cc_final: 0.7529 (ttpt) REVERT: H 38 LYS cc_start: 0.7865 (tttp) cc_final: 0.7442 (ttpt) REVERT: J 172 SER cc_start: 0.8651 (t) cc_final: 0.8364 (m) REVERT: K 126 ILE cc_start: 0.4856 (OUTLIER) cc_final: 0.4419 (tt) REVERT: L 85 ASP cc_start: 0.7604 (m-30) cc_final: 0.7173 (t0) REVERT: L 147 ASN cc_start: 0.8536 (t0) cc_final: 0.8228 (t0) REVERT: M 34 ASP cc_start: 0.7214 (m-30) cc_final: 0.6908 (m-30) REVERT: M 85 ASP cc_start: 0.7369 (m-30) cc_final: 0.6899 (t0) REVERT: P 38 LYS cc_start: 0.7794 (tttp) cc_final: 0.6996 (ttmt) REVERT: P 67 MET cc_start: 0.7784 (mtp) cc_final: 0.7518 (mtm) REVERT: Q 48 MET cc_start: 0.7671 (tmm) cc_final: 0.7442 (tmm) REVERT: R 145 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7781 (pttp) REVERT: U 20 MET cc_start: 0.6149 (ptm) cc_final: 0.5576 (mtm) REVERT: U 177 MET cc_start: 0.7852 (tpp) cc_final: 0.7427 (tpp) REVERT: V 79 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7892 (ttmt) REVERT: V 85 ASP cc_start: 0.7375 (m-30) cc_final: 0.7061 (t0) REVERT: W 34 ASP cc_start: 0.7192 (m-30) cc_final: 0.6552 (m-30) REVERT: W 67 MET cc_start: 0.7609 (mtp) cc_final: 0.7363 (mtt) REVERT: W 79 LYS cc_start: 0.7617 (ttpp) cc_final: 0.7322 (mttt) REVERT: W 80 MET cc_start: 0.7530 (mmp) cc_final: 0.7154 (mmp) REVERT: Y 20 MET cc_start: 0.6371 (ptm) cc_final: 0.5603 (ptm) REVERT: Y 38 LYS cc_start: 0.8134 (tttp) cc_final: 0.7922 (tttt) REVERT: Z 23 ASP cc_start: 0.7667 (p0) cc_final: 0.7284 (p0) REVERT: a 79 LYS cc_start: 0.7514 (ttpp) cc_final: 0.7025 (mttp) REVERT: c 80 MET cc_start: 0.8044 (mmp) cc_final: 0.7826 (mmt) REVERT: c 108 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.7056 (mp) REVERT: d 67 MET cc_start: 0.8262 (mtp) cc_final: 0.7982 (mtm) REVERT: e 79 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7289 (mttt) REVERT: h 22 TYR cc_start: 0.7771 (m-80) cc_final: 0.7490 (m-80) REVERT: h 79 LYS cc_start: 0.7939 (ttpp) cc_final: 0.6963 (mttm) REVERT: h 108 ILE cc_start: 0.7045 (OUTLIER) cc_final: 0.6829 (pt) REVERT: j 88 ILE cc_start: 0.7369 (mt) cc_final: 0.7144 (tt) REVERT: k 172 SER cc_start: 0.8658 (t) cc_final: 0.8451 (m) REVERT: l 177 MET cc_start: 0.8561 (tpt) cc_final: 0.8295 (tpt) REVERT: m 145 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8067 (tttp) REVERT: n 80 MET cc_start: 0.6636 (mmp) cc_final: 0.6398 (mmt) REVERT: n 177 MET cc_start: 0.8613 (tpp) cc_final: 0.8292 (tpt) REVERT: o 30 ASP cc_start: 0.6881 (m-30) cc_final: 0.6553 (t0) REVERT: o 79 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7338 (mttt) REVERT: o 85 ASP cc_start: 0.7766 (m-30) cc_final: 0.7510 (t0) REVERT: p 34 ASP cc_start: 0.7429 (m-30) cc_final: 0.6868 (m-30) REVERT: p 39 LEU cc_start: 0.8003 (mt) cc_final: 0.7765 (mp) REVERT: p 79 LYS cc_start: 0.7273 (ttpp) cc_final: 0.6870 (mttt) REVERT: r 27 MET cc_start: 0.9041 (mtp) cc_final: 0.8622 (mtp) REVERT: s 30 ASP cc_start: 0.7381 (m-30) cc_final: 0.7063 (t0) REVERT: s 163 MET cc_start: 0.7454 (mtt) cc_final: 0.7203 (mtt) REVERT: t 38 LYS cc_start: 0.7930 (tttp) cc_final: 0.7220 (ttmt) REVERT: u 80 MET cc_start: 0.7798 (mmt) cc_final: 0.7350 (mmt) REVERT: u 172 SER cc_start: 0.8741 (t) cc_final: 0.8295 (m) REVERT: u 176 ASP cc_start: 0.8307 (m-30) cc_final: 0.8091 (m-30) REVERT: u 185 ILE cc_start: 0.8751 (mm) cc_final: 0.8476 (mm) REVERT: v 52 MET cc_start: 0.8039 (mtm) cc_final: 0.7830 (mtp) REVERT: v 145 LYS cc_start: 0.8097 (tttp) cc_final: 0.7485 (mtpp) REVERT: v 177 MET cc_start: 0.8664 (tpt) cc_final: 0.8195 (tpt) REVERT: w 145 LYS cc_start: 0.8374 (ttpp) cc_final: 0.7900 (mmtm) outliers start: 173 outliers final: 40 residues processed: 1164 average time/residue: 0.5565 time to fit residues: 1146.3061 Evaluate side-chains 901 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 856 time to evaluate : 5.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain V residue 127 ASN Chi-restraints excluded: chain V residue 181 GLN Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 126 ILE Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain c residue 108 ILE Chi-restraints excluded: chain d residue 145 LYS Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain f residue 96 ASP Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain i residue 88 ILE Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain q residue 117 ASP Chi-restraints excluded: chain s residue 88 ILE Chi-restraints excluded: chain t residue 23 ASP Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain u residue 23 ASP Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain w residue 83 LEU Chi-restraints excluded: chain w residue 179 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 428 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 642 optimal weight: 8.9990 chunk 525 optimal weight: 10.0000 chunk 212 optimal weight: 0.0980 chunk 773 optimal weight: 20.0000 chunk 835 optimal weight: 8.9990 chunk 688 optimal weight: 6.9990 chunk 766 optimal weight: 7.9990 chunk 263 optimal weight: 8.9990 chunk 620 optimal weight: 8.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 154 ASN C 161 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN D 154 ASN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 154 ASN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 GLN ** G 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN H 56 GLN H 68 ASN ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 GLN H 162 GLN H 168 ASN I 68 ASN I 78 GLN ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN J 181 GLN K 68 ASN K 154 ASN K 161 GLN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN L 161 GLN ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN M 154 ASN M 161 GLN ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 ASN N 68 ASN N 154 ASN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 ASN O 154 ASN ** O 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 GLN P 68 ASN ** P 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 GLN ** P 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 ASN Q 127 ASN Q 161 GLN Q 168 ASN R 56 GLN R 68 ASN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 GLN ** R 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 168 ASN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 127 ASN ** T 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 161 GLN V 68 ASN ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 GLN ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 161 GLN ** W 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 154 ASN ** X 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 168 ASN Y 68 ASN Y 154 ASN ** Y 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 ASN Z 161 GLN ** Z 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 168 ASN a 68 ASN a 154 ASN ** a 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN b 56 GLN b 68 ASN ** b 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 GLN ** b 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 GLN ** c 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 168 ASN d 127 ASN e 68 ASN ** e 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 ASN f 161 GLN ** f 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 ASN h 154 ASN ** h 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 168 ASN i 68 ASN ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 168 ASN j 68 ASN ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 154 ASN ** j 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 168 ASN k 68 ASN ** k 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 147 ASN ** k 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 161 GLN ** k 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 68 ASN ** l 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 168 ASN m 56 GLN m 127 ASN o 68 ASN p 68 ASN p 161 GLN q 68 ASN q 154 ASN q 181 GLN r 68 ASN r 161 GLN ** r 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 ASN ** s 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN t 68 ASN ** t 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 168 ASN u 68 ASN ** u 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 161 GLN ** u 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 68 ASN ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 168 ASN ** w 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 54 GLN Total number of N/Q/H flips: 103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 66050 Z= 0.399 Angle : 0.722 9.705 89150 Z= 0.369 Chirality : 0.044 0.216 10700 Planarity : 0.004 0.053 11650 Dihedral : 6.142 25.082 9050 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.59 % Allowed : 9.99 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: -0.76 (0.09), residues: 8600 helix: 0.47 (0.07), residues: 6250 sheet: None (None), residues: 0 loop : -3.18 (0.10), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE u 49 TYR 0.019 0.002 TYR Z 22 ARG 0.006 0.001 ARG a 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 850 time to evaluate : 5.786 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.8085 (mtt) cc_final: 0.7764 (mtt) REVERT: B 34 ASP cc_start: 0.7272 (m-30) cc_final: 0.6744 (m-30) REVERT: B 38 LYS cc_start: 0.8016 (tttp) cc_final: 0.7743 (tttm) REVERT: B 85 ASP cc_start: 0.7615 (m-30) cc_final: 0.7059 (t0) REVERT: C 118 ILE cc_start: 0.8425 (tp) cc_final: 0.8140 (tt) REVERT: C 172 SER cc_start: 0.8892 (t) cc_final: 0.8690 (t) REVERT: D 79 LYS cc_start: 0.7897 (ttpp) cc_final: 0.6712 (tptm) REVERT: D 161 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8138 (tp-100) REVERT: E 161 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: E 177 MET cc_start: 0.8234 (tpt) cc_final: 0.7963 (tpt) REVERT: F 79 LYS cc_start: 0.7710 (ttpp) cc_final: 0.6977 (mttp) REVERT: F 161 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: F 169 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8029 (mp) REVERT: F 177 MET cc_start: 0.8634 (tpt) cc_final: 0.8301 (tpt) REVERT: G 23 ASP cc_start: 0.7316 (p0) cc_final: 0.6884 (t0) REVERT: G 38 LYS cc_start: 0.8339 (tttp) cc_final: 0.7777 (ttmt) REVERT: G 79 LYS cc_start: 0.7330 (ttpp) cc_final: 0.7050 (mttt) REVERT: G 80 MET cc_start: 0.7646 (mmt) cc_final: 0.7443 (mmt) REVERT: G 161 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: H 20 MET cc_start: 0.7110 (ptm) cc_final: 0.6728 (ttp) REVERT: H 38 LYS cc_start: 0.7949 (tttp) cc_final: 0.7571 (ttpt) REVERT: I 161 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: J 31 ASP cc_start: 0.7949 (m-30) cc_final: 0.7729 (m-30) REVERT: J 176 ASP cc_start: 0.8200 (m-30) cc_final: 0.7995 (m-30) REVERT: L 39 LEU cc_start: 0.7734 (mt) cc_final: 0.7525 (mt) REVERT: L 147 ASN cc_start: 0.8849 (t0) cc_final: 0.8423 (t0) REVERT: M 34 ASP cc_start: 0.7149 (m-30) cc_final: 0.6903 (m-30) REVERT: M 85 ASP cc_start: 0.7678 (m-30) cc_final: 0.7174 (t0) REVERT: M 161 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: N 161 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: O 177 MET cc_start: 