Starting phenix.real_space_refine on Thu Nov 20 09:43:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yi5_6830/11_2025/5yi5_6830.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yi5_6830/11_2025/5yi5_6830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5yi5_6830/11_2025/5yi5_6830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yi5_6830/11_2025/5yi5_6830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5yi5_6830/11_2025/5yi5_6830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yi5_6830/11_2025/5yi5_6830.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.021 sd= 0.084 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 168 5.16 5 C 21216 2.51 5 N 5928 2.21 5 O 6504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33816 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 7.65, per 1000 atoms: 0.23 Number of scatterers: 33816 At special positions: 0 Unit cell: (139.73, 138.333, 141.127, 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 168 16.00 O 6504 8.00 N 5928 7.00 C 21216 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 - 3.00 Amino acid : True - 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: 3.19 Conformation dependent library (CDL) restraints added in 1.4 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 62 " --> pdb=" O HIS A 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN A 110 " --> pdb=" O HIS A 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 62 " --> pdb=" O HIS B 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 110 " --> pdb=" O HIS B 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR B 138 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 173 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C 62 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN C 110 " --> pdb=" O HIS C 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR C 138 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS C 173 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 175 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU D 62 " --> pdb=" O HIS D 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 removed outlier: 3.587A pdb=" N CYS D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 173 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR D 175 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 36 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU E 62 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN E 110 " --> pdb=" O HIS E 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS E 125 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS E 173 " --> pdb=" O TYR E 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR E 175 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER F 37 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU F 62 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN F 76 " --> pdb=" O LYS F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS F 103 " --> pdb=" O ASN F 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN F 110 " --> pdb=" O HIS F 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS F 144 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU F 168 " --> pdb=" O SER F 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 173 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR F 175 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG G 23 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER G 37 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS G 54 " --> pdb=" O LYS G 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU G 62 " --> pdb=" O HIS G 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 125 removed outlier: 3.587A pdb=" N CYS G 103 " --> pdb=" O ASN G 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN G 110 " --> pdb=" O HIS G 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS G 125 " --> pdb=" O LEU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR G 138 " --> pdb=" O ILE G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS G 144 " --> pdb=" O ASN G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU G 168 " --> pdb=" O SER G 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS G 173 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR G 175 " --> pdb=" O PHE G 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG H 23 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU H 36 " --> pdb=" O SER H 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER H 37 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU H 62 " --> pdb=" O HIS H 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS H 103 " --> pdb=" O ASN H 99 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN H 110 " --> pdb=" O HIS H 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU H 117 " --> pdb=" O GLN H 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS H 125 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR H 138 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS H 144 " --> pdb=" O ASN H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU H 168 " --> pdb=" O SER H 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS H 173 " --> pdb=" O TYR H 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR H 175 " --> pdb=" O PHE H 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY H 177 " --> pdb=" O LYS H 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN I 22 " --> pdb=" O GLU I 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU I 36 " --> pdb=" O SER I 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER I 37 " --> pdb=" O TYR I 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS I 54 " --> pdb=" O LYS I 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU I 62 " --> pdb=" O HIS I 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN I 76 " --> pdb=" O LYS I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 125 removed outlier: 3.587A pdb=" N CYS I 103 " --> pdb=" O ASN I 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN I 110 " --> pdb=" O HIS I 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU I 117 " --> pdb=" O GLN I 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS I 125 " --> pdb=" O LEU I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR I 138 " --> pdb=" O ILE I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL I 143 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS I 144 " --> pdb=" O ASN I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU I 168 " --> pdb=" O SER I 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS I 173 " --> pdb=" O TYR I 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR I 175 " --> pdb=" O PHE I 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY I 177 " --> pdb=" O LYS I 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN J 22 " --> pdb=" O GLU J 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG J 23 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 36 " --> pdb=" O SER J 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER J 37 " --> pdb=" O TYR J 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS J 54 " --> pdb=" O LYS J 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS J 61 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU J 62 " --> pdb=" O HIS J 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN J 76 " --> pdb=" O LYS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS J 103 " --> pdb=" O ASN J 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN J 110 " --> pdb=" O HIS J 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS J 125 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR J 138 " --> pdb=" O ILE J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS J 144 " --> pdb=" O ASN J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU J 168 " --> pdb=" O SER J 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS J 173 " --> pdb=" O TYR J 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR J 175 " --> pdb=" O PHE J 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY J 177 " --> pdb=" O LYS J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG K 23 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU K 36 " --> pdb=" O SER K 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER K 37 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS K 54 " --> pdb=" O LYS K 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU K 62 " --> pdb=" O HIS K 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET K 71 " --> pdb=" O ALA K 67 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN K 76 " --> pdb=" O LYS K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS K 103 " --> pdb=" O ASN K 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN K 110 " --> pdb=" O HIS K 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU K 117 " --> pdb=" O GLN K 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR K 138 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL K 143 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS K 144 " --> pdb=" O ASN K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU K 168 " --> pdb=" O SER K 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS K 173 " --> pdb=" O TYR K 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR K 175 " --> pdb=" O PHE K 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY K 177 " --> pdb=" O LYS K 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN L 22 " --> pdb=" O GLU L 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG L 23 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU L 36 " --> pdb=" O SER L 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER L 37 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS L 54 " --> pdb=" O LYS L 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU L 