0.8263 (tpt) cc_final: 0.8004 (tpt) REVERT: P 38 LYS cc_start: 0.7875 (tttp) cc_final: 0.7117 (ttmt) REVERT: P 161 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: P 169 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8217 (mp) REVERT: Q 161 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: R 31 ASP cc_start: 0.7800 (t0) cc_final: 0.7585 (t0) REVERT: R 68 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7497 (m110) REVERT: R 145 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7975 (pttp) REVERT: R 188 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8052 (mt) REVERT: S 161 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: U 20 MET cc_start: 0.6558 (ptm) cc_final: 0.5433 (mtp) REVERT: V 38 LYS cc_start: 0.7957 (tttp) cc_final: 0.7153 (mttt) REVERT: V 79 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7893 (ttmt) REVERT: V 85 ASP cc_start: 0.7585 (m-30) cc_final: 0.7139 (t0) REVERT: V 147 ASN cc_start: 0.8845 (t0) cc_final: 0.8641 (t0) REVERT: W 34 ASP cc_start: 0.7086 (m-30) cc_final: 0.6419 (m-30) REVERT: W 79 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7364 (mttt) REVERT: W 80 MET cc_start: 0.7675 (mmp) cc_final: 0.7383 (mmp) REVERT: Y 163 MET cc_start: 0.7749 (mtt) cc_final: 0.7377 (mtt) REVERT: Y 177 MET cc_start: 0.8509 (tpp) cc_final: 0.8294 (tpp) REVERT: Z 161 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: a 79 LYS cc_start: 0.7674 (ttpp) cc_final: 0.7068 (mttp) REVERT: d 67 MET cc_start: 0.8013 (mtp) cc_final: 0.7740 (mtm) REVERT: e 79 LYS cc_start: 0.7973 (ttpp) cc_final: 0.7298 (mttt) REVERT: f 47 LEU cc_start: 0.8865 (tt) cc_final: 0.8663 (tp) REVERT: f 79 LYS cc_start: 0.7902 (ttpp) cc_final: 0.7342 (mttt) REVERT: f 145 LYS cc_start: 0.7858 (ttpp) cc_final: 0.7434 (ttmm) REVERT: g 120 ILE cc_start: 0.5553 (mt) cc_final: 0.5259 (mt) REVERT: h 79 LYS cc_start: 0.7979 (ttpp) cc_final: 0.7242 (ttmm) REVERT: h 108 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6536 (pt) REVERT: i 161 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: k 31 ASP cc_start: 0.8195 (m-30) cc_final: 0.7861 (m-30) REVERT: k 68 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7494 (m110) REVERT: k 177 MET cc_start: 0.8364 (tpp) cc_final: 0.8045 (mmt) REVERT: l 161 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: l 177 MET cc_start: 0.8586 (tpt) cc_final: 0.8297 (tpt) REVERT: m 145 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8156 (tttp) REVERT: m 161 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: m 169 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8302 (mp) REVERT: n 177 MET cc_start: 0.8650 (tpp) cc_final: 0.8401 (tpt) REVERT: o 20 MET cc_start: 0.7572 (ptm) cc_final: 0.7370 (ptm) REVERT: o 79 LYS cc_start: 0.7988 (ttpp) cc_final: 0.7282 (mttt) REVERT: o 85 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7451 (t0) REVERT: p 38 LYS cc_start: 0.8598 (tttp) cc_final: 0.8133 (tttm) REVERT: p 79 LYS cc_start: 0.7555 (ttpp) cc_final: 0.6961 (mttt) REVERT: q 161 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: r 161 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: s 82 ASN cc_start: 0.6899 (m-40) cc_final: 0.6559 (m-40) REVERT: s 169 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8305 (mp) REVERT: t 38 LYS cc_start: 0.8039 (tttp) cc_final: 0.7322 (ttmt) REVERT: v 145 LYS cc_start: 0.8394 (tttp) cc_final: 0.7973 (ttmm) REVERT: v 172 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8351 (p) REVERT: v 177 MET cc_start: 0.8726 (tpt) cc_final: 0.8337 (tpt) REVERT: w 145 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8086 (mmtm) outliers start: 262 outliers final: 127 residues processed: 1051 average time/residue: 0.5729 time to fit residues: 1058.1767 Evaluate side-chains 946 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 792 time to evaluate : 5.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 161 GLN Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 161 GLN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 161 GLN Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 161 GLN Chi-restraints excluded: chain N residue 161 GLN Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 161 GLN Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain Q residue 161 GLN Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 68 ASN Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain S residue 161 GLN Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain V residue 181 GLN Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 184 THR Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 126 ILE Chi-restraints excluded: chain Z residue 161 GLN Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain a residue 52 MET Chi-restraints excluded: chain a residue 68 ASN Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain a residue 161 GLN Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 88 ILE Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 142 ILE Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain d residue 20 MET Chi-restraints excluded: chain d residue 71 SER Chi-restraints excluded: chain d residue 80 MET Chi-restraints excluded: chain d residue 145 LYS Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain e residue 59 LEU Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 118 ILE Chi-restraints excluded: chain e residue 181 GLN Chi-restraints excluded: chain e residue 184 THR Chi-restraints excluded: chain f residue 96 ASP Chi-restraints excluded: chain f residue 117 ASP Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 184 THR Chi-restraints excluded: chain g residue 88 ILE Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain h residue 48 MET Chi-restraints excluded: chain h residue 68 ASN Chi-restraints excluded: chain h residue 88 ILE Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain i residue 88 ILE Chi-restraints excluded: chain i residue 111 ILE Chi-restraints excluded: chain i residue 161 GLN Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 161 GLN Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain k residue 68 ASN Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain k residue 184 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 161 GLN Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 108 ILE Chi-restraints excluded: chain m residue 161 GLN Chi-restraints excluded: chain m residue 169 LEU Chi-restraints excluded: chain m residue 172 SER Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain n residue 184 THR Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain p residue 90 ASP Chi-restraints excluded: chain p residue 181 GLN Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain q residue 117 ASP Chi-restraints excluded: chain q residue 126 ILE Chi-restraints excluded: chain q residue 161 GLN Chi-restraints excluded: chain q residue 184 THR Chi-restraints excluded: chain r residue 161 GLN Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain s residue 161 GLN Chi-restraints excluded: chain s residue 169 LEU Chi-restraints excluded: chain s residue 172 SER Chi-restraints excluded: chain t residue 23 ASP Chi-restraints excluded: chain t residue 161 GLN Chi-restraints excluded: chain t residue 172 SER Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain u residue 23 ASP Chi-restraints excluded: chain u residue 108 ILE Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain v residue 172 SER Chi-restraints excluded: chain v residue 184 THR Chi-restraints excluded: chain w residue 83 LEU Chi-restraints excluded: chain w residue 179 SER Chi-restraints excluded: chain x residue 172 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 764 optimal weight: 1.9990 chunk 581 optimal weight: 0.8980 chunk 401 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 369 optimal weight: 6.9990 chunk 519 optimal weight: 4.9990 chunk 776 optimal weight: 20.0000 chunk 821 optimal weight: 3.9990 chunk 405 optimal weight: 2.9990 chunk 735 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 154 ASN B 68 ASN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN D 68 ASN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN E 56 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN F 68 ASN F 78 GLN ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN ** H 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 GLN ** I 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN J 54 GLN K 68 ASN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** L 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN N 56 GLN N 68 ASN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 GLN O 161 GLN ** O 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 GLN ** P 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 GLN Q 56 GLN ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN R 68 ASN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 168 ASN S 56 GLN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 168 ASN T 56 GLN ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 68 ASN ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 127 ASN ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 56 GLN X 68 ASN ** X 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 GLN ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 161 GLN Z 56 GLN ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 168 ASN a 56 GLN a 68 ASN a 162 GLN b 68 ASN b 154 ASN ** b 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 168 ASN c 54 GLN c 68 ASN c 168 ASN d 56 GLN ** e 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 ASN g 56 GLN h 68 ASN ** h 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 168 ASN i 56 GLN i 68 ASN ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 168 ASN ** j 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 168 ASN k 56 GLN k 68 ASN ** k 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 162 GLN k 168 ASN l 56 GLN ** l 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 56 GLN o 68 ASN p 68 ASN q 136 GLN r 68 ASN r 162 GLN s 56 GLN s 68 ASN ** s 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN t 68 ASN ** t 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 168 ASN u 56 GLN ** u 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 56 GLN v 154 ASN ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 168 ASN w 56 GLN ** w 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 66050 Z= 0.193 Angle : 0.553 8.096 89150 Z= 0.292 Chirality : 0.039 0.185 10700 Planarity : 0.003 0.048 11650 Dihedral : 5.541 23.980 9050 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.52 % Allowed : 11.75 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: -0.10 (0.09), residues: 8600 helix: 1.10 (0.07), residues: 5950 sheet: None (None), residues: 0 loop : -2.89 (0.10), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE u 49 TYR 0.014 0.001 TYR s 22 ARG 0.004 0.000 ARG n 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 856 time to evaluate : 5.505 Fit side-chains REVERT: A 163 MET cc_start: 0.7990 (mtt) cc_final: 0.7729 (mtt) REVERT: A 177 MET cc_start: 0.8138 (tpt) cc_final: 0.7795 (tpt) REVERT: B 34 ASP cc_start: 0.7178 (m-30) cc_final: 0.6655 (m-30) REVERT: B 38 LYS cc_start: 0.7941 (tttp) cc_final: 0.7576 (tttm) REVERT: B 85 ASP cc_start: 0.7381 (m-30) cc_final: 0.6848 (t0) REVERT: C 118 ILE cc_start: 0.8427 (tp) cc_final: 0.8131 (tt) REVERT: C 161 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: C 185 ILE cc_start: 0.9037 (mm) cc_final: 0.8835 (mm) REVERT: D 79 LYS cc_start: 0.7957 (ttpp) cc_final: 0.6746 (tptm) REVERT: E 177 MET cc_start: 0.8295 (tpt) cc_final: 0.7924 (tpt) REVERT: F 79 LYS cc_start: 0.7758 (ttpp) cc_final: 0.7013 (mttp) REVERT: F 169 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8080 (mp) REVERT: G 23 ASP cc_start: 0.7202 (p0) cc_final: 0.6842 (t0) REVERT: G 31 ASP cc_start: 0.7888 (m-30) cc_final: 0.7687 (m-30) REVERT: G 38 LYS cc_start: 0.8415 (tttp) cc_final: 0.7756 (ttmt) REVERT: G 79 LYS cc_start: 0.7290 (ttpp) cc_final: 0.7005 (mttt) REVERT: G 172 SER cc_start: 0.8792 (t) cc_final: 0.8582 (t) REVERT: H 20 MET cc_start: 0.6994 (ptm) cc_final: 0.6556 (ttp) REVERT: H 38 LYS cc_start: 0.8052 (tttp) cc_final: 0.7675 (ttmt) REVERT: J 172 SER cc_start: 0.8890 (t) cc_final: 0.8467 (m) REVERT: L 63 LYS cc_start: 0.9036 (tptt) cc_final: 0.8786 (tptm) REVERT: M 34 ASP cc_start: 0.7098 (m-30) cc_final: 0.6817 (m-30) REVERT: M 85 ASP cc_start: 0.7549 (m-30) cc_final: 0.6936 (t0) REVERT: N 135 LEU cc_start: 0.6724 (tp) cc_final: 0.6519 (mt) REVERT: O 163 MET cc_start: 0.7723 (mtt) cc_final: 0.7495 (mtt) REVERT: P 38 LYS cc_start: 0.7891 (tttp) cc_final: 0.7107 (ttmt) REVERT: P 67 MET cc_start: 0.8003 (mtp) cc_final: 0.7788 (mtm) REVERT: P 135 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7277 (mp) REVERT: P 169 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8305 (mp) REVERT: Q 48 MET cc_start: 0.7986 (tmm) cc_final: 0.7586 (tmm) REVERT: Q 169 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8403 (mp) REVERT: R 68 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.7145 (m110) REVERT: R 145 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7908 (pttp) REVERT: S 85 ASP cc_start: 0.7220 (m-30) cc_final: 0.6844 (m-30) REVERT: S 163 MET cc_start: 0.7867 (mtt) cc_final: 0.7405 (mtt) REVERT: U 20 MET cc_start: 0.6596 (ptm) cc_final: 0.5754 (mtp) REVERT: V 38 LYS cc_start: 0.7907 (tttp) cc_final: 0.7128 (mttt) REVERT: V 79 LYS cc_start: 0.8234 (ttpp) cc_final: 0.7910 (ttmt) REVERT: V 85 ASP cc_start: 0.7681 (m-30) cc_final: 0.7206 (t0) REVERT: V 90 ASP cc_start: 0.6655 (m-30) cc_final: 0.6406 (m-30) REVERT: W 34 ASP cc_start: 0.7044 (m-30) cc_final: 0.6380 (m-30) REVERT: W 79 LYS cc_start: 0.7764 (ttpp) cc_final: 0.7363 (mttt) REVERT: Y 163 MET cc_start: 0.7601 (mtt) cc_final: 0.7261 (mtt) REVERT: Y 177 MET cc_start: 0.8499 (tpp) cc_final: 0.8250 (tpp) REVERT: Z 126 ILE cc_start: 0.5571 (OUTLIER) cc_final: 0.5340 (tp) REVERT: a 79 LYS cc_start: 0.7675 (ttpp) cc_final: 0.7151 (mttt) REVERT: a 169 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8347 (mt) REVERT: a 188 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7934 (mt) REVERT: b 67 MET cc_start: 0.8301 (mtp) cc_final: 0.8095 (mtp) REVERT: c 108 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7154 (mp) REVERT: d 67 MET cc_start: 0.8030 (mtp) cc_final: 0.7748 (mtm) REVERT: e 79 LYS cc_start: 0.8019 (ttpp) cc_final: 0.7330 (mttt) REVERT: f 79 LYS cc_start: 0.7940 (ttpp) cc_final: 0.7403 (mttt) REVERT: f 145 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7392 (ttmm) REVERT: g 27 MET cc_start: 0.9087 (mtp) cc_final: 0.8822 (mtp) REVERT: g 47 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8363 (tp) REVERT: h 67 MET cc_start: 0.7890 (mtp) cc_final: 0.7626 (mtp) REVERT: h 79 LYS cc_start: 0.7941 (ttpp) cc_final: 0.7226 (ttmm) REVERT: h 145 LYS cc_start: 0.7752 (tttm) cc_final: 0.7298 (ttmm) REVERT: i 48 MET cc_start: 0.7803 (tmm) cc_final: 0.7533 (ttp) REVERT: j 88 ILE cc_start: 0.7430 (mt) cc_final: 0.7188 (tt) REVERT: k 31 ASP cc_start: 0.8176 (m-30) cc_final: 0.7859 (m-30) REVERT: k 172 SER cc_start: 0.8617 (t) cc_final: 0.8361 (m) REVERT: k 177 MET cc_start: 0.8386 (tpp) cc_final: 0.8098 (mmt) REVERT: l 30 ASP cc_start: 0.7878 (m-30) cc_final: 0.7667 (m-30) REVERT: l 177 MET cc_start: 0.8602 (tpt) cc_final: 0.8249 (tpt) REVERT: m 145 LYS cc_start: 0.8559 (ttpp) cc_final: 0.8091 (tttp) REVERT: n 19 SER cc_start: 0.5999 (m) cc_final: 0.5643 (t) REVERT: n 80 MET cc_start: 0.6965 (mmp) cc_final: 0.6637 (mmt) REVERT: n 177 MET cc_start: 0.8646 (tpp) cc_final: 0.8382 (tpt) REVERT: o 79 LYS cc_start: 0.7982 (ttpp) cc_final: 0.7352 (mttt) REVERT: o 85 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7519 (t0) REVERT: o 177 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8266 (mmt) REVERT: p 79 LYS cc_start: 0.7601 (ttpp) cc_final: 0.6954 (mttt) REVERT: r 68 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7437 (t0) REVERT: s 23 ASP cc_start: 0.7016 (p0) cc_final: 0.6772 (p0) REVERT: u 172 SER cc_start: 0.8764 (t) cc_final: 0.8520 (m) REVERT: v 172 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8606 (m) REVERT: v 177 MET cc_start: 0.8749 (tpt) cc_final: 0.8296 (tpt) REVERT: w 145 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8062 (mmtm) REVERT: x 177 MET cc_start: 0.8468 (tpt) cc_final: 0.8221 (tpt) outliers start: 257 outliers final: 113 residues processed: 1061 average time/residue: 0.5550 time to fit residues: 1036.8113 Evaluate side-chains 910 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 781 time to evaluate : 5.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 188 ILE Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 181 GLN Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 68 ASN Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 188 ILE Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 184 THR Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 181 GLN Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 184 THR Chi-restraints excluded: chain X residue 117 ASP Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 27 MET Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 126 ILE Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain a residue 169 LEU Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 188 ILE Chi-restraints excluded: chain c residue 48 MET Chi-restraints excluded: chain c residue 88 ILE Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 108 ILE Chi-restraints excluded: chain c residue 142 ILE Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain d residue 20 MET Chi-restraints excluded: chain d residue 80 MET Chi-restraints excluded: chain e residue 68 ASN Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 181 GLN Chi-restraints excluded: chain f residue 68 ASN Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 184 THR Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 88 ILE Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain h residue 48 MET Chi-restraints excluded: chain h residue 88 ILE Chi-restraints excluded: chain i residue 68 ASN Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 88 ILE Chi-restraints excluded: chain m residue 172 SER Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain n residue 184 THR Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain o residue 172 SER Chi-restraints excluded: chain o residue 177 MET Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain o residue 185 ILE Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain p residue 181 GLN Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 188 ILE Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 117 ASP Chi-restraints excluded: chain q residue 126 ILE Chi-restraints excluded: chain r residue 68 ASN Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain t residue 23 ASP Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain v residue 142 ILE Chi-restraints excluded: chain v residue 172 SER Chi-restraints excluded: chain w residue 179 SER Chi-restraints excluded: chain x residue 169 LEU Chi-restraints excluded: chain x residue 188 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 684 optimal weight: 9.9990 chunk 466 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 611 optimal weight: 5.9990 chunk 339 optimal weight: 8.9990 chunk 701 optimal weight: 8.9990 chunk 567 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 419 optimal weight: 2.9990 chunk 737 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN B 68 ASN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 127 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN G 68 ASN G 154 ASN ** G 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** H 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN H 168 ASN ** I 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN M 68 ASN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN ** P 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 ASN Q 154 ASN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 ASN R 54 GLN R 68 ASN R 154 ASN ** R 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 168 ASN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 168 ASN ** T 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 155 ASN ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 168 ASN V 68 ASN V 154 ASN ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 154 ASN X 68 ASN ** X 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 168 ASN b 68 ASN b 162 GLN b 168 ASN c 162 GLN c 168 ASN e 154 ASN f 68 ASN g 68 ASN g 168 ASN h 68 ASN ** h 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 168 ASN i 68 ASN ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 161 GLN i 168 ASN ** j 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 168 ASN k 154 ASN k 168 ASN ** l 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 162 GLN l 168 ASN ** o 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 ASN ** r 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 168 ASN s 154 ASN ** s 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN t 68 ASN t 154 ASN t 161 GLN t 168 ASN u 154 ASN ** u 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 168 ASN w 168 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 66050 Z= 0.346 Angle : 0.663 9.317 89150 Z= 0.342 Chirality : 0.043 0.254 10700 Planarity : 0.004 0.050 11650 Dihedral : 5.796 28.127 9050 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.49 % Allowed : 13.55 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: -0.46 (0.09), residues: 8600 helix: 0.71 (0.07), residues: 6200 sheet: None (None), residues: 0 loop : -3.07 (0.10), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE u 49 TYR 0.017 0.002 TYR j 22 ARG 0.004 0.001 ARG d 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 814 time to evaluate : 5.742 Fit side-chains revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8344 (tp) cc_final: 0.8031 (tt) REVERT: A 163 MET cc_start: 0.8107 (mtt) cc_final: 0.7802 (mtt) REVERT: A 169 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9047 (mp) REVERT: A 188 ILE cc_start: 0.2998 (OUTLIER) cc_final: 0.2701 (mt) REVERT: B 34 ASP cc_start: 0.7264 (m-30) cc_final: 0.6748 (m-30) REVERT: B 38 LYS cc_start: 0.7939 (tttp) cc_final: 0.7652 (tttm) REVERT: B 85 ASP cc_start: 0.7590 (m-30) cc_final: 0.6978 (t0) REVERT: C 48 MET cc_start: 0.8134 (tmm) cc_final: 0.7767 (ttp) REVERT: C 118 ILE cc_start: 0.8564 (tp) cc_final: 0.8319 (tt) REVERT: C 161 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: D 79 LYS cc_start: 0.7893 (ttpp) cc_final: 0.6776 (tptm) REVERT: D 161 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: D 188 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8674 (mt) REVERT: E 177 MET cc_start: 0.8231 (tpt) cc_final: 0.7831 (mmt) REVERT: F 79 LYS cc_start: 0.7767 (ttpp) cc_final: 0.6952 (mttp) REVERT: F 169 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8165 (mp) REVERT: G 20 MET cc_start: 0.6834 (ptm) cc_final: 0.6103 (ttp) REVERT: G 38 LYS cc_start: 0.8342 (tttp) cc_final: 0.7776 (ttmt) REVERT: G 79 LYS cc_start: 0.7390 (ttpp) cc_final: 0.6986 (mttt) REVERT: G 145 LYS cc_start: 0.8401 (tttp) cc_final: 0.8051 (ttmm) REVERT: H 20 MET cc_start: 0.7036 (ptm) cc_final: 0.6616 (ttp) REVERT: H 38 LYS cc_start: 0.7979 (tttp) cc_final: 0.7686 (ttpt) REVERT: I 161 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: M 34 ASP cc_start: 0.7065 (m-30) cc_final: 0.6824 (m-30) REVERT: M 85 ASP cc_start: 0.7794 (m-30) cc_final: 0.7141 (t0) REVERT: P 38 LYS cc_start: 0.7877 (tttp) cc_final: 0.7098 (ttmt) REVERT: P 169 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8170 (mp) REVERT: Q 169 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8359 (mp) REVERT: S 31 ASP cc_start: 0.8038 (m-30) cc_final: 0.7630 (m-30) REVERT: S 161 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: S 163 MET cc_start: 0.8062 (mtt) cc_final: 0.7533 (mtt) REVERT: U 20 MET cc_start: 0.6717 (ptm) cc_final: 0.5538 (mtp) REVERT: V 38 LYS cc_start: 0.7781 (tttp) cc_final: 0.6986 (mttt) REVERT: V 79 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7882 (ttmt) REVERT: V 85 ASP cc_start: 0.7759 (m-30) cc_final: 0.7254 (t0) REVERT: V 90 ASP cc_start: 0.6675 (m-30) cc_final: 0.6439 (m-30) REVERT: W 79 LYS cc_start: 0.7784 (ttpp) cc_final: 0.7334 (mttt) REVERT: W 80 MET cc_start: 0.7798 (mmt) cc_final: 0.7506 (mmt) REVERT: Y 163 MET cc_start: 0.7780 (mtt) cc_final: 0.7373 (mtt) REVERT: Z 126 ILE cc_start: 0.5612 (OUTLIER) cc_final: 0.5406 (tp) REVERT: a 79 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7167 (mttt) REVERT: a 188 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8151 (mt) REVERT: c 108 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.7107 (mp) REVERT: d 20 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6409 (ptt) REVERT: d 67 MET cc_start: 0.8033 (mtp) cc_final: 0.7790 (mtm) REVERT: e 79 LYS cc_start: 0.8050 (ttpp) cc_final: 0.7329 (mttt) REVERT: f 79 LYS cc_start: 0.7760 (ttpp) cc_final: 0.7163 (mttt) REVERT: f 145 LYS cc_start: 0.7890 (ttpp) cc_final: 0.7456 (ttmm) REVERT: g 47 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8392 (tp) REVERT: h 79 LYS cc_start: 0.7899 (ttpp) cc_final: 0.7315 (ttmm) REVERT: h 145 LYS cc_start: 0.7983 (tttm) cc_final: 0.7530 (ttmm) REVERT: k 20 MET cc_start: 0.6569 (ptm) cc_final: 0.6365 (ptt) REVERT: k 177 MET cc_start: 0.8337 (tpp) cc_final: 0.8018 (mmt) REVERT: l 161 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8525 (tt0) REVERT: m 145 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8069 (tttp) REVERT: m 149 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8462 (mm) REVERT: m 161 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: n 19 SER cc_start: 0.6187 (m) cc_final: 0.5733 (t) REVERT: n 177 MET cc_start: 0.8604 (tpp) cc_final: 0.8392 (tpt) REVERT: o 68 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7473 (m-40) REVERT: o 79 LYS cc_start: 0.8045 (ttpp) cc_final: 0.7351 (mttt) REVERT: o 85 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7435 (t0) REVERT: p 79 LYS cc_start: 0.7682 (ttpp) cc_final: 0.6913 (mttt) REVERT: q 59 LEU cc_start: 0.8718 (mt) cc_final: 0.8464 (mp) REVERT: q 161 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: r 68 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7710 (t0) REVERT: u 27 MET cc_start: 0.8706 (mtp) cc_final: 0.8503 (mtt) REVERT: u 177 MET cc_start: 0.8563 (tpp) cc_final: 0.7847 (mmt) REVERT: v 67 MET cc_start: 0.8402 (mtp) cc_final: 0.8106 (mtp) REVERT: v 145 LYS cc_start: 0.8467 (tttp) cc_final: 0.7992 (ttmm) REVERT: v 172 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8441 (p) REVERT: v 177 MET cc_start: 0.8743 (tpt) cc_final: 0.8257 (tpt) REVERT: w 145 LYS cc_start: 0.8454 (ttpp) cc_final: 0.8126 (mmtm) outliers start: 255 outliers final: 148 residues processed: 1007 average time/residue: 0.5783 time to fit residues: 1016.7644 Evaluate side-chains 944 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 773 time to evaluate : 5.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 161 GLN Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 188 ILE Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 161 GLN Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 184 THR Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain V residue 30 ASP Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 181 GLN Chi-restraints excluded: chain W residue 61 ILE Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 184 THR Chi-restraints excluded: chain X residue 117 ASP Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 188 ILE Chi-restraints excluded: chain Z residue 38 LYS Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 126 ILE Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain a residue 52 MET Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 188 ILE Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 88 ILE Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 108 ILE Chi-restraints excluded: chain c residue 142 ILE Chi-restraints excluded: chain c residue 149 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain d residue 20 MET Chi-restraints excluded: chain d residue 80 MET Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain e residue 68 ASN Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 118 ILE Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 181 GLN Chi-restraints excluded: chain f residue 68 ASN Chi-restraints excluded: chain f residue 117 ASP Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 184 THR Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 88 ILE Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain h residue 48 MET Chi-restraints excluded: chain h residue 68 ASN Chi-restraints excluded: chain h residue 88 ILE Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 119 THR Chi-restraints excluded: chain i residue 59 LEU Chi-restraints excluded: chain i residue 68 ASN Chi-restraints excluded: chain i residue 88 ILE Chi-restraints excluded: chain i residue 109 SER Chi-restraints excluded: chain i residue 111 ILE Chi-restraints excluded: chain i residue 119 THR Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 161 GLN Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 88 ILE Chi-restraints excluded: chain m residue 118 ILE Chi-restraints excluded: chain m residue 149 LEU Chi-restraints excluded: chain m residue 161 GLN Chi-restraints excluded: chain m residue 172 SER Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 52 MET Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain n residue 184 THR Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain o residue 172 SER Chi-restraints excluded: chain o residue 175 SER Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain p residue 181 GLN Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 188 ILE Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 117 ASP Chi-restraints excluded: chain q residue 126 ILE Chi-restraints excluded: chain q residue 161 GLN Chi-restraints excluded: chain r residue 68 ASN Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain s residue 172 SER Chi-restraints excluded: chain t residue 23 ASP Chi-restraints excluded: chain t residue 172 SER Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain u residue 23 ASP Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain v residue 20 MET Chi-restraints excluded: chain v residue 142 ILE Chi-restraints excluded: chain v residue 172 SER Chi-restraints excluded: chain w residue 179 SER Chi-restraints excluded: chain x residue 172 SER Chi-restraints excluded: chain x residue 188 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 276 optimal weight: 4.9990 chunk 739 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 482 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 822 optimal weight: 5.9990 chunk 682 optimal weight: 10.0000 chunk 380 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 272 optimal weight: 7.9990 chunk 431 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN B 154 ASN C 68 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN H 68 ASN ** H 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 ASN ** I 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN M 68 ASN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 GLN Q 78 GLN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 ASN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 168 ASN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 168 ASN T 54 GLN ** T 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 155 ASN U 154 ASN ** X 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 168 ASN a 68 ASN b 54 GLN b 68 ASN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 168 ASN c 168 ASN f 181 GLN g 127 ASN g 168 ASN ** h 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 168 ASN ** j 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 78 GLN ** j 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 168 ASN k 54 GLN k 168 ASN ** l 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 168 ASN ** o 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 68 ASN q 68 ASN r 68 ASN r 162 GLN r 168 ASN ** s 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 161 GLN ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 68 ASN ** t 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 168 ASN ** u 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 168 ASN w 168 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 66050 Z= 0.421 Angle : 0.702 9.401 89150 Z= 0.362 Chirality : 0.045 0.245 10700 Planarity : 0.004 0.053 11650 Dihedral : 5.931 27.388 9050 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.64 % Allowed : 14.48 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: -0.69 (0.09), residues: 8600 helix: 0.54 (0.07), residues: 6150 sheet: None (None), residues: 