62 " --> pdb=" O HIS L 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN L 76 " --> pdb=" O LYS L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 125 removed outlier: 3.587A pdb=" N CYS L 103 " --> pdb=" O ASN L 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN L 110 " --> pdb=" O HIS L 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU L 117 " --> pdb=" O GLN L 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS L 125 " --> pdb=" O LEU L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR L 138 " --> pdb=" O ILE L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS L 144 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU L 168 " --> pdb=" O SER L 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS L 173 " --> pdb=" O TYR L 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR L 175 " --> pdb=" O PHE L 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY L 177 " --> pdb=" O LYS L 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN M 22 " --> pdb=" O GLU M 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU M 36 " --> pdb=" O SER M 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER M 37 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS M 54 " --> pdb=" O LYS M 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU M 62 " --> pdb=" O HIS M 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN M 76 " --> pdb=" O LYS M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS M 103 " --> pdb=" O ASN M 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN M 110 " --> pdb=" O HIS M 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU M 117 " --> pdb=" O GLN M 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS M 125 " --> pdb=" O LEU M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR M 138 " --> pdb=" O ILE M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL M 143 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS M 144 " --> pdb=" O ASN M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU M 168 " --> pdb=" O SER M 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS M 173 " --> pdb=" O TYR M 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR M 175 " --> pdb=" O PHE M 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY M 177 " --> pdb=" O LYS M 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU N 36 " --> pdb=" O SER N 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER N 37 " --> pdb=" O TYR N 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS N 54 " --> pdb=" O LYS N 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU N 62 " --> pdb=" O HIS N 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET N 71 " --> pdb=" O ALA N 67 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN N 76 " --> pdb=" O LYS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS N 103 " --> pdb=" O ASN N 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN N 110 " --> pdb=" O HIS N 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU N 117 " --> pdb=" O GLN N 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS N 125 " --> pdb=" O LEU N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR N 138 " --> pdb=" O ILE N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL N 143 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS N 144 " --> pdb=" O ASN N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU N 168 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS N 173 " --> pdb=" O TYR N 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR N 175 " --> pdb=" O PHE N 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY N 177 " --> pdb=" O LYS N 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN O 22 " --> pdb=" O GLU O 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG O 23 " --> pdb=" O ALA O 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU O 36 " --> pdb=" O SER O 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER O 37 " --> pdb=" O TYR O 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA O 53 " --> pdb=" O LEU O 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS O 54 " --> pdb=" O LYS O 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU O 62 " --> pdb=" O HIS O 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN O 76 " --> pdb=" O LYS O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 125 removed outlier: 3.587A pdb=" N CYS O 103 " --> pdb=" O ASN O 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN O 110 " --> pdb=" O HIS O 106 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS O 125 " --> pdb=" O LEU O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR O 138 " --> pdb=" O ILE O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL O 143 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS O 144 " --> pdb=" O ASN O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS O 173 " --> pdb=" O TYR O 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR O 175 " --> pdb=" O PHE O 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY O 177 " --> pdb=" O LYS O 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN P 22 " --> pdb=" O GLU P 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG P 23 " --> pdb=" O ALA P 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU P 36 " --> pdb=" O SER P 32 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER P 37 " --> pdb=" O TYR P 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS P 54 " --> pdb=" O LYS P 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU P 62 " --> pdb=" O HIS P 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET P 71 " --> pdb=" O ALA P 67 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN P 76 " --> pdb=" O LYS P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS P 103 " --> pdb=" O ASN P 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN P 110 " --> pdb=" O HIS P 106 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS P 125 " --> pdb=" O LEU P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR P 138 " --> pdb=" O ILE P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL P 143 " --> pdb=" O LEU P 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS P 144 " --> pdb=" O ASN P 140 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU P 168 " --> pdb=" O SER P 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS P 173 " --> pdb=" O TYR P 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR P 175 " --> pdb=" O PHE P 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY P 177 " --> pdb=" O LYS P 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN Q 22 " --> pdb=" O GLU Q 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG Q 23 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU Q 36 " --> pdb=" O SER Q 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER Q 37 " --> pdb=" O TYR Q 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU Q 62 " --> pdb=" O HIS Q 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN Q 76 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS Q 103 " --> pdb=" O ASN Q 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN Q 110 " --> pdb=" O HIS Q 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS Q 125 " --> pdb=" O LEU Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR Q 138 " --> pdb=" O ILE Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS Q 144 " --> pdb=" O ASN Q 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS Q 173 " --> pdb=" O TYR Q 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR Q 175 " --> pdb=" O PHE Q 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY Q 177 " --> pdb=" O LYS Q 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG R 23 " --> pdb=" O ALA R 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU R 36 " --> pdb=" O SER R 32 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER R 37 " --> pdb=" O TYR R 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS R 54 " --> pdb=" O LYS R 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU R 62 " --> pdb=" O HIS R 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET R 71 " --> pdb=" O ALA R 67 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN R 76 " --> pdb=" O LYS R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS R 103 " --> pdb=" O ASN R 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN R 110 " --> pdb=" O HIS R 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU R 117 " --> pdb=" O GLN R 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS R 125 " --> pdb=" O LEU R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR R 138 " --> pdb=" O ILE R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL R 143 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS R 144 " --> pdb=" O ASN R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU R 168 " --> pdb=" O SER R 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS R 173 " --> pdb=" O TYR R 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR R 175 " --> pdb=" O PHE R 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY R 177 " --> pdb=" O LYS R 173 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN S 22 " --> pdb=" O GLU S 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG S 23 " --> pdb=" O ALA S 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU S 36 " --> pdb=" O SER S 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER S 37 " --> pdb=" O TYR S 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA S 53 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS S 54 " --> pdb=" O LYS S 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU S 62 " --> pdb=" O HIS S 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN S 76 " --> pdb=" O LYS S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS S 103 " --> pdb=" O ASN S 