0 loop : -3.05 (0.10), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE b 49 TYR 0.019 0.002 TYR F 22 ARG 0.004 0.001 ARG a 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 782 time to evaluate : 5.534 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.8112 (mtt) cc_final: 0.7765 (mtt) REVERT: A 177 MET cc_start: 0.8229 (tpt) cc_final: 0.7855 (tpt) REVERT: A 188 ILE cc_start: 0.3111 (OUTLIER) cc_final: 0.2847 (mt) REVERT: B 38 LYS cc_start: 0.7934 (tttp) cc_final: 0.7646 (tttm) REVERT: B 85 ASP cc_start: 0.7512 (m-30) cc_final: 0.6806 (t0) REVERT: C 118 ILE cc_start: 0.8551 (tp) cc_final: 0.8330 (tt) REVERT: C 161 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: D 48 MET cc_start: 0.7839 (tmm) cc_final: 0.7470 (tmm) REVERT: D 188 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8725 (mt) REVERT: E 177 MET cc_start: 0.8345 (tpt) cc_final: 0.7876 (mmt) REVERT: F 79 LYS cc_start: 0.7780 (ttpp) cc_final: 0.6982 (mttp) REVERT: F 169 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8149 (mp) REVERT: G 43 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8362 (mm-40) REVERT: G 79 LYS cc_start: 0.7428 (ttpp) cc_final: 0.7024 (mttt) REVERT: G 145 LYS cc_start: 0.8467 (tttp) cc_final: 0.8127 (ttmm) REVERT: H 20 MET cc_start: 0.7117 (ptm) cc_final: 0.6790 (ttp) REVERT: H 38 LYS cc_start: 0.8039 (tttp) cc_final: 0.7560 (ttpt) REVERT: I 161 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: I 192 LYS cc_start: 0.7705 (mttt) cc_final: 0.7476 (mttm) REVERT: J 20 MET cc_start: 0.8281 (ttm) cc_final: 0.7912 (ttp) REVERT: M 34 ASP cc_start: 0.7080 (m-30) cc_final: 0.6826 (m-30) REVERT: M 85 ASP cc_start: 0.7891 (m-30) cc_final: 0.7135 (t0) REVERT: P 38 LYS cc_start: 0.7902 (tttp) cc_final: 0.7125 (ttmt) REVERT: P 169 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8127 (mp) REVERT: Q 169 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8418 (mp) REVERT: R 31 ASP cc_start: 0.7859 (t0) cc_final: 0.7644 (t0) REVERT: R 79 LYS cc_start: 0.7977 (ttpp) cc_final: 0.7149 (mttm) REVERT: S 31 ASP cc_start: 0.8072 (m-30) cc_final: 0.7657 (m-30) REVERT: S 161 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: S 163 MET cc_start: 0.8067 (mtt) cc_final: 0.7520 (mtt) REVERT: T 147 ASN cc_start: 0.8800 (t0) cc_final: 0.8553 (t0) REVERT: U 20 MET cc_start: 0.6909 (ptm) cc_final: 0.5598 (mtp) REVERT: V 38 LYS cc_start: 0.7783 (tttp) cc_final: 0.6986 (mttt) REVERT: V 79 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7893 (ttmt) REVERT: V 85 ASP cc_start: 0.7796 (m-30) cc_final: 0.7254 (t0) REVERT: W 79 LYS cc_start: 0.7835 (ttpp) cc_final: 0.7383 (mttt) REVERT: W 80 MET cc_start: 0.7832 (mmt) cc_final: 0.7595 (mmt) REVERT: Y 163 MET cc_start: 0.7812 (mtt) cc_final: 0.7397 (mtt) REVERT: Z 126 ILE cc_start: 0.5566 (OUTLIER) cc_final: 0.5336 (tp) REVERT: a 79 LYS cc_start: 0.7703 (ttpp) cc_final: 0.7227 (mttt) REVERT: a 170 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8117 (mp) REVERT: a 188 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8145 (mt) REVERT: b 135 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.5871 (mp) REVERT: b 139 LYS cc_start: 0.7723 (tmmt) cc_final: 0.7516 (tttp) REVERT: c 108 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.7105 (mp) REVERT: d 20 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6517 (ptt) REVERT: d 67 MET cc_start: 0.7960 (mtp) cc_final: 0.7726 (mtm) REVERT: e 79 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7341 (mttt) REVERT: f 79 LYS cc_start: 0.7809 (ttpp) cc_final: 0.7164 (mttt) REVERT: h 79 LYS cc_start: 0.7925 (ttpp) cc_final: 0.7318 (ttmm) REVERT: h 145 LYS cc_start: 0.7855 (tttm) cc_final: 0.7407 (ttmm) REVERT: k 68 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7476 (m110) REVERT: k 79 LYS cc_start: 0.7613 (ttpp) cc_final: 0.6955 (mttt) REVERT: k 177 MET cc_start: 0.8409 (tpp) cc_final: 0.7993 (mmt) REVERT: l 161 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8498 (tt0) REVERT: m 145 LYS cc_start: 0.8669 (ttpp) cc_final: 0.8157 (tttp) REVERT: m 161 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8480 (tt0) REVERT: n 19 SER cc_start: 0.6459 (m) cc_final: 0.5904 (t) REVERT: n 80 MET cc_start: 0.6314 (mmt) cc_final: 0.5980 (mmp) REVERT: o 79 LYS cc_start: 0.8076 (ttpp) cc_final: 0.7377 (mttt) REVERT: o 85 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7421 (t0) REVERT: p 79 LYS cc_start: 0.7701 (ttpp) cc_final: 0.6902 (mttt) REVERT: q 59 LEU cc_start: 0.8773 (mt) cc_final: 0.8477 (mp) REVERT: q 161 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: q 170 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7923 (mp) REVERT: s 135 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6376 (mp) REVERT: s 188 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8396 (mt) REVERT: t 79 LYS cc_start: 0.7497 (ttpp) cc_final: 0.6816 (mttt) REVERT: v 67 MET cc_start: 0.8408 (mtp) cc_final: 0.8110 (mtp) REVERT: v 115 ARG cc_start: 0.6536 (ptt-90) cc_final: 0.6262 (ptt-90) REVERT: v 145 LYS cc_start: 0.8480 (tttp) cc_final: 0.8075 (ttmm) REVERT: v 172 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8408 (p) REVERT: v 177 MET cc_start: 0.8734 (tpt) cc_final: 0.8266 (tpt) REVERT: w 34 ASP cc_start: 0.7139 (m-30) cc_final: 0.6716 (m-30) REVERT: w 145 LYS cc_start: 0.8455 (ttpp) cc_final: 0.8077 (mmtm) REVERT: w 177 MET cc_start: 0.8560 (mmm) cc_final: 0.8296 (mmt) outliers start: 266 outliers final: 173 residues processed: 988 average time/residue: 0.5942 time to fit residues: 1030.9729 Evaluate side-chains 959 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 762 time to evaluate : 5.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 161 GLN Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 188 ILE Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 161 GLN Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 184 THR Chi-restraints excluded: chain U residue 111 ILE Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 181 GLN Chi-restraints excluded: chain W residue 61 ILE Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 109 SER Chi-restraints excluded: chain W residue 184 THR Chi-restraints excluded: chain X residue 111 ILE Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 188 ILE Chi-restraints excluded: chain Z residue 38 LYS Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 126 ILE Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain a residue 52 MET Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain a residue 170 LEU Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 188 ILE Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 88 ILE Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 108 ILE Chi-restraints excluded: chain c residue 142 ILE Chi-restraints excluded: chain c residue 149 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain d residue 20 MET Chi-restraints excluded: chain d residue 80 MET Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain e residue 68 ASN Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 118 ILE Chi-restraints excluded: chain e residue 143 SER Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain e residue 181 GLN Chi-restraints excluded: chain e residue 184 THR Chi-restraints excluded: chain f residue 96 ASP Chi-restraints excluded: chain f residue 117 ASP Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 184 THR Chi-restraints excluded: chain g residue 20 MET Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain h residue 119 THR Chi-restraints excluded: chain h residue 169 LEU Chi-restraints excluded: chain i residue 59 LEU Chi-restraints excluded: chain i residue 88 ILE Chi-restraints excluded: chain i residue 109 SER Chi-restraints excluded: chain i residue 111 ILE Chi-restraints excluded: chain i residue 119 THR Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 88 ILE Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain k residue 68 ASN Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain k residue 184 THR Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 161 GLN Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 88 ILE Chi-restraints excluded: chain m residue 161 GLN Chi-restraints excluded: chain m residue 172 SER Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 52 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain n residue 184 THR Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain o residue 172 SER Chi-restraints excluded: chain o residue 175 SER Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain o residue 185 ILE Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 142 ILE Chi-restraints excluded: chain p residue 181 GLN Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 188 ILE Chi-restraints excluded: chain q residue 48 MET Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 117 ASP Chi-restraints excluded: chain q residue 126 ILE Chi-restraints excluded: chain q residue 161 GLN Chi-restraints excluded: chain q residue 170 LEU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain s residue 135 LEU Chi-restraints excluded: chain s residue 150 THR Chi-restraints excluded: chain s residue 172 SER Chi-restraints excluded: chain s residue 188 ILE Chi-restraints excluded: chain t residue 23 ASP Chi-restraints excluded: chain t residue 172 SER Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain u residue 23 ASP Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain v residue 20 MET Chi-restraints excluded: chain v residue 142 ILE Chi-restraints excluded: chain v residue 172 SER Chi-restraints excluded: chain w residue 83 LEU Chi-restraints excluded: chain w residue 179 SER Chi-restraints excluded: chain x residue 27 MET Chi-restraints excluded: chain x residue 172 SER Chi-restraints excluded: chain x residue 184 THR Chi-restraints excluded: chain x residue 188 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 792 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 468 optimal weight: 9.9990 chunk 600 optimal weight: 0.9990 chunk 465 optimal weight: 4.9990 chunk 692 optimal weight: 3.9990 chunk 459 optimal weight: 8.9990 chunk 819 optimal weight: 0.7980 chunk 512 optimal weight: 0.9980 chunk 499 optimal weight: 6.9990 chunk 378 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 68 ASN B 68 ASN C 68 ASN ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN G 56 GLN ** H 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN J 56 GLN K 68 ASN ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN M 56 GLN M 68 ASN M 161 GLN O 168 ASN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN R 127 ASN R 168 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 168 ASN U 56 GLN X 78 GLN X 162 GLN ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 GLN Z 168 ASN a 68 ASN a 168 ASN b 68 ASN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 162 GLN b 168 ASN f 56 GLN f 181 GLN g 168 ASN h 68 ASN ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 168 ASN ** j 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 168 ASN k 168 ASN ** l 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN ** o 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 56 GLN q 168 ASN r 68 ASN r 161 GLN r 168 ASN ** s 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 56 GLN t 68 ASN ** t 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 168 ASN ** u 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 168 ASN w 168 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 66050 Z= 0.189 Angle : 0.547 9.668 89150 Z= 0.287 Chirality : 0.039 0.297 10700 Planarity : 0.003 0.053 11650 Dihedral : 5.323 25.476 9050 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.93 % Allowed : 15.60 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: 0.03 (0.09), residues: 8600 helix: 1.15 (0.07), residues: 6000 sheet: None (None), residues: 0 loop : -2.78 (0.10), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE L 49 TYR 0.016 0.001 TYR w 110 ARG 0.004 0.000 ARG d 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 799 time to evaluate : 5.503 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.8003 (mtt) cc_final: 0.7584 (mtt) REVERT: A 175 SER cc_start: 0.8637 (t) cc_final: 0.8250 (p) REVERT: A 177 MET cc_start: 0.8061 (tpt) cc_final: 0.7776 (tpt) REVERT: A 188 ILE cc_start: 0.3102 (OUTLIER) cc_final: 0.2847 (mt) REVERT: B 34 ASP cc_start: 0.7178 (m-30) cc_final: 0.6728 (m-30) REVERT: B 38 LYS cc_start: 0.7934 (tttp) cc_final: 0.7680 (tttm) REVERT: B 85 ASP cc_start: 0.7329 (m-30) cc_final: 0.6762 (t0) REVERT: B 177 MET cc_start: 0.8818 (tpp) cc_final: 0.8508 (tpt) REVERT: D 48 MET cc_start: 0.7755 (tmm) cc_final: 0.7407 (tmm) REVERT: D 79 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7850 (tttt) REVERT: E 177 MET cc_start: 0.8244 (tpt) cc_final: 0.7904 (tpt) REVERT: F 79 LYS cc_start: 0.7810 (ttpp) cc_final: 0.7025 (mttp) REVERT: F 169 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8176 (mp) REVERT: G 79 LYS cc_start: 0.7390 (ttpp) cc_final: 0.7062 (mttt) REVERT: G 172 SER cc_start: 0.8799 (t) cc_final: 0.8580 (t) REVERT: H 38 LYS cc_start: 0.8057 (tttp) cc_final: 0.7734 (ttpt) REVERT: I 192 LYS cc_start: 0.7688 (mttt) cc_final: 0.7451 (mttm) REVERT: J 20 MET cc_start: 0.8192 (ttm) cc_final: 0.7784 (ttp) REVERT: L 63 LYS cc_start: 0.9058 (tptt) cc_final: 0.8759 (tptm) REVERT: M 34 ASP cc_start: 0.7076 (m-30) cc_final: 0.6848 (m-30) REVERT: M 85 ASP cc_start: 0.7715 (m-30) cc_final: 0.6939 (t0) REVERT: O 79 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7591 (ttmm) REVERT: P 38 LYS cc_start: 0.7908 (tttp) cc_final: 0.7142 (ttmt) REVERT: P 169 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8207 (mp) REVERT: Q 169 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8448 (mp) REVERT: R 79 LYS cc_start: 0.7756 (ttpp) cc_final: 0.7160 (mttm) REVERT: S 30 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: S 163 MET cc_start: 0.7904 (mtt) cc_final: 0.7429 (mtt) REVERT: T 147 ASN cc_start: 0.8695 (t0) cc_final: 0.8481 (t0) REVERT: U 20 MET cc_start: 0.6863 (ptm) cc_final: 0.5734 (mtp) REVERT: U 145 LYS cc_start: 0.8991 (ttmm) cc_final: 0.8584 (mtpp) REVERT: V 38 LYS cc_start: 0.7772 (tttp) cc_final: 0.6988 (mttt) REVERT: V 79 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7881 (ttmt) REVERT: V 85 ASP cc_start: 0.7756 (m-30) cc_final: 0.7182 (t0) REVERT: V 177 MET cc_start: 0.8886 (mmm) cc_final: 0.8493 (mmt) REVERT: W 79 LYS cc_start: 0.7848 (ttpp) cc_final: 0.7355 (mttt) REVERT: W 80 MET cc_start: 0.7755 (mmt) cc_final: 0.7429 (mmt) REVERT: Y 163 MET cc_start: 0.7653 (mtt) cc_final: 0.7362 (mtt) REVERT: Z 38 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7700 (tmtt) REVERT: a 79 LYS cc_start: 0.7653 (ttpp) cc_final: 0.7189 (mttt) REVERT: a 188 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8050 (mt) REVERT: b 135 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5826 (mp) REVERT: d 20 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6438 (ptt) REVERT: d 67 MET cc_start: 0.8029 (mtp) cc_final: 0.7714 (mtm) REVERT: e 79 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7287 (mttt) REVERT: e 177 MET cc_start: 0.8361 (mmm) cc_final: 0.7807 (mmt) REVERT: f 20 MET cc_start: 0.7137 (ttp) cc_final: 0.6778 (ptm) REVERT: f 79 LYS cc_start: 0.7761 (ttpp) cc_final: 0.7197 (mttt) REVERT: h 68 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7392 (t0) REVERT: i 48 MET cc_start: 0.8044 (tmm) cc_final: 0.7720 (ttp) REVERT: k 31 ASP cc_start: 0.8123 (m-30) cc_final: 0.7909 (m-30) REVERT: k 68 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.7318 (m110) REVERT: k 79 LYS cc_start: 0.7570 (ttpp) cc_final: 0.6948 (mttt) REVERT: k 172 SER cc_start: 0.8629 (t) cc_final: 0.8402 (m) REVERT: k 177 MET cc_start: 0.8401 (tpp) cc_final: 0.8055 (mmt) REVERT: o 35 LEU cc_start: 0.8124 (tp) cc_final: 0.7871 (tp) REVERT: o 79 LYS cc_start: 0.7994 (ttpp) cc_final: 0.7419 (mttt) REVERT: o 85 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7432 (t0) REVERT: p 79 LYS cc_start: 0.7632 (ttpp) cc_final: 0.6986 (mttt) REVERT: q 59 LEU cc_start: 0.8647 (mt) cc_final: 0.8409 (mp) REVERT: r 27 MET cc_start: 0.8997 (mtp) cc_final: 0.8593 (mtp) REVERT: r 30 ASP cc_start: 0.7751 (m-30) cc_final: 0.7447 (m-30) REVERT: u 145 LYS cc_start: 0.8584 (tttp) cc_final: 0.8353 (tttp) REVERT: u 172 SER cc_start: 0.8735 (t) cc_final: 0.8519 (m) REVERT: v 67 MET cc_start: 0.8105 (mtp) cc_final: 0.7831 (mtp) REVERT: v 145 LYS cc_start: 0.8399 (tttp) cc_final: 0.7964 (ttmm) REVERT: v 172 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8597 (m) REVERT: v 177 MET cc_start: 0.8759 (tpt) cc_final: 0.8302 (tpt) REVERT: w 145 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8060 (mmtm) REVERT: x 67 MET cc_start: 0.6767 (mtt) cc_final: 0.6521 (mtt) outliers start: 214 outliers final: 130 residues processed: 964 average time/residue: 0.5687 time to fit residues: 960.5311 Evaluate side-chains 905 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 762 time to evaluate : 5.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 27 MET Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 181 GLN Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain S residue 30 ASP Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 188 ILE Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 184 THR Chi-restraints excluded: chain U residue 48 MET Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 181 GLN Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 117 ASP Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 38 LYS Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 188 ILE Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 88 ILE Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain d residue 20 MET Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain e residue 68 ASN Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 184 THR Chi-restraints excluded: chain g residue 88 ILE Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 127 ASN Chi-restraints excluded: chain h residue 68 ASN Chi-restraints excluded: chain h residue 88 ILE Chi-restraints excluded: chain i residue 59 LEU Chi-restraints excluded: chain i residue 111 ILE Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 88 ILE Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain k residue 68 ASN Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain k residue 184 THR Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 88 ILE Chi-restraints excluded: chain m residue 172 SER Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain n residue 184 THR Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain o residue 172 SER Chi-restraints excluded: chain o residue 175 SER Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain o residue 185 ILE Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain p residue 142 ILE Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 188 ILE Chi-restraints excluded: chain q residue 48 MET Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 117 ASP Chi-restraints excluded: chain q residue 126 ILE Chi-restraints excluded: chain q residue 151 THR Chi-restraints excluded: chain r residue 169 LEU Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain s residue 143 SER Chi-restraints excluded: chain s residue 172 SER Chi-restraints excluded: chain t residue 23 ASP Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain v residue 20 MET Chi-restraints excluded: chain v residue 172 SER Chi-restraints excluded: chain w residue 83 LEU Chi-restraints excluded: chain w residue 179 SER Chi-restraints excluded: chain x residue 188 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 506 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 489 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 160 optimal weight: 0.0070 chunk 158 optimal weight: 2.9990 chunk 520 optimal weight: 0.0060 chunk 558 optimal weight: 2.9990 chunk 405 optimal weight: 5.9990 chunk 76 optimal weight: 0.0470 chunk 643 optimal weight: 0.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 68 ASN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 161 GLN F 168 ASN H 162 GLN ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN K 56 GLN K 68 ASN ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 56 GLN L 68 ASN ** L 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 GLN M 68 ASN N 68 ASN P 54 GLN P 68 ASN P 78 GLN ** P 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 168 ASN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN R 168 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 GLN U 161 GLN ** V 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 168 ASN Z 68 ASN Z 168 ASN b 78 GLN b 168 ASN f 68 ASN ** f 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 ASN h 56 GLN h 68 ASN h 161 GLN i 68 ASN ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 GLN ** j 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 54 GLN ** k 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 127 ASN ** o 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 68 ASN p 56 GLN q 136 GLN q 168 ASN r 54 GLN r 56 GLN r 168 ASN s 54 GLN s 127 ASN t 54 GLN t 162 GLN u 54 GLN ** u 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 168 ASN x 56 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 66050 Z= 0.106 Angle : 0.482 9.319 89150 Z= 0.259 Chirality : 0.036 0.256 10700 Planarity : 0.003 0.052 11650 Dihedral : 4.720 24.934 9050 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.22 % Allowed : 17.16 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: 0.72 (0.09), residues: 8600 helix: 1.70 (0.07), residues: 5950 sheet: None (None), residues: 0 loop : -2.54 (0.10), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 42 TYR 0.018 0.001 TYR m 110 ARG 0.002 0.000 ARG v 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 915 time to evaluate : 5.