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN S 110 " --> pdb=" O HIS S 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU S 117 " --> pdb=" O GLN S 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS S 125 " --> pdb=" O LEU S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR S 138 " --> pdb=" O ILE S 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL S 143 " --> pdb=" O LEU S 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS S 144 " --> pdb=" O ASN S 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU S 168 " --> pdb=" O SER S 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS S 173 " --> pdb=" O TYR S 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR S 175 " --> pdb=" O PHE S 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY S 177 " --> pdb=" O LYS S 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG T 23 " --> pdb=" O ALA T 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU T 36 " --> pdb=" O SER T 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER T 37 " --> pdb=" O TYR T 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR T 40 " --> pdb=" O LEU T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA T 53 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS T 61 " --> pdb=" O LEU T 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU T 62 " --> pdb=" O HIS T 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET T 71 " --> pdb=" O ALA T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS T 103 " --> pdb=" O ASN T 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN T 110 " --> pdb=" O HIS T 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU T 117 " --> pdb=" O GLN T 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS T 125 " --> pdb=" O LEU T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR T 138 " --> pdb=" O ILE T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 138 through 160 removed outlier: 3.553A pdb=" N VAL T 143 " --> pdb=" O LEU T 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS T 144 " --> pdb=" O ASN T 140 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU T 168 " --> pdb=" O SER T 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS T 173 " --> pdb=" O TYR T 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR T 175 " --> pdb=" O PHE T 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY T 177 " --> pdb=" O LYS T 173 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN U 22 " --> pdb=" O GLU U 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG U 23 " --> pdb=" O ALA U 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU U 36 " --> pdb=" O SER U 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER U 37 " --> pdb=" O TYR U 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA U 53 " --> pdb=" O LEU U 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS U 54 " --> pdb=" O LYS U 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS U 61 " --> pdb=" O LEU U 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU U 62 " --> pdb=" O HIS U 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET U 71 " --> pdb=" O ALA U 67 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN U 76 " --> pdb=" O LYS U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS U 103 " --> pdb=" O ASN U 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN U 110 " --> pdb=" O HIS U 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU U 117 " --> pdb=" O GLN U 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS U 125 " --> pdb=" O LEU U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR U 138 " --> pdb=" O ILE U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL U 143 " --> pdb=" O LEU U 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS U 144 " --> pdb=" O ASN U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU U 168 " --> pdb=" O SER U 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS U 173 " --> pdb=" O TYR U 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR U 175 " --> pdb=" O PHE U 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY U 177 " --> pdb=" O LYS U 173 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN V 22 " --> pdb=" O GLU V 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG V 23 " --> pdb=" O ALA V 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU V 36 " --> pdb=" O SER V 32 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER V 37 " --> pdb=" O TYR V 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR V 40 " --> pdb=" O LEU V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA V 53 " --> pdb=" O LEU V 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS V 54 " --> pdb=" O LYS V 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS V 61 " --> pdb=" O LEU V 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU V 62 " --> pdb=" O HIS V 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET V 71 " --> pdb=" O ALA V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS V 103 " --> pdb=" O ASN V 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN V 110 " --> pdb=" O HIS V 106 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU V 117 " --> pdb=" O GLN V 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS V 125 " --> pdb=" O LEU V 121 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR V 138 " --> pdb=" O ILE V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL V 143 " --> pdb=" O LEU V 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS V 144 " --> pdb=" O ASN V 140 " (cutoff:3.500A) Processing helix chain 'V' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU V 168 " --> pdb=" O SER V 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS V 173 " --> pdb=" O TYR V 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR V 175 " --> pdb=" O PHE V 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY V 177 " --> pdb=" O LYS V 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN W 22 " --> pdb=" O GLU W 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG W 23 " --> pdb=" O ALA W 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU W 36 " --> pdb=" O SER W 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER W 37 " --> pdb=" O TYR W 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR W 40 " --> pdb=" O LEU W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA W 53 " --> pdb=" O LEU W 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS W 54 " --> pdb=" O LYS W 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS W 61 " --> pdb=" O LEU W 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU W 62 " --> pdb=" O HIS W 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET W 71 " --> pdb=" O ALA W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 125 removed outlier: 3.587A pdb=" N CYS W 103 " --> pdb=" O ASN W 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN W 110 " --> pdb=" O HIS W 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU W 117 " --> pdb=" O GLN W 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS W 125 " --> pdb=" O LEU W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR W 138 " --> pdb=" O ILE W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS W 144 " --> pdb=" O ASN W 140 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS W 173 " --> pdb=" O TYR W 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR W 175 " --> pdb=" O PHE W 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY W 177 " --> pdb=" O LYS W 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN X 22 " --> pdb=" O GLU X 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG X 23 " --> pdb=" O ALA X 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU X 36 " --> pdb=" O SER X 32 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER X 37 " --> pdb=" O TYR X 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR X 40 " --> pdb=" O LEU X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA X 53 " --> pdb=" O LEU X 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS X 54 " --> pdb=" O LYS X 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS X 61 " --> pdb=" O LEU X 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU X 62 " --> pdb=" O HIS X 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET X 71 " --> pdb=" O ALA X 67 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN X 76 " --> pdb=" O LYS X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS X 103 " --> pdb=" O ASN X 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN X 110 " --> pdb=" O HIS X 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU X 117 " --> pdb=" O GLN X 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS X 125 " --> pdb=" O LEU X 121 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR X 138 " --> pdb=" O ILE X 134 " (cutoff:3.500A) Processing helix chain 'X' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL X 143 " --> pdb=" O LEU X 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS X 144 " --> pdb=" O ASN X 140 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU X 168 " --> pdb=" O SER X 164 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS X 173 " --> pdb=" O TYR X 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR X 175 " --> pdb=" O PHE X 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY X 177 " --> pdb=" O LYS X 173 " (cutoff:3.500A) 2139 hydrogen bonds defined for protein. 