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8115 (tp) cc_final: 0.7846 (tt) REVERT: A 163 MET cc_start: 0.7859 (mtt) cc_final: 0.7443 (mtt) REVERT: A 175 SER cc_start: 0.8555 (t) cc_final: 0.8185 (p) REVERT: A 188 ILE cc_start: 0.3254 (OUTLIER) cc_final: 0.3010 (mt) REVERT: B 34 ASP cc_start: 0.7103 (m-30) cc_final: 0.6718 (m-30) REVERT: B 38 LYS cc_start: 0.7872 (tttp) cc_final: 0.7645 (tttm) REVERT: B 85 ASP cc_start: 0.7282 (m-30) cc_final: 0.6699 (t0) REVERT: C 177 MET cc_start: 0.8319 (mmm) cc_final: 0.8007 (mmt) REVERT: D 48 MET cc_start: 0.7515 (tmm) cc_final: 0.7228 (tmm) REVERT: E 85 ASP cc_start: 0.6837 (m-30) cc_final: 0.6478 (t0) REVERT: E 135 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6102 (mp) REVERT: E 177 MET cc_start: 0.8298 (tpt) cc_final: 0.7861 (tpt) REVERT: F 79 LYS cc_start: 0.7734 (ttpp) cc_final: 0.6920 (mttp) REVERT: G 79 LYS cc_start: 0.7348 (ttpp) cc_final: 0.7035 (mttt) REVERT: H 38 LYS cc_start: 0.8042 (tttp) cc_final: 0.7641 (ttpt) REVERT: H 79 LYS cc_start: 0.8031 (ttpp) cc_final: 0.7626 (mttm) REVERT: H 155 ASN cc_start: 0.8401 (m-40) cc_final: 0.7856 (m-40) REVERT: J 172 SER cc_start: 0.8879 (t) cc_final: 0.8482 (m) REVERT: M 85 ASP cc_start: 0.7798 (m-30) cc_final: 0.6911 (t0) REVERT: M 176 ASP cc_start: 0.8425 (m-30) cc_final: 0.7987 (m-30) REVERT: O 79 LYS cc_start: 0.7867 (ttpp) cc_final: 0.7521 (ttmm) REVERT: O 163 MET cc_start: 0.7607 (mtt) cc_final: 0.7350 (mtt) REVERT: P 20 MET cc_start: 0.7172 (ptm) cc_final: 0.6885 (ttp) REVERT: P 38 LYS cc_start: 0.7736 (tttp) cc_final: 0.7121 (ttmt) REVERT: R 79 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7155 (mttm) REVERT: R 82 ASN cc_start: 0.8303 (t0) cc_final: 0.7973 (t0) REVERT: S 85 ASP cc_start: 0.7229 (m-30) cc_final: 0.6480 (m-30) REVERT: S 163 MET cc_start: 0.7698 (mtt) cc_final: 0.7361 (mtt) REVERT: T 181 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: U 20 MET cc_start: 0.6760 (ptm) cc_final: 0.5793 (mtp) REVERT: U 27 MET cc_start: 0.7011 (mpp) cc_final: 0.6427 (mtp) REVERT: U 145 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8473 (mtpp) REVERT: V 79 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7866 (ttmt) REVERT: V 85 ASP cc_start: 0.7742 (m-30) cc_final: 0.7159 (t0) REVERT: W 79 LYS cc_start: 0.7730 (ttpp) cc_final: 0.7361 (mttt) REVERT: W 147 ASN cc_start: 0.8211 (t0) cc_final: 0.7995 (t0) REVERT: Y 163 MET cc_start: 0.7488 (mtt) cc_final: 0.7286 (mtt) REVERT: Z 20 MET cc_start: 0.7117 (ptm) cc_final: 0.6566 (ttm) REVERT: Z 38 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7688 (tmtt) REVERT: a 79 LYS cc_start: 0.7616 (ttpp) cc_final: 0.6981 (mttp) REVERT: a 172 SER cc_start: 0.8899 (t) cc_final: 0.8614 (m) REVERT: a 188 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7812 (mt) REVERT: b 135 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6051 (mp) REVERT: d 67 MET cc_start: 0.7826 (mtp) cc_final: 0.7515 (mtt) REVERT: e 79 LYS cc_start: 0.8051 (ttpp) cc_final: 0.7304 (mttt) REVERT: f 79 LYS cc_start: 0.7807 (ttpp) cc_final: 0.7347 (mttt) REVERT: g 27 MET cc_start: 0.9065 (mtp) cc_final: 0.8615 (mtp) REVERT: k 79 LYS cc_start: 0.7474 (ttpp) cc_final: 0.6821 (mttt) REVERT: k 177 MET cc_start: 0.8502 (tpp) cc_final: 0.8226 (mmt) REVERT: l 30 ASP cc_start: 0.7596 (m-30) cc_final: 0.7336 (m-30) REVERT: o 79 LYS cc_start: 0.7905 (ttpp) cc_final: 0.7396 (mttt) REVERT: o 85 ASP cc_start: 0.7635 (m-30) cc_final: 0.7249 (t0) REVERT: p 79 LYS cc_start: 0.7516 (ttpp) cc_final: 0.6958 (mttt) REVERT: s 30 ASP cc_start: 0.7149 (m-30) cc_final: 0.6899 (t0) REVERT: s 90 ASP cc_start: 0.6801 (m-30) cc_final: 0.6178 (p0) REVERT: t 67 MET cc_start: 0.8116 (mtp) cc_final: 0.7858 (mtt) REVERT: v 52 MET cc_start: 0.8225 (mtm) cc_final: 0.7890 (mtp) REVERT: v 66 ASP cc_start: 0.8044 (m-30) cc_final: 0.7778 (m-30) REVERT: v 172 SER cc_start: 0.8757 (t) cc_final: 0.8526 (m) REVERT: v 176 ASP cc_start: 0.8344 (m-30) cc_final: 0.8139 (m-30) REVERT: x 177 MET cc_start: 0.8393 (tpt) cc_final: 0.8189 (tpt) outliers start: 89 outliers final: 51 residues processed: 987 average time/residue: 0.5734 time to fit residues: 993.8602 Evaluate side-chains 890 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 833 time to evaluate : 5.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 68 ASN Chi-restraints excluded: chain I residue 188 ILE Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 181 GLN Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 150 THR Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain Z residue 38 LYS Chi-restraints excluded: chain Z residue 68 ASN Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain a residue 188 ILE Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain e residue 68 ASN Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain i residue 68 ASN Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain o residue 172 SER Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain q residue 48 MET Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain v residue 20 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 745 optimal weight: 4.9990 chunk 784 optimal weight: 2.9990 chunk 716 optimal weight: 3.9990 chunk 763 optimal weight: 6.9990 chunk 459 optimal weight: 10.0000 chunk 332 optimal weight: 0.0670 chunk 599 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 689 optimal weight: 6.9990 chunk 722 optimal weight: 5.9990 chunk 760 optimal weight: 0.9980 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN C 68 ASN C 78 GLN ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 ASN F 168 ASN G 43 GLN H 54 GLN H 162 GLN H 168 ASN ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 168 ASN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN M 68 ASN M 127 ASN P 78 GLN P 155 ASN P 162 GLN P 168 ASN Q 162 GLN Q 168 ASN R 78 GLN R 168 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 168 ASN T 43 GLN X 168 ASN ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 78 GLN Z 162 GLN b 68 ASN b 168 ASN f 181 GLN ** g 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 ASN ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 168 ASN ** j 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 168 ASN k 162 GLN l 154 ASN l 155 ASN o 54 GLN p 78 GLN r 168 ASN s 54 GLN s 168 ASN t 68 ASN t 168 ASN u 162 GLN u 168 ASN v 168 ASN w 168 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 66050 Z= 0.218 Angle : 0.554 9.337 89150 Z= 0.287 Chirality : 0.040 0.328 10700 Planarity : 0.003 0.053 11650 Dihedral : 4.927 24.256 9050 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.56 % Allowed : 17.41 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: 0.56 (0.09), residues: 8600 helix: 1.57 (0.07), residues: 6050 sheet: None (None), residues: 0 loop : -2.74 (0.10), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE i 49 TYR 0.016 0.001 TYR w 110 ARG 0.006 0.000 ARG v 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 799 time to evaluate : 5.541 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.6543 (m110) cc_final: 0.5845 (t0) REVERT: A 163 MET cc_start: 0.8063 (mtt) cc_final: 0.7666 (mtt) REVERT: A 175 SER cc_start: 0.8740 (t) cc_final: 0.8308 (p) REVERT: A 177 MET cc_start: 0.8207 (tpt) cc_final: 0.7970 (tpt) REVERT: A 188 ILE cc_start: 0.3284 (OUTLIER) cc_final: 0.3014 (mt) REVERT: B 38 LYS cc_start: 0.7928 (tttp) cc_final: 0.7668 (tttm) REVERT: B 85 ASP cc_start: 0.7548 (m-30) cc_final: 0.6836 (t0) REVERT: C 48 MET cc_start: 0.8024 (tmm) cc_final: 0.7531 (ttp) REVERT: D 22 TYR cc_start: 0.7536 (m-80) cc_final: 0.6900 (m-80) REVERT: E 135 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6143 (mp) REVERT: F 79 LYS cc_start: 0.7771 (ttpp) cc_final: 0.7008 (mttp) REVERT: G 20 MET cc_start: 0.6933 (ptt) cc_final: 0.6106 (ttp) REVERT: G 79 LYS cc_start: 0.7366 (ttpp) cc_final: 0.7022 (mttt) REVERT: H 38 LYS cc_start: 0.8126 (tttp) cc_final: 0.7733 (ttpt) REVERT: J 20 MET cc_start: 0.7934 (ttp) cc_final: 0.7622 (ttp) REVERT: J 172 SER cc_start: 0.8903 (t) cc_final: 0.8552 (m) REVERT: K 27 MET cc_start: 0.7202 (mtt) cc_final: 0.6832 (mtp) REVERT: M 85 ASP cc_start: 0.7960 (m-30) cc_final: 0.7079 (t0) REVERT: O 79 LYS cc_start: 0.7967 (ttpp) cc_final: 0.7599 (ttmm) REVERT: P 20 MET cc_start: 0.7241 (ptm) cc_final: 0.6889 (ttp) REVERT: P 38 LYS cc_start: 0.7983 (tttp) cc_final: 0.7210 (ttmt) REVERT: Q 169 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8326 (mp) REVERT: R 31 ASP cc_start: 0.7765 (t0) cc_final: 0.7527 (t0) REVERT: R 67 MET cc_start: 0.8155 (mtp) cc_final: 0.7904 (mtp) REVERT: R 79 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7226 (mttm) REVERT: R 82 ASN cc_start: 0.8262 (t0) cc_final: 0.7914 (t0) REVERT: S 163 MET cc_start: 0.7891 (mtt) cc_final: 0.7432 (mtt) REVERT: U 20 MET cc_start: 0.6945 (ptm) cc_final: 0.5829 (mtp) REVERT: V 79 LYS cc_start: 0.8240 (ttpp) cc_final: 0.7906 (ttmt) REVERT: V 85 ASP cc_start: 0.7784 (m-30) cc_final: 0.7191 (t0) REVERT: W 34 ASP cc_start: 0.7200 (t0) cc_final: 0.6682 (m-30) REVERT: W 79 LYS cc_start: 0.7769 (ttpp) cc_final: 0.7327 (mttt) REVERT: W 80 MET cc_start: 0.7795 (mmt) cc_final: 0.7375 (mmt) REVERT: X 177 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8599 (tpp) REVERT: Y 163 MET cc_start: 0.7718 (mtt) cc_final: 0.7400 (mtt) REVERT: Z 38 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7760 (tttt) REVERT: Z 135 LEU cc_start: 0.7111 (tp) cc_final: 0.6848 (mp) REVERT: Z 169 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.7940 (mp) REVERT: a 79 LYS cc_start: 0.7586 (ttpp) cc_final: 0.7156 (mttt) REVERT: a 82 ASN cc_start: 0.7262 (m-40) cc_final: 0.6963 (m110) REVERT: a 188 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7989 (mt) REVERT: b 135 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6047 (mp) REVERT: c 48 MET cc_start: 0.8021 (tmm) cc_final: 0.7481 (ttp) REVERT: d 67 MET cc_start: 0.8081 (mtp) cc_final: 0.7709 (mtm) REVERT: e 79 LYS cc_start: 0.8065 (ttpp) cc_final: 0.7340 (mttt) REVERT: f 79 LYS cc_start: 0.7687 (ttpp) cc_final: 0.7149 (mttt) REVERT: f 135 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6253 (mp) REVERT: f 188 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7981 (mp) REVERT: h 177 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8270 (mmt) REVERT: i 23 ASP cc_start: 0.7789 (p0) cc_final: 0.7486 (p0) REVERT: k 31 ASP cc_start: 0.8125 (m-30) cc_final: 0.7809 (m-30) REVERT: k 79 LYS cc_start: 0.7590 (ttpp) cc_final: 0.6921 (mttt) REVERT: k 172 SER cc_start: 0.8583 (t) cc_final: 0.8380 (m) REVERT: k 177 MET cc_start: 0.8417 (tpp) cc_final: 0.7986 (mmt) REVERT: n 80 MET cc_start: 0.6771 (mmp) cc_final: 0.6356 (mmt) REVERT: o 79 LYS cc_start: 0.7954 (ttpp) cc_final: 0.7430 (mttt) REVERT: o 85 ASP cc_start: 0.7716 (m-30) cc_final: 0.7354 (t0) REVERT: p 79 LYS cc_start: 0.7664 (ttpp) cc_final: 0.7034 (mttt) REVERT: r 30 ASP cc_start: 0.7670 (m-30) cc_final: 0.7373 (t0) REVERT: w 34 ASP cc_start: 0.6979 (m-30) cc_final: 0.6544 (m-30) REVERT: x 177 MET cc_start: 0.8437 (tpt) cc_final: 0.8213 (tpt) outliers start: 114 outliers final: 76 residues processed: 884 average time/residue: 0.5777 time to fit residues: 892.1876 Evaluate side-chains 870 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 783 time to evaluate : 5.