6417 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: 5.64 Time building geometry restraints manager: 4.27 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: 11500 1.34 - 1.46: 6203 1.46 - 1.57: 16545 1.57 - 1.69: 0 1.69 - 1.80: 264 Bond restraints: 34512 Sorted by residual: bond pdb=" CG TYR H 40 " pdb=" CD2 TYR H 40 " ideal model delta sigma weight residual 1.389 1.362 0.027 2.10e-02 2.27e+03 1.63e+00 bond pdb=" CG TYR E 40 " pdb=" CD2 TYR E 40 " ideal model delta sigma weight residual 1.389 1.363 0.026 2.10e-02 2.27e+03 1.48e+00 bond pdb=" CG TYR B 40 " pdb=" CD2 TYR B 40 " ideal model delta sigma weight residual 1.389 1.364 0.025 2.10e-02 2.27e+03 1.41e+00 bond pdb=" CG TYR W 40 " pdb=" CD2 TYR W 40 " ideal model delta sigma weight residual 1.389 1.364 0.025 2.10e-02 2.27e+03 1.39e+00 bond pdb=" CG TYR O 40 " pdb=" CD2 TYR O 40 " ideal model delta sigma weight residual 1.389 1.364 0.025 2.10e-02 2.27e+03 1.38e+00 ... (remaining 34507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 44279 1.38 - 2.77: 1732 2.77 - 4.15: 381 4.15 - 5.53: 72 5.53 - 6.91: 24 Bond angle restraints: 46488 Sorted by residual: angle pdb=" N GLU P 95 " pdb=" CA GLU P 95 " pdb=" C GLU P 95 " ideal model delta sigma weight residual 110.80 115.71 -4.91 2.13e+00 2.20e-01 5.31e+00 angle pdb=" N GLU C 95 " pdb=" CA GLU C 95 " pdb=" C GLU C 95 " ideal model delta sigma weight residual 110.80 115.70 -4.90 2.13e+00 2.20e-01 5.29e+00 angle pdb=" N GLU M 95 " pdb=" CA GLU M 95 " pdb=" C GLU M 95 " ideal model delta sigma weight residual 110.80 115.70 -4.90 2.13e+00 2.20e-01 5.29e+00 angle pdb=" N GLU Q 95 " pdb=" CA GLU Q 95 " pdb=" C GLU Q 95 " ideal model delta sigma weight residual 110.80 115.69 -4.89 2.13e+00 2.20e-01 5.26e+00 angle pdb=" N GLU I 95 " pdb=" CA GLU I 95 " pdb=" C GLU I 95 " ideal model delta sigma weight residual 110.80 115.69 -4.89 2.13e+00 2.20e-01 5.26e+00 ... (remaining 46483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 20310 15.77 - 31.54: 282 31.54 - 47.31: 144 47.31 - 63.08: 24 63.08 - 78.85: 96 Dihedral angle restraints: 20856 sinusoidal: 8616 harmonic: 12240 Sorted by residual: dihedral pdb=" CA TRP B 94 " pdb=" C TRP B 94 " pdb=" N GLU B 95 " pdb=" CA GLU B 95 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA TRP K 94 " pdb=" C TRP K 94 " pdb=" N GLU K 95 " pdb=" CA GLU K 95 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA TRP N 94 " pdb=" C TRP N 94 " pdb=" N GLU N 95 " pdb=" CA GLU N 95 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 20853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1671 0.024 - 0.047: 1795 0.047 - 0.071: 1077 0.071 - 0.094: 230 0.094 - 0.118: 123 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA HIS H 174 " pdb=" N HIS H 174 " pdb=" C HIS H 174 " pdb=" CB HIS H 174 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA HIS W 174 " pdb=" N HIS W 174 " pdb=" C HIS W 174 " pdb=" CB HIS W 174 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.46e-01 chirality pdb=" CA HIS C 174 " pdb=" N HIS C 174 " pdb=" C HIS C 174 " pdb=" CB HIS C 174 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 4893 not shown) Planarity restraints: 6120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE X 82 " -0.050 2.00e-02 2.50e+03 4.46e-02 3.48e+01 pdb=" CG PHE X 82 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 PHE X 82 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE X 82 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE X 82 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE X 82 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHE X 82 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 82 " 0.051 2.00e-02 2.50e+03 4.40e-02 3.38e+01 pdb=" CG PHE J 82 " -0.101 2.00e-02 2.50e+03 pdb=" CD1 PHE J 82 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE J 82 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE J 82 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE J 82 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE J 82 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 82 " 0.048 2.00e-02 2.50e+03 4.26e-02 3.18e+01 pdb=" CG PHE L 82 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 PHE L 82 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE L 82 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE L 82 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE L 82 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE L 82 " -0.002 2.00e-02 2.50e+03 ... (remaining 6117 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 10985 2.83 - 3.35: 34886 3.35 - 3.87: 52450 3.87 - 4.38: 61299 4.38 - 4.90: 101032 Nonbonded interactions: 260652 Sorted by model distance: nonbonded pdb=" OD1 ASP J 85 " pdb=" N LYS V 88 " model vdw 2.314 3.120 nonbonded pdb=" O GLY B 79 " pdb=" NH1 ARG B 80 " model vdw 2.326 3.120 nonbonded pdb=" O GLY K 79 " pdb=" NH1 ARG K 80 " model vdw 2.326 3.120 nonbonded pdb=" O GLY D 79 " pdb=" NH1 ARG D 80 " model vdw 2.327 3.120 nonbonded pdb=" O GLY S 79 " pdb=" NH1 ARG S 80 " model vdw 2.327 3.120 ... (remaining 260647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.760 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.007 0.033 34512 Z= 0.321 Angle : 0.682 6.913 46488 Z= 0.364 Chirality : 0.043 0.118 4896 Planarity : 0.004 0.045 6120 Dihedral : 10.513 78.853 12936 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.10), residues: 4080 helix: -2.91 (0.06), residues: 3000 sheet: None (None), residues: 0 loop : -1.03 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 44 TYR 0.013 0.002 TYR G 40 PHE 0.103 0.005 PHE X 82 TRP 0.012 0.003 TRP A 94 HIS 0.004 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00699 (34512) covalent geometry : angle 0.68180 (46488) hydrogen bonds : bond 0.28737 ( 2139) hydrogen bonds : angle 10.07813 ( 6417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1845 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1845 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7608 (m-30) cc_final: 0.7273 (t0) REVERT: A 64 ARG cc_start: 0.8482 (ttt90) cc_final: 0.8097 (ttp-170) REVERT: B 45 ASP cc_start: 0.8239 (p0) cc_final: 0.7889 (t0) REVERT: B 95 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7503 (tt0) REVERT: C 18 GLU cc_start: 0.8447 (tt0) cc_final: 0.7615 (tm-30) REVERT: C 68 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8535 (tm-30) REVERT: C 86 ILE cc_start: 0.9135 (mt) cc_final: 0.8329 (tt) REVERT: C 90 ASP cc_start: 0.8185 (m-30) cc_final: 0.7916 (p0) REVERT: C 127 ASP cc_start: 0.8155 (t0) cc_final: 0.7844 (t0) REVERT: C 173 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8242 (tptp) REVERT: D 16 ASP cc_start: 0.7696 (m-30) cc_final: 0.7433 (t0) REVERT: D 43 ASP cc_start: 0.9099 (t70) cc_final: 0.8896 (t0) REVERT: D 46 ASP cc_start: 0.9126 (p0) cc_final: 0.8818 (m-30) REVERT: D 86 ILE cc_start: 0.7937 (mt) cc_final: 0.7553 (pt) REVERT: D 87 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7672 (mttt) REVERT: D 127 ASP cc_start: 0.7181 (t0) cc_final: 0.6324 (p0) REVERT: D 154 THR cc_start: 0.8984 (m) cc_final: 0.8725 (p) REVERT: E 14 HIS cc_start: 0.6776 (t-90) cc_final: 0.6536 (t70) REVERT: E 16 ASP cc_start: 0.8609 (m-30) cc_final: 0.8269 (t0) REVERT: E 18 GLU cc_start: 0.9193 (tt0) cc_final: 0.8816 (pt0) REVERT: E 24 GLN cc_start: 0.8748 (tp40) cc_final: 0.8512 (tm-30) REVERT: E 45 ASP cc_start: 0.7452 (p0) cc_final: 0.7047 (t70) REVERT: E 175 THR cc_start: 0.8179 (m) cc_final: 0.7808 (p) REVERT: F 85 ASP cc_start: 0.8115 (m-30) cc_final: 0.7888 (m-30) REVERT: F 86 ILE cc_start: 0.7985 (mt) cc_final: 0.7525 (tp) REVERT: F 90 ASP cc_start: 0.8364 (m-30) cc_final: 0.8014 (p0) REVERT: F 99 ASN cc_start: 0.9014 (t0) cc_final: 0.8789 (t0) REVERT: F 101 MET cc_start: 0.9098 (mmt) cc_final: 0.8897 (mmt) REVERT: F 117 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8204 (tp30) REVERT: F 127 ASP cc_start: 0.7823 (t0) cc_final: 0.7544 (t0) REVERT: G 45 ASP cc_start: 0.7428 (p0) cc_final: 0.7177 (t0) REVERT: G 85 ASP cc_start: 0.8152 (m-30) cc_final: 0.6900 (p0) REVERT: G 86 ILE cc_start: 0.8648 (mt) cc_final: 0.8404 (mp) REVERT: G 109 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8850 (mtpt) REVERT: G 123 THR cc_start: 0.8501 (m) cc_final: 0.8178 (p) REVERT: H 46 ASP cc_start: 0.8121 (p0) cc_final: 0.7726 (t0) REVERT: H 86 ILE cc_start: 0.8154 (mt) cc_final: 0.7860 (tp) REVERT: H 93 ASP cc_start: 0.8621 (t0) cc_final: 0.8394 (p0) REVERT: H 95 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8072 (tm-30) REVERT: H 127 ASP cc_start: 0.8477 (t0) cc_final: 0.8127 (t0) REVERT: I 18 GLU cc_start: 0.8607 (tt0) cc_final: 0.8316 (tm-30) REVERT: I 90 ASP cc_start: 0.8278 (m-30) cc_final: 0.7767 (p0) REVERT: I 95 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8223 (tm-30) REVERT: I 127 ASP cc_start: 0.8607 (t0) cc_final: 0.8291 (OUTLIER) REVERT: I 159 MET cc_start: 0.7905 (mtp) cc_final: 0.6843 (ttm) REVERT: I 175 THR cc_start: 0.7636 (m) cc_final: 0.7170 (p) REVERT: J 24 GLN cc_start: 0.9072 (tp40) cc_final: 0.8754 (tm-30) REVERT: J 64 ARG cc_start: 0.8306 (ttt90) cc_final: 0.7980 (ttp-170) REVERT: J 102 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7637 (tm-30) REVERT: J 113 GLN cc_start: 0.8569 (tp-100) cc_final: 0.8283 (tm-30) REVERT: K 12 ASN cc_start: 0.8727 (t0) cc_final: 0.8424 (t0) REVERT: K 68 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8417 (tm-30) REVERT: K 76 GLN cc_start: 0.9371 (mt0) cc_final: 0.9111 (mp10) REVERT: K 115 LEU cc_start: 0.7998 (mt) cc_final: 0.7696 (tm) REVERT: K 117 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7826 (pp20) REVERT: K 126 ASN cc_start: 0.7672 (m-40) cc_final: 0.7245 (p0) REVERT: K 168 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8804 (mt-10) REVERT: L 23 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.7125 (tpp80) REVERT: L 84 GLN cc_start: 0.7769 (mm110) cc_final: 0.7501 (mm-40) REVERT: L 90 ASP cc_start: 0.7974 (m-30) cc_final: 0.7626 (p0) REVERT: L 91 CYS cc_start: 0.7657 (m) cc_final: 0.7325 (t) REVERT: L 92 ASP cc_start: 0.8777 (m-30) cc_final: 0.8525 (t0) REVERT: L 102 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7930 (pp20) REVERT: M 68 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8878 (tp30) REVERT: M 108 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7927 (tm-30) REVERT: N 12 ASN cc_start: 0.8767 (t0) cc_final: 0.8198 (t0) REVERT: N 14 HIS cc_start: 0.6405 (t-90) cc_final: 0.6189 (t-90) REVERT: N 45 ASP cc_start: 0.8263 (p0) cc_final: 0.7459 (t70) REVERT: N 62 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7437 (tm-30) REVERT: N 82 PHE cc_start: 0.8132 (m-80) cc_final: 0.7871 (m-80) REVERT: N 84 GLN cc_start: 0.8327 (mm110) cc_final: 0.8015 (mm-40) REVERT: N 92 ASP cc_start: 0.6276 (m-30) cc_final: 0.6016 (m-30) REVERT: P 22 ASN cc_start: 0.8766 (m-40) cc_final: 0.8561 (m110) REVERT: P 45 ASP cc_start: 0.8064 (p0) cc_final: 0.7543 (t70) REVERT: P 68 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8644 (mt-10) REVERT: P 87 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7801 (ttpt) REVERT: Q 18 GLU cc_start: 0.8903 (tt0) cc_final: 0.8650 (tp30) REVERT: Q 34 VAL cc_start: 0.7859 (t) cc_final: 0.7370 (t) REVERT: Q 55 TYR cc_start: 0.8380 (t80) cc_final: 0.8178 (t80) REVERT: Q 85 ASP cc_start: 0.8905 (m-30) cc_final: 0.8443 (p0) REVERT: Q 88 LYS cc_start: 0.8381 (pttp) cc_final: 0.8122 (ptpp) REVERT: Q 95 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7426 (tp30) REVERT: Q 138 TYR cc_start: 0.8240 (m-80) cc_final: 0.8008 (m-80) REVERT: Q 140 ASN cc_start: 0.8873 (t0) cc_final: 0.8660 (t0) REVERT: Q 158 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8979 (ttmm) REVERT: R 11 GLN cc_start: 0.8121 (tt0) cc_final: 0.7481 (tm130) REVERT: R 64 ARG cc_start: 0.8033 (ttt90) cc_final: 0.7754 (ttt90) REVERT: R 85 ASP cc_start: 0.7662 (m-30) cc_final: 0.7350 (m-30) REVERT: R 92 ASP cc_start: 0.8030 (m-30) cc_final: 0.7659 (p0) REVERT: R 138 TYR cc_start: 0.8406 (m-80) cc_final: 0.8189 (m-80) REVERT: R 169 TYR cc_start: 0.8460 (t80) cc_final: 0.8083 (t80) REVERT: S 55 TYR cc_start: 0.8571 (t80) cc_final: 0.7573 (t80) REVERT: S 58 HIS cc_start: 0.7535 (t70) cc_final: 0.7276 (t70) REVERT: S 68 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8792 (mt-10) REVERT: S 87 LYS cc_start: 0.7124 (mmtt) cc_final: 0.6436 (pttp) REVERT: S 88 LYS cc_start: 0.8007 (pttp) cc_final: 0.7784 (pttm) REVERT: T 11 GLN cc_start: 0.8555 (tt0) cc_final: 0.8331 (tt0) REVERT: T 12 ASN cc_start: 0.7875 (t0) cc_final: 0.7649 (t0) REVERT: T 92 ASP cc_start: 0.7554 (m-30) cc_final: 0.6961 (p0) REVERT: T 102 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8718 (tm-30) REVERT: U 14 HIS cc_start: 0.7827 (t-90) cc_final: 0.7592 (t-90) REVERT: U 18 GLU cc_start: 0.8199 (tt0) cc_final: 0.7953 (tm-30) REVERT: U 47 VAL cc_start: 0.8096 (t) cc_final: 0.7815 (m) REVERT: U 54 LYS cc_start: 0.8570 (mttt) cc_final: 0.8328 (mtmp) REVERT: U 85 ASP cc_start: 0.8475 (m-30) cc_final: 0.8167 (m-30) REVERT: V 18 GLU cc_start: 0.8791 (tt0) cc_final: 0.8565 (tp30) REVERT: V 24 GLN cc_start: 0.8965 (tp40) cc_final: 0.8693 (tp40) REVERT: V 72 LYS cc_start: 0.8330 (tttt) cc_final: 0.7965 (ttpp) REVERT: V 80 ARG cc_start: 0.7001 (mmt-90) cc_final: 0.6610 (mpt-90) REVERT: V 88 LYS cc_start: 0.8839 (pttp) cc_final: 0.8285 (pmtt) REVERT: V 117 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8125 (mp0) REVERT: V 164 SER cc_start: 0.7087 (t) cc_final: 0.6254 (m) REVERT: W 68 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8774 (tt0) REVERT: W 90 ASP cc_start: 0.8141 (m-30) cc_final: 0.7391 (t0) REVERT: W 92 ASP cc_start: 0.6660 (m-30) cc_final: 0.6307 (p0) REVERT: W 99 ASN cc_start: 0.8941 (t0) cc_final: 0.8720 (t0) REVERT: X 13 TYR cc_start: 0.6374 (t80) cc_final: 0.6021 (t80) REVERT: X 80 ARG cc_start: 0.7662 (mmt-90) cc_final: 0.7088 (pmm150) REVERT: X 85 ASP cc_start: 0.7885 (m-30) cc_final: 0.7139 (p0) REVERT: X 94 TRP cc_start: 0.7928 (m100) cc_final: 0.7629 (m100) REVERT: X 95 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7737 (tm-30) outliers start: 0 outliers final: 9 residues processed: 1845 average time/residue: 0.8018 time to fit residues: 1727.4926 Evaluate side-chains 691 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 683 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain K residue 155 ASN Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain V residue 41 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN A 106 HIS A 140 ASN A 152 HIS ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 HIS B 26 ASN B 51 ASN C 12 ASN C 22 ASN C 126 ASN C 140 ASN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN E 61 HIS E 126 ASN F 22 ASN F 66 HIS ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 66 HIS G 113 GLN G 126 ASN H 12 ASN H 22 ASN H 24 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 ASN I 51 ASN I 140 ASN J 126 ASN J 137 HIS J 155 ASN K 22 ASN K 51 ASN K 59 GLN K 137 HIS K 155 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 GLN M 137 HIS ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN N 24 GLN O 22 ASN O 26 ASN O 99 ASN O 155 ASN P 113 GLN P 126 ASN Q 99 ASN R 12 ASN R 14 HIS R 26 ASN R 61 HIS R 155 ASN ** R 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 GLN ** S 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 GLN U 61 HIS U 119 HIS V 59 GLN W 22 ASN W 119 HIS ** W 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 ASN X 126 ASN ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.125086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.111546 restraints weight = 70436.091| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.22 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34512 Z= 0.191 Angle : 0.706 8.413 46488 Z= 0.371 Chirality : 0.041 0.189 4896 Planarity : 0.004 0.050 6120 Dihedral : 4.762 55.558 4504 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 6.80 % Allowed : 21.41 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.12), residues: 4080 helix: 0.74 (0.08), residues: 3144 sheet: None (None), residues: 0 loop : -0.83 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 80 TYR 0.025 0.002 TYR R 138 PHE 0.016 0.001 PHE R 171 TRP 0.019 0.002 TRP K 94 HIS 0.011 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00399 (34512) covalent geometry : angle 0.70618 (46488) hydrogen bonds : bond 0.07231 ( 2139) hydrogen bonds : angle 5.05350 ( 6417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 939 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: A 22 ASN cc_start: 0.8082 (m-40) cc_final: 0.7871 (m-40) REVERT: A 64 ARG cc_start: 0.7940 (ttt90) cc_final: 0.7684 (ttp-170) REVERT: A 154 THR cc_start: 0.8626 (m) cc_final: 0.8381 (t) REVERT: A 164 SER cc_start: 0.7188 (t) cc_final: 0.6740 (p) REVERT: B 24 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7709 (tm-30) REVERT: B 58 HIS cc_start: 0.7192 (t70) cc_final: 0.6801 (t70) REVERT: B 141 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8511 (mt-10) REVERT: C 13 TYR cc_start: 0.7215 (t80) cc_final: 0.6941 (t80) REVERT: C 22 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8389 (m110) REVERT: C 45 ASP cc_start: 0.7892 (p0) cc_final: 0.5875 (t0) REVERT: C 62 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6659 (tp30) REVERT: C 86 ILE cc_start: 0.9169 (mt) cc_final: 0.8342 (tt) REVERT: C 90 ASP cc_start: 0.8497 (m-30) cc_final: 0.7995 (p0) REVERT: C 101 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8417 (mmm) REVERT: C 124 ASP cc_start: 0.6572 (OUTLIER) cc_final: 0.5210 (p0) REVERT: C 127 ASP cc_start: 0.7431 (t0) cc_final: 0.6836 (t0) REVERT: C 173 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8555 (mmtp) REVERT: D 16 ASP cc_start: 0.7521 (m-30) cc_final: 0.7039 (t0) REVERT: D 43 ASP cc_start: 0.9014 (t70) cc_final: 0.8175 (t0) REVERT: D 62 GLU cc_start: 0.7456 (mp0) cc_final: 0.6998 (mm-30) REVERT: D 76 GLN cc_start: 0.8567 (mt0) cc_final: 0.8092 (mt0) REVERT: D 80 ARG cc_start: 0.7834 (mmt-90) cc_final: 0.7531 (mpt180) REVERT: D 86 ILE cc_start: 0.7655 (mt) cc_final: 0.7390 (mp) REVERT: D 127 ASP cc_start: 0.6279 (t0) cc_final: 0.5523 (p0) REVERT: D 140 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7999 (m110) REVERT: D 168 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8065 (pm20) REVERT: E 16 ASP cc_start: 0.8972 (m-30) cc_final: 0.8758 (m-30) REVERT: E 18 GLU cc_start: 0.8850 (tt0) cc_final: 0.8368 (tt0) REVERT: E 24 GLN cc_start: 0.8422 (tp40) cc_final: 0.8075 (tm-30) REVERT: E 45 ASP cc_start: 0.6152 (p0) cc_final: 0.5728 (t70) REVERT: E 86 ILE cc_start: 0.7977 (mm) cc_final: 0.7339 (mp) REVERT: E 92 ASP cc_start: 0.8626 (m-30) cc_final: 0.7515 (t0) REVERT: E 113 GLN cc_start: 0.8309 (tp-100) cc_final: 0.7990 (tm-30) REVERT: E 142 GLN cc_start: 0.8220 (mm110) cc_final: 0.7968 (mm-40) REVERT: E 157 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7342 (ttp-110) REVERT: F 11 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7187 (tm-30) REVERT: F 17 SER cc_start: 0.8803 (m) cc_final: 0.8496 (p) REVERT: F 24 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8097 (tm-30) REVERT: F 26 ASN cc_start: 0.8132 (t0) cc_final: 0.7926 (t0) REVERT: F 38 MET cc_start: 0.8570 (mtp) cc_final: 0.7964 (ttm) REVERT: F 47 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8498 (m) REVERT: F 85 ASP cc_start: 0.7518 (m-30) cc_final: 0.7309 (m-30) REVERT: F 86 ILE cc_start: 0.7886 (mt) cc_final: 0.7559 (mt) REVERT: F 90 ASP cc_start: 0.8520 (m-30) cc_final: 0.7964 (p0) REVERT: F 117 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8057 (tp30) REVERT: F 144 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7552 (mttp) REVERT: G 38 MET cc_start: 0.8900 (mmm) cc_final: 0.8593 (mmm) REVERT: G 59 GLN cc_start: 0.9153 (tp40) cc_final: 0.8803 (tp40) REVERT: G 85 ASP cc_start: 0.7993 (m-30) cc_final: 0.6016 (p0) REVERT: G 86 ILE cc_start: 0.7942 (mt) cc_final: 0.7511 (mp) REVERT: G 90 ASP cc_start: 0.5487 (OUTLIER) cc_final: 0.5244 (p0) REVERT: G 113 GLN cc_start: 0.8052 (tp40) cc_final: 0.7077 (tm-30) REVERT: G 172 ASP cc_start: 0.8347 (m-30) cc_final: 0.8011 (m-30) REVERT: H 46 ASP cc_start: 0.8252 (p0) cc_final: 0.7914 (t0) REVERT: H 65 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7922 (mm-30) REVERT: H 75 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8497 (t0) REVERT: H 86 ILE cc_start: 0.8409 (mt) cc_final: 0.7766 (tp) REVERT: H 93 ASP cc_start: 0.8267 (t0) cc_final: 0.7936 (p0) REVERT: H 117 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8556 (pp20) REVERT: H 127 ASP cc_start: 0.8106 (t0) cc_final: 0.7713 (t0) REVERT: I 18 GLU cc_start: 0.8538 (tt0) cc_final: 0.7878 (tp30) REVERT: I 76 GLN cc_start: 0.8475 (mt0) cc_final: 0.8221 (mt0) REVERT: I 90 ASP cc_start: 0.8428 (m-30) cc_final: 0.7488 (t0) REVERT: I 108 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: I 159 MET cc_start: 0.7676 (mtp) cc_final: 0.7396 (mtm) REVERT: J 23 ARG cc_start: 0.8861 (mtp85) cc_final: 0.8646 (mpp80) REVERT: J 24 GLN cc_start: 0.9142 (tp40) cc_final: 0.8418 (tm-30) REVERT: J 43 ASP cc_start: 0.8328 (t0) cc_final: 0.8099 (t0) REVERT: J 64 ARG cc_start: 0.7915 (ttt90) cc_final: 0.7451 (ttt90) REVERT: J 68 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8104 (tm-30) REVERT: J 71 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8457 (ttm) REVERT: J 76 GLN cc_start: 0.8948 (mt0) cc_final: 0.8475 (mt0) REVERT: J 102 GLU cc_start: 0.8802 (mt-10) cc_final: 0.7658 (tm-30) REVERT: J 113 GLN cc_start: 0.8436 (tp-100) cc_final: 0.8150 (tm-30) REVERT: K 51 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7875 (t0) REVERT: K 65 GLU cc_start: 0.9061 (tt0) cc_final: 0.8858 (tm-30) REVERT: K 138 TYR cc_start: 0.8047 (m-80) cc_final: 0.7830 (m-80) REVERT: K 168 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7925 (mp0) REVERT: K 173 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8796 (mmtp) REVERT: L 39 SER cc_start: 0.9297 (t) cc_final: 0.9066 (t) REVERT: L 84 GLN cc_start: 0.7132 (mm110) cc_final: 0.6816 (mm-40) REVERT: L 85 ASP cc_start: 0.8070 (p0) cc_final: 0.7783 (p0) REVERT: L 90 ASP cc_start: 0.7568 (m-30) cc_final: 0.6892 (p0) REVERT: L 92 ASP cc_start: 0.8816 (m-30) cc_final: 0.8167 (t0) REVERT: L 102 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7337 (pp20) REVERT: L 113 GLN cc_start: 0.8729 (tt0) cc_final: 0.8298 (pt0) REVERT: L 132 ASP cc_start: 0.8164 (p0) cc_final: 0.7958 (m-30) REVERT: L 133 PHE cc_start: 0.7788 (t80) cc_final: 0.7511 (t80) REVERT: L 157 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7563 (mtm-85) REVERT: M 65 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7252 (tm-30) REVERT: M 68 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8222 (mt-10) REVERT: M 70 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7228 (mm) REVERT: M 99 ASN cc_start: 0.7574 (t0) cc_final: 0.7249 (t0) REVERT: M 108 GLU cc_start: 0.7845 (mm-30) cc_final: 0.6767 (tm-30) REVERT: N 45 ASP cc_start: 0.7808 (p0) cc_final: 0.6733 (t0) REVERT: N 62 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6942 (tm-30) REVERT: N 71 MET cc_start: 0.8054 (mtp) cc_final: 0.7815 (mtp) REVERT: N 84 GLN cc_start: 0.8019 (mm110) cc_final: 0.7633 (mm-40) REVERT: N 102 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7254 (tm-30) REVERT: N 168 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: O 7 SER cc_start: 0.7865 (m) cc_final: 0.7449 (p) REVERT: O 38 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.9031 (mmm) REVERT: O 144 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8516 (mtmp) REVERT: P 38 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8339 (ttm) REVERT: P 43 ASP cc_start: 0.8141 (t70) cc_final: 0.7604 (t0) REVERT: P 45 ASP cc_start: 0.7755 (p0) cc_final: 0.6715 (t0) REVERT: P 64 ARG cc_start: 0.7769 (tmt170) cc_final: 0.7521 (tmt170) REVERT: P 77 ARG cc_start: 0.7997 (mmp80) cc_final: 0.7317 (mmm160) REVERT: P 151 ASP cc_start: 0.8561 (m-30) cc_final: 0.8320 (t0) REVERT: P 158 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8768 (mtmt) REVERT: Q 18 GLU cc_start: 0.8423 (tt0) cc_final: 0.7921 (tp30) REVERT: Q 24 GLN cc_start: 0.9214 (tp-100) cc_final: 0.8815 (tp-100) REVERT: Q 34 VAL cc_start: 0.8038 (t) cc_final: 0.7735 (p) REVERT: Q 55 TYR cc_start: 0.7834 (t80) cc_final: 0.7563 (t80) REVERT: Q 59 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8575 (mm110) REVERT: Q 80 ARG cc_start: 0.7385 (mmm160) cc_final: 0.6934 (mmm160) REVERT: Q 132 ASP cc_start: 0.8158 (p0) cc_final: 0.7926 (m-30) REVERT: Q 169 TYR cc_start: 0.8578 (t80) cc_final: 0.8326 (t80) REVERT: R 11 GLN cc_start: 0.8078 (tt0) cc_final: 0.7135 (tp-100) REVERT: R 43 ASP cc_start: 0.9091 (t0) cc_final: 0.8874 (t0) REVERT: R 92 ASP cc_start: 0.8229 (m-30) cc_final: 0.7514 (t0) REVERT: R 154 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7836 (t) REVERT: S 11 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8325 (tm-30) REVERT: S 24 GLN cc_start: 0.7432 (tp40) cc_final: 0.6994 (tp-100) REVERT: S 58 HIS cc_start: 0.7082 (t70) cc_final: 0.6767 (t70) REVERT: S 68 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7588 (mt-10) REVERT: S 74 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6740 (tt0) REVERT: S 85 ASP cc_start: 0.8516 (m-30) cc_final: 0.8312 (m-30) REVERT: S 87 LYS cc_start: 0.6227 (mmtt) cc_final: 0.5473 (pttp) REVERT: S 110 ASN cc_start: 0.7830 (m-40) cc_final: 0.7470 (t0) REVERT: T 38 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7404 (ttm) REVERT: T 45 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7263 (p0) REVERT: T 54 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7936 (mttp) REVERT: T 64 ARG cc_start: 0.7885 (ttt-90) cc_final: 0.7653 (ttt90) REVERT: T 84 GLN cc_start: 0.7339 (mm110) cc_final: 0.7094 (mm110) REVERT: T 92 ASP cc_start: 0.8070 (m-30) cc_final: 0.6777 (p0) REVERT: T 133 PHE cc_start: 0.8141 (t80) cc_final: 0.7577 (t80) REVERT: T 138 TYR cc_start: 0.8061 (m-80) cc_final: 0.7842 (m-80) REVERT: U 18 GLU cc_start: 0.7586 (tt0) cc_final: 0.7341 (tp30) REVERT: U 54 LYS cc_start: 0.8403 (mttt) cc_final: 0.8002 (mtmp) REVERT: U 74 GLN cc_start: 0.7734 (tp40) cc_final: 0.7434 (tp40) REVERT: U 113 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7748 (tp40) REVERT: V 18 GLU cc_start: 0.8187 (tt0) cc_final: 0.7387 (tp30) REVERT: V 24 GLN cc_start: 0.8908 (tp40) cc_final: 0.8619 (tp40) REVERT: V 64 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.7058 (tmm-80) REVERT: V 72 LYS cc_start: 0.8179 (tttt) cc_final: 0.7792 (ttpp) REVERT: V 74 GLN cc_start: 0.8220 (tp-100) cc_final: 0.7131 (tm-30) REVERT: V 80 ARG cc_start: 0.6436 (mmt-90) cc_final: 0.5464 (mmt180) REVERT: V 117 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7462 (mp0) REVERT: W 64 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6897 (tmm-80) REVERT: W 68 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8255 (tt0) REVERT: W 74 GLN cc_start: 0.8526 (tp-100) cc_final: 0.8171 (tp-100) REVERT: W 76 GLN cc_start: 0.9213 (mt0) cc_final: 0.8896 (mt0) REVERT: W 80 ARG cc_start: 0.8680 (mmm-85) cc_final: 0.8269 (mpt180) REVERT: W 92 ASP cc_start: 0.6441 (m-30) cc_final: 0.6014 (p0) REVERT: X 11 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7802 (tp-100) REVERT: X 62 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6833 (tm-30) REVERT: X 80 ARG cc_start: 0.7317 (mmt-90) cc_final: 0.6845 (tpp-160) REVERT: X 84 GLN cc_start: 0.8660 (mp10) cc_final: 0.8438 (mm-40) outliers start: 248 outliers final: 48 residues processed: 1101 average time/residue: 0.6896 time to fit residues: 910.9078 Evaluate side-chains 722 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 646 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 71 MET Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 106 HIS Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 157 ARG Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 38 MET Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 144 LYS Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 144 LYS Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain T residue 38 MET Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 54 LYS Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 157 ARG Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 64 ARG Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 130 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 31 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 361 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 269 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 314 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 326 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 106 HIS A 110 ASN B 26 ASN C 126 ASN C 140 ASN C 155 ASN D 74 GLN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN G 126 ASN G 142 GLN J 8 GLN J 140 ASN K 24 GLN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS M 84 GLN M 152 HIS ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN O 22 ASN O 26 ASN O 76 GLN O 99 ASN O 152 HIS P 106 HIS P 126 ASN R 12 ASN R 14 HIS R 24 GLN S 75 ASN S 76 GLN ** S 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 ASN ** U 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 HIS V 59 GLN ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN ** X 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.121827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.108719 restraints weight = 71103.796| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.99 r_work: 0.3594 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34512 Z= 0.186 Angle : 0.664 10.076 46488 Z= 0.348 Chirality : 0.042 0.216 4896 Planarity : 0.004 0.053 6120 Dihedral : 4.445 24.463 4492 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 6.85 % Allowed : 25.47 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.12), residues: 4080 helix: 1.70 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.68 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 80 TYR 0.029 0.002 TYR M 169 PHE 0.012 0.001 PHE B 133 TRP 0.023 0.001 TRP C 94 HIS 0.014 0.001 HIS L 106 Details of bonding type rmsd covalent geometry : bond 0.00405 (34512) covalent geometry : angle 0.66363 (46488) hydrogen bonds : bond 0.06551 ( 2139) hydrogen bonds : angle 4.47296 ( 6417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 713 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: A 12 ASN cc_start: 0.9419 (t0) cc_final: 0.8472 (t0) REVERT: A 22 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7893 (m-40) REVERT: A 40 TYR cc_start: 0.8924 (m-10) cc_final: 0.8624 (m-10) REVERT: A 64 ARG cc_start: 0.8461 (ttt90) cc_final: 0.8154 (ttp-170) REVERT: B 24 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7591 (tm-30) REVERT: B 58 HIS cc_start: 0.7414 (t70) cc_final: 0.7015 (t70) REVERT: B 71 MET cc_start: 0.8930 (mtp) cc_final: 0.8660 (ttm) REVERT: B 90 ASP cc_start: 0.8398 (m-30) cc_final: 0.7858 (p0) REVERT: B 135 GLU cc_start: 0.5402 (mt-10) cc_final: 0.4955 (mt-10) REVERT: C 13 TYR cc_start: 0.7548 (t80) cc_final: 0.7190 (t80) REVERT: C 40 TYR cc_start: 0.8422 (m-10) cc_final: 0.7922 (m-10) REVERT: C 45 ASP cc_start: 0.8378 (p0) cc_final: 0.6965 (t0) REVERT: C 62 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6916 (tp30) REVERT: C 68 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7676 (tm-30) REVERT: C 86 ILE cc_start: 0.9028 (mt) cc_final: 0.8304 (tt) REVERT: C 90 ASP cc_start: 0.8540 (m-30) cc_final: 0.7898 (p0) REVERT: C 101 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8260 (mpp) REVERT: C 123 THR cc_start: 0.7198 (t) cc_final: 0.6986 (t) REVERT: C 124 ASP cc_start: 0.6109 (OUTLIER) cc_final: 0.4975 (p0) REVERT: C 127 ASP cc_start: 0.7877 (t0) cc_final: 0.7163 (t0) REVERT: C 168 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8326 (mp0) REVERT: C 173 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8697 (mmtp) REVERT: D 16 ASP cc_start: 0.7686 (m-30) cc_final: 0.7120 (t0) REVERT: D 43 ASP cc_start: 0.9140 (t70) cc_final: 0.8523 (t0) REVERT: D 62 GLU cc_start: 0.7362 (mp0) cc_final: 0.6973 (mm-30) REVERT: D 80 ARG cc_start: 0.7959 (mmt-90) cc_final: 0.7611 (mmp80) REVERT: D 127 ASP cc_start: 0.6913 (t0) cc_final: 0.5549 (p0) REVERT: D 140 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8201 (m110) REVERT: E 11 GLN cc_start: 0.8398 (tp-100) cc_final: 0.8105 (tp-100) REVERT: E 18 GLU cc_start: 0.9049 (tt0) cc_final: 0.8435 (tt0) REVERT: E 24 GLN cc_start: 0.8296 (tp40) cc_final: 0.7958 (tm-30) REVERT: E 45 ASP cc_start: 0.6580 (p0) cc_final: 0.5868 (t70) REVERT: E 62 GLU cc_start: 0.7954 (tt0) cc_final: 0.7663 (tm-30) REVERT: E 80 ARG cc_start: 0.8663 (mtp85) cc_final: 0.8447 (mtp85) REVERT: E 85 ASP cc_start: 0.7636 (m-30) cc_final: 0.6862 (p0) REVERT: E 92 ASP cc_start: 0.8636 (m-30) cc_final: 0.7728 (t0) REVERT: E 113 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7887 (tm-30) REVERT: E 142 GLN cc_start: 0.8249 (mm110) cc_final: 0.8018 (mm-40) REVERT: F 11 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7332 (tm-30) REVERT: F 24 GLN cc_start: 0.8271 (tm-30) cc_final: 0.8000 (tm-30) REVERT: F 26 ASN cc_start: 0.7958 (t0) cc_final: 0.7748 (t0) REVERT: F 38 MET cc_start: 0.8757 (mtp) cc_final: 0.8291 (ttm) REVERT: F 47 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8524 (m) REVERT: F 80 ARG cc_start: 0.7962 (mmm160) cc_final: 0.6805 (mmt90) REVERT: F 85 ASP cc_start: 0.7429 (m-30) cc_final: 0.7099 (m-30) REVERT: F 90 ASP cc_start: 0.8684 (m-30) cc_final: 0.8040 (p0) REVERT: F 92 ASP cc_start: 0.8306 (m-30) cc_final: 0.7070 (t0) REVERT: F 117 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8071 (tp30) REVERT: F 144 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7724 (mttm) REVERT: G 38 MET cc_start: 0.8989 (mmm) cc_final: 0.8618 (mmm) REVERT: G 51 ASN cc_start: 0.8075 (m-40) cc_final: 0.7871 (m-40) REVERT: G 54 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7607 (tmmt) REVERT: G 59 GLN cc_start: 0.9157 (tp40) cc_final: 0.8791 (tp40) REVERT: G 75 ASN cc_start: 0.9040 (m-40) cc_final: 0.8780 (t0) REVERT: G 132 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8171 (p0) REVERT: G 172 ASP cc_start: 0.8564 (m-30) cc_final: 0.8240 (m-30) REVERT: H 46 ASP cc_start: 0.8298 (p0) cc_final: 0.7966 (t0) REVERT: H 65 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7977 (mm-30) REVERT: H 86 ILE cc_start: 0.8432 (mt) cc_final: 0.7826 (tp) REVERT: H 117 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8616 (pp20) REVERT: H 127 ASP cc_start: 0.8287 (t0) cc_final: 0.7831 (t0) REVERT: I 18 GLU cc_start: 0.8691 (tt0) cc_final: 0.8453 (tt0) REVERT: I 21 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8283 (tt) REVERT: I 74 GLN cc_start: 0.8467 (tp40) cc_final: 0.7770 (tm-30) REVERT: I 76 GLN cc_start: 0.8596 (mt0) cc_final: 0.8317 (mt0) REVERT: I 90 ASP cc_start: 0.8553 (m-30) cc_final: 0.7565 (t0) REVERT: I 108 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: J 24 GLN cc_start: 0.9260 (tp40) cc_final: 0.8454 (tm-30) REVERT: J 64 ARG cc_start: 0.8351 (ttt90) cc_final: 0.8068 (ttt90) REVERT: J 68 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7728 (tm-30) REVERT: J 71 MET cc_start: 0.9227 (mtm) cc_final: 0.8625 (ttm) REVERT: J 102 GLU cc_start: 0.8774 (mt-10) cc_final: 0.7695 (tm-30) REVERT: J 113 GLN cc_start: 0.8412 (tp-100) cc_final: 0.8146 (tm-30) REVERT: K 65 GLU cc_start: 0.9214 (tt0) cc_final: 0.8906 (tm-30) REVERT: K 168 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7991 (mp0) REVERT: L 24 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7943 (tp40) REVERT: L 39 SER cc_start: 0.9188 (t) cc_final: 0.8958 (t) REVERT: L 84 GLN cc_start: 0.7237 (mm110) cc_final: 0.6882 (mm-40) REVERT: L 85 ASP cc_start: 0.8171 (p0) cc_final: 0.7822 (p0) REVERT: L 90 ASP cc_start: 0.7687 (m-30) cc_final: 0.6861 (p0) REVERT: L 92 ASP cc_start: 0.9003 (m-30) cc_final: 0.8288 (t0) REVERT: L 102 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7323 (pp20) REVERT: L 113 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: L 132 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: L 134 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7923 (tp) REVERT: L 148 GLU cc_start: 0.8664 (tp30) cc_final: 0.8438 (tp30) REVERT: M 65 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7525 (tm-30) REVERT: M 68 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8338 (tt0) REVERT: M 108 GLU cc_start: 0.7893 (mm-30) cc_final: 0.6806 (tm-30) REVERT: N 22 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8942 (t0) REVERT: N 71 MET cc_start: 0.8368 (mtp) cc_final: 0.8132 (mtp) REVERT: N 102 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7025 (tm-30) REVERT: N 132 ASP cc_start: 0.5736 (OUTLIER) cc_final: 0.5111 (m-30) REVERT: N 168 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: O 7 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7414 (p) REVERT: O 62 GLU cc_start: 0.8262 (mp0) cc_final: 0.8030 (mp0) REVERT: P 38 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8562 (ttm) REVERT: P 43 ASP cc_start: 0.8417 (t70) cc_final: 0.7955 (t0) REVERT: P 45 ASP cc_start: 0.8048 (p0) cc_final: 0.7615 (p0) REVERT: P 51 ASN cc_start: 0.8824 (m110) cc_final: 0.8501 (m110) REVERT: P 65 GLU cc_start: 0.9112 (tp30) cc_final: 0.8595 (tp30) REVERT: P 68 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8077 (pp20) REVERT: P 76 GLN cc_start: 0.9023 (mt0) cc_final: 0.8342 (mp10) REVERT: P 132 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6912 (t70) REVERT: P 158 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8795 (mtmt) REVERT: Q 18 GLU cc_start: 0.8456 (tt0) cc_final: 0.7969 (tp30) REVERT: Q 24 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8473 (tp-100) REVERT: Q 35 TYR cc_start: 0.7943 (m-10) cc_final: 0.7370 (m-80) REVERT: Q 59 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8002 (mm-40) REVERT: Q 60 SER cc_start: 0.8758 (OUTLIER) cc_final: 0.8413 (p) REVERT: Q 76 GLN cc_start: 0.8926 (mt0) cc_final: 0.8679 (mt0) REVERT: Q 127 ASP cc_start: 0.8066 (t0) cc_final: 0.7682 (t0) REVERT: Q 169 TYR cc_start: 0.8909 (t80) cc_final: 0.8449 (t80) REVERT: R 11 GLN cc_start: 0.8518 (tt0) cc_final: 0.7517 (tp-100) REVERT: R 71 MET cc_start: 0.8231 (mtp) cc_final: 0.7691 (mpp) REVERT: R 74 GLN cc_start: 0.7494 (tp-100) cc_final: 0.7083 (tp-100) REVERT: R 75 ASN cc_start: 0.8729 (t0) cc_final: 0.8238 (t0) REVERT: R 92 ASP cc_start: 0.8277 (m-30) cc_final: 0.7712 (p0) REVERT: R 154 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7640 (t) REVERT: R 159 MET cc_start: 0.8246 (mtp) cc_final: 0.7819 (ttm) REVERT: S 11 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8345 (tm-30) REVERT: S 13 TYR cc_start: 0.8258 (t80) cc_final: 0.8043 (t80) REVERT: S 24 GLN cc_start: 0.7689 (tp40) cc_final: 0.7431 (tp40) REVERT: S 58 HIS cc_start: 0.7170 (t70) cc_final: 0.6888 (t-90) REVERT: S 68 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7892 (mt-10) REVERT: S 74 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7250 (tp-100) REVERT: S 87 LYS cc_start: 0.6309 (mmtt) cc_final: 0.5597 (pttp) REVERT: S 110 ASN cc_start: 0.7771 (m-40) cc_final: 0.7386 (t0) REVERT: T 14 HIS cc_start: 0.7107 (t-90) cc_final: 0.6781 (t-90) REVERT: T 45 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7087 (p0) REVERT: T 84 GLN cc_start: 0.7296 (mm110) cc_final: 0.7033 (mm110) REVERT: T 138 TYR cc_start: 0.8441 (m-80) cc_final: 0.8069 (m-80) REVERT: U 11 GLN cc_start: 0.7873 (mp10) cc_final: 0.7653 (mm110) REVERT: U 54 LYS cc_start: 0.8473 (mttt) cc_final: 0.8078 (mtmp) REVERT: U 74 GLN cc_start: 0.8009 (tp40) cc_final: 0.7761 (tm130) REVERT: U 86 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7945 (tp) REVERT: U 113 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7661 (tp40) REVERT: U 144 LYS cc_start: 0.8771 (mppt) cc_final: 0.8491 (mttt) REVERT: V 18 GLU cc_start: 0.8218 (tt0) cc_final: 0.7550 (tp30) REVERT: V 24 GLN cc_start: 0.8957 (tp40) cc_final: 0.8740 (tp40) REVERT: V 35 TYR cc_start: 0.8284 (m-80) cc_final: 0.7814 (m-10) REVERT: V 64 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7360 (tmm-80) REVERT: V 72 LYS cc_start: 0.8560 (tttt) cc_final: 0.7985 (ttpp) REVERT: V 74 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7777 (tm-30) REVERT: V 80 ARG cc_start: 0.6699 (mmt-90) cc_final: 0.5890 (mmt180) REVERT: V 85 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: V 117 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7610 (mp0) REVERT: W 62 GLU cc_start: 0.8310 (tt0) cc_final: 0.7930 (tp30) REVERT: W 64 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6997 (tmm-80) REVERT: W 68 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8369 (tt0) REVERT: W 74 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8497 (tp-100) REVERT: W 76 GLN cc_start: 0.9223 (mt0) cc_final: 0.8930 (mt0) REVERT: W 80 ARG cc_start: 0.8876 (mmm-85) cc_final: 0.8412 (mpt180) REVERT: W 92 ASP cc_start: 0.6707 (m-30) cc_final: 0.6063 (p0) REVERT: X 70 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8398 (mm) REVERT: X 80 ARG cc_start: 0.7881 (mmt-90) cc_final: 0.7015 (pmm150) outliers start: 250 outliers final: 81 residues processed: 897 average time/residue: 0.7184 time to fit residues: 769.1366 Evaluate side-chains 725 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 614 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain N residue 22 ASN Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 132 ASP Chi-restraints excluded: chain P residue 147 LYS Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 172 ASP Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 144 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 64 ARG Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 130 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 146 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 221 optimal weight: 30.0000 chunk 302 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 219 optimal weight: 30.0000 chunk 145 optimal weight: 8.9990 chunk 386 optimal weight: 0.0870 chunk 157 optimal weight: 20.0000 chunk 274 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 overall best weight: 6.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 106 HIS B 26 ASN B 74 GLN C 66 HIS C 106 HIS C 140 ASN C 142 GLN C 155 ASN D 24 GLN D 75 ASN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN E 76 GLN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 HIS G 110 ASN G 126 ASN H 126 ASN I 142 GLN J 140 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN O 22 ASN O 24 GLN O 26 ASN O 99 ASN P 106 HIS P 126 ASN R 12 ASN R 14 HIS R 74 GLN ** S 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 ASN ** S 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 113 GLN T 126 ASN V 59 GLN V 75 ASN ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.121522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.108503 restraints weight = 71024.167| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.95 r_work: 0.3593 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 34512 Z= 0.179 Angle : 0.642 10.464 46488 Z= 0.337 Chirality : 0.041 0.195 4896 Planarity : 0.004 0.060 6120 Dihedral : 4.396 24.607 4488 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 6.83 % Allowed : 26.59 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.12), residues: 4080 helix: 2.03 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.64 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 80 TYR 0.022 0.002 TYR M 169 PHE 0.025 0.001 PHE R 133 TRP 0.009 0.001 TRP I 94 HIS 0.013 0.001 HIS L 106 Details of bonding type rmsd covalent geometry : bond 0.00389 (34512) covalent geometry : angle 0.64242 (46488) hydrogen bonds : bond 0.06103 ( 2139) hydrogen bonds : angle 4.23898 ( 6417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 670 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: A 12 ASN cc_start: 0.9384 (t0) cc_final: 0.8452 (t0) REVERT: A 22 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7868 (m-40) REVERT: A 40 TYR cc_start: 0.9035 (m-10) cc_final: 0.8683 (m-10) REVERT: A 64 ARG cc_start: 0.8491 (ttt90) cc_final: 0.8176 (ttp-170) REVERT: A 172 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8763 (t0) REVERT: B 24 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7435 (tm-30) REVERT: B 58 HIS cc_start: 0.7362 (t70) cc_final: 0.6985 (t70) REVERT: B 76 GLN cc_start: 0.8172 (mt0) cc_final: 0.7693 (mt0) REVERT: B 90 ASP cc_start: 0.8365 (m-30) cc_final: 0.7801 (p0) REVERT: B 135 GLU cc_start: 0.5514 (mt-10) cc_final: 0.5109 (mt-10) REVERT: C 40 TYR cc_start: 0.8504 (m-10) cc_final: 0.7827 (m-10) REVERT: C 45 ASP cc_start: 0.8411 (p0) cc_final: 0.7109 (t0) REVERT: C 62 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7003 (tp30) REVERT: C 86 ILE cc_start: 0.9082 (mt) cc_final: 0.8384 (tt) REVERT: C 90 ASP cc_start: 0.8575 (m-30) cc_final: 0.7963 (p0) REVERT: C 101 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8231 (mpp) REVERT: C 124 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5105 (p0) REVERT: C 127 ASP cc_start: 0.7588 (t0) cc_final: 0.6719 (t0) REVERT: C 173 LYS cc_start: 0.9211 (mmtt) cc_final: 0.8755 (mmtp) REVERT: D 16 ASP cc_start: 0.7799 (m-30) cc_final: 0.7245 (t0) REVERT: D 43 ASP cc_start: 0.9251 (t70) cc_final: 0.8572 (OUTLIER) REVERT: D 62 GLU cc_start: 0.7376 (mp0) cc_final: 0.6964 (tm-30) REVERT: D 75 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.7663 (t0) REVERT: D 80 ARG cc_start: 0.7999 (mmt-90) cc_final: 0.7589 (mmp80) REVERT: D 99 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7910 (m110) REVERT: D 127 ASP cc_start: 0.6883 (t0) cc_final: 0.5514 (p0) REVERT: E 11 GLN cc_start: 0.8412 (tp-100) cc_final: 0.8103 (tp-100) REVERT: E 18 GLU cc_start: 0.9006 (tt0) cc_final: 0.8377 (tt0) REVERT: E 24 GLN cc_start: 0.8202 (tp40) cc_final: 0.7808 (tm-30) REVERT: E 45 ASP cc_start: 0.6779 (p0) cc_final: 0.6123 (t70) REVERT: E 62 GLU cc_start: 0.7988 (tt0) cc_final: 0.7660 (tm-30) REVERT: E 76 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: E 85 ASP cc_start: 0.7626 (m-30) cc_final: 0.6928 (p0) REVERT: E 91 CYS cc_start: 0.6017 (m) cc_final: 0.5766 (m) REVERT: E 92 ASP cc_start: 0.8594 (m-30) cc_final: 0.7743 (t0) REVERT: E 99 ASN cc_start: 0.7494 (t0) cc_final: 0.7117 (t0) REVERT: E 113 GLN cc_start: 0.8263 (tp-100) cc_final: 0.7871 (tm-30) REVERT: E 157 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7314 (ttp-110) REVERT: F 24 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8101 (tm-30) REVERT: F 26 ASN cc_start: 0.8083 (t0) cc_final: 0.7816 (t0) REVERT: F 38 MET cc_start: 0.8686 (mtp) cc_final: 0.8257 (ttm) REVERT: F 45 ASP cc_start: 0.7864 (p0) cc_final: 0.7279 (p0) REVERT: F 47 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8563 (m) REVERT: F 85 ASP cc_start: 0.7502 (m-30) cc_final: 0.7177 (m-30) REVERT: F 90 ASP cc_start: 0.8702 (m-30) cc_final: 0.8068 (p0) REVERT: F 92 ASP cc_start: 0.8361 (m-30) cc_final: 0.7015 (t0) REVERT: F 106 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.6670 (t70) REVERT: F 117 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8154 (tp30) REVERT: F 144 LYS cc_start: 0.8174 (mtmt) cc_final: 0.7844 (mttm) REVERT: G 38 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8181 (mmt) REVERT: G 54 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7670 (tmmt) REVERT: G 59 GLN cc_start: 0.9171 (tp40) cc_final: 0.8834 (tp40) REVERT: G 71 MET cc_start: 0.8929 (mtm) cc_final: 0.8649 (mtm) REVERT: G 75 ASN cc_start: 0.9110 (OUTLIER) cc_final: 0.8559 (t0) REVERT: G 132 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8151 (p0) REVERT: G 172 ASP cc_start: 0.8635 (m-30) cc_final: 0.8165 (m-30) REVERT: H 46 ASP cc_start: 0.8330 (p0) cc_final: 0.8083 (t0) REVERT: H 50 LYS cc_start: 0.7625 (tppt) cc_final: 0.7392 (tppt) REVERT: H 65 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8083 (mm-30) REVERT: H 72 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7617 (tppt) REVERT: H 86 ILE cc_start: 0.8404 (mt) cc_final: 0.7756 (tp) REVERT: H 117 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8541 (pp20) REVERT: I 74 GLN cc_start: 0.8497 (tp40) cc_final: 0.7672 (tm-30) REVERT: I 90 ASP cc_start: 0.8350 (m-30) cc_final: 0.7225 (t0) REVERT: I 108 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: J 23 ARG cc_start: 0.8802 (mpp80) cc_final: 0.8483 (mpp80) REVERT: J 24 GLN cc_start: 0.9260 (tp40) cc_final: 0.8451 (tm-30) REVERT: J 64 ARG cc_start: 0.8178 (ttt90) cc_final: 0.7896 (ttt90) REVERT: J 68 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7936 (tm-30) REVERT: J 71 MET cc_start: 0.9120 (mtm) cc_final: 0.8824 (ttm) REVERT: J 102 GLU cc_start: 0.8801 (mt-10) cc_final: 0.7701 (tm-30) REVERT: J 113 GLN cc_start: 0.8452 (tp-100) cc_final: 0.8171 (tm-30) REVERT: J 132 ASP cc_start: 0.7596 (t70) cc_final: 0.7117 (m-30) REVERT: K 65 GLU cc_start: 0.9263 (tt0) cc_final: 0.8955 (tm-30) REVERT: K 86 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7805 (tp) REVERT: K 168 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7930 (mp0) REVERT: L 