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 68 ASN Chi-restraints excluded: chain I residue 188 ILE Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain U residue 48 MET Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain X residue 177 MET Chi-restraints excluded: chain Z residue 38 LYS Chi-restraints excluded: chain Z residue 169 LEU Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain a residue 80 MET Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 188 ILE Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 149 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain e residue 68 ASN Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain f residue 30 ASP Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 135 LEU Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain h residue 177 MET Chi-restraints excluded: chain i residue 59 LEU Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 118 ILE Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain o residue 172 SER Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain p residue 142 ILE Chi-restraints excluded: chain q residue 48 MET Chi-restraints excluded: chain q residue 67 MET Chi-restraints excluded: chain q residue 151 THR Chi-restraints excluded: chain s residue 23 ASP Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain u residue 23 ASP Chi-restraints excluded: chain v residue 20 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 501 optimal weight: 20.0000 chunk 807 optimal weight: 3.9990 chunk 492 optimal weight: 5.9990 chunk 382 optimal weight: 7.9990 chunk 561 optimal weight: 9.9990 chunk 846 optimal weight: 5.9990 chunk 779 optimal weight: 0.8980 chunk 674 optimal weight: 50.0000 chunk 70 optimal weight: 0.8980 chunk 520 optimal weight: 3.9990 chunk 413 optimal weight: 0.8980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN C 68 ASN ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN F 168 ASN H 54 GLN H 168 ASN ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 155 ASN I 168 ASN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN M 68 ASN N 162 GLN Q 168 ASN R 168 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 168 ASN X 168 ASN ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 ASN c 154 ASN f 181 GLN ** g 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 54 GLN ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 168 ASN ** j 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 168 ASN ** k 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 68 ASN r 54 GLN s 168 ASN t 68 ASN t 168 ASN v 82 ASN v 127 ASN v 168 ASN w 168 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 66050 Z= 0.187 Angle : 0.533 9.062 89150 Z= 0.278 Chirality : 0.039 0.332 10700 Planarity : 0.003 0.055 11650 Dihedral : 4.845 23.163 9050 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.48 % Allowed : 17.53 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: 0.61 (0.09), residues: 8600 helix: 1.61 (0.07), residues: 6050 sheet: None (None), residues: 0 loop : -2.70 (0.10), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE t 49 TYR 0.017 0.001 TYR w 110 ARG 0.005 0.000 ARG v 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 792 time to evaluate : 5.480 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8370 (tp) cc_final: 0.8164 (tp) REVERT: A 127 ASN cc_start: 0.6586 (m110) cc_final: 0.5991 (t0) REVERT: A 163 MET cc_start: 0.8085 (mtt) cc_final: 0.7702 (mtt) REVERT: A 175 SER cc_start: 0.8727 (t) cc_final: 0.8276 (p) REVERT: A 177 MET cc_start: 0.8195 (tpt) cc_final: 0.7944 (tpt) REVERT: A 188 ILE cc_start: 0.3290 (OUTLIER) cc_final: 0.3029 (mt) REVERT: B 34 ASP cc_start: 0.7167 (m-30) cc_final: 0.6692 (m-30) REVERT: B 38 LYS cc_start: 0.7899 (tttp) cc_final: 0.7658 (tttm) REVERT: B 85 ASP cc_start: 0.7538 (m-30) cc_final: 0.6821 (t0) REVERT: C 48 MET cc_start: 0.7981 (tmm) cc_final: 0.7617 (ttp) REVERT: D 22 TYR cc_start: 0.7530 (m-80) cc_final: 0.6979 (m-80) REVERT: E 135 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6200 (mp) REVERT: E 177 MET cc_start: 0.8257 (tpt) cc_final: 0.7858 (tpt) REVERT: F 79 LYS cc_start: 0.7794 (ttpp) cc_final: 0.7016 (mttp) REVERT: G 20 MET cc_start: 0.6897 (ptt) cc_final: 0.6034 (ttp) REVERT: G 79 LYS cc_start: 0.7373 (ttpp) cc_final: 0.7021 (mttt) REVERT: H 38 LYS cc_start: 0.8141 (tttp) cc_final: 0.7757 (ttpt) REVERT: J 20 MET cc_start: 0.7885 (ttp) cc_final: 0.7591 (ttp) REVERT: J 48 MET cc_start: 0.8166 (tmm) cc_final: 0.7782 (ttt) REVERT: J 172 SER cc_start: 0.8905 (t) cc_final: 0.8559 (m) REVERT: K 27 MET cc_start: 0.7188 (mtt) cc_final: 0.6834 (mtp) REVERT: M 85 ASP cc_start: 0.7937 (m-30) cc_final: 0.7059 (t0) REVERT: O 79 LYS cc_start: 0.7923 (ttpp) cc_final: 0.7571 (ttmm) REVERT: P 38 LYS cc_start: 0.8054 (tttp) cc_final: 0.7263 (ttmt) REVERT: R 67 MET cc_start: 0.8075 (mtp) cc_final: 0.7770 (mtp) REVERT: R 79 LYS cc_start: 0.8005 (ttpp) cc_final: 0.7215 (mttm) REVERT: R 82 ASN cc_start: 0.8257 (t0) cc_final: 0.7910 (t0) REVERT: S 85 ASP cc_start: 0.7297 (m-30) cc_final: 0.6443 (m-30) REVERT: S 163 MET cc_start: 0.7904 (mtt) cc_final: 0.7488 (mtt) REVERT: T 20 MET cc_start: 0.7502 (ttp) cc_final: 0.7272 (ptm) REVERT: U 20 MET cc_start: 0.6925 (ptm) cc_final: 0.5770 (mtp) REVERT: V 79 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7874 (ttmt) REVERT: V 85 ASP cc_start: 0.7746 (m-30) cc_final: 0.7146 (t0) REVERT: W 34 ASP cc_start: 0.7183 (t0) cc_final: 0.6659 (m-30) REVERT: W 79 LYS cc_start: 0.7756 (ttpp) cc_final: 0.7327 (mttt) REVERT: W 80 MET cc_start: 0.7789 (mmt) cc_final: 0.7382 (mmt) REVERT: Y 163 MET cc_start: 0.7659 (mtt) cc_final: 0.7374 (mtt) REVERT: Z 38 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7760 (tmtt) REVERT: Z 135 LEU cc_start: 0.7158 (tp) cc_final: 0.6922 (mp) REVERT: a 79 LYS cc_start: 0.7583 (ttpp) cc_final: 0.7145 (mttt) REVERT: a 82 ASN cc_start: 0.7273 (m-40) cc_final: 0.6960 (m110) REVERT: a 188 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7988 (mt) REVERT: b 135 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6070 (mp) REVERT: c 48 MET cc_start: 0.8038 (tmm) cc_final: 0.7555 (ttp) REVERT: d 67 MET cc_start: 0.8059 (mtp) cc_final: 0.7674 (mtm) REVERT: e 79 LYS cc_start: 0.8062 (ttpp) cc_final: 0.7332 (mttt) REVERT: f 79 LYS cc_start: 0.7716 (ttpp) cc_final: 0.7177 (mttt) REVERT: f 188 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7958 (mp) REVERT: h 67 MET cc_start: 0.7994 (mtp) cc_final: 0.7669 (mtp) REVERT: i 23 ASP cc_start: 0.7766 (p0) cc_final: 0.7526 (p0) REVERT: k 31 ASP cc_start: 0.8119 (m-30) cc_final: 0.7799 (m-30) REVERT: k 79 LYS cc_start: 0.7580 (ttpp) cc_final: 0.6910 (mttt) REVERT: k 177 MET cc_start: 0.8432 (tpp) cc_final: 0.8028 (mmt) REVERT: n 80 MET cc_start: 0.6774 (mmp) cc_final: 0.6370 (mmt) REVERT: o 79 LYS cc_start: 0.7968 (ttpp) cc_final: 0.7432 (mttt) REVERT: o 85 ASP cc_start: 0.7699 (m-30) cc_final: 0.7341 (t0) REVERT: p 79 LYS cc_start: 0.7622 (ttpp) cc_final: 0.6991 (mttt) REVERT: r 30 ASP cc_start: 0.7635 (m-30) cc_final: 0.7329 (t0) REVERT: t 79 LYS cc_start: 0.7409 (ttpp) cc_final: 0.6712 (mttt) REVERT: v 52 MET cc_start: 0.8204 (mtm) cc_final: 0.7887 (mtp) outliers start: 108 outliers final: 82 residues processed: 875 average time/residue: 0.5758 time to fit residues: 878.8504 Evaluate side-chains 866 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 778 time to evaluate : 5.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 68 ASN Chi-restraints excluded: chain I residue 188 ILE Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 181 GLN Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain U residue 48 MET Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 150 THR Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Z residue 38 LYS Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain a residue 80 MET Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 188 ILE Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain e residue 68 ASN Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 127 ASN Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain i residue 59 LEU Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 52 MET Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 118 ILE Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain o residue 172 SER Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain p residue 142 ILE Chi-restraints excluded: chain q residue 48 MET Chi-restraints excluded: chain q residue 67 MET Chi-restraints excluded: chain q residue 151 THR Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 23 ASP Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain t residue 23 ASP Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain v residue 20 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 535 optimal weight: 0.0370 chunk 718 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 621 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 675 optimal weight: 9.9990 chunk 282 optimal weight: 0.7980 chunk 693 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 overall best weight: 3.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN C 68 ASN ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN F 168 ASN H 168 ASN ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 168 ASN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN L 161 GLN M 68 ASN Q 168 ASN R 68 ASN R 168 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 168 ASN X 168 ASN ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 54 GLN ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 ASN g 127 ASN ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 168 ASN ** j 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 168 ASN s 168 ASN t 68 ASN t 168 ASN ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 168 ASN w 168 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.185742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.146403 restraints weight = 62584.925| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.22 r_work: 0.3006 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 66050 Z= 0.265 Angle : 0.586 8.874 89150 Z= 0.303 Chirality : 0.041 0.332 10700 Planarity : 0.003 0.055 11650 Dihedral : 5.066 24.800 9050 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.78 % Allowed : 17.15 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: 0.39 (0.09), residues: 8600 helix: 1.43 (0.07), residues: 6050 sheet: None (None), residues: 0 loop : -2.73 (0.10), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE t 49 TYR 0.017 0.001 TYR w 110 ARG 0.006 0.000 ARG v 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15728.31 seconds wall clock time: 277 minutes 28.20 seconds (16648.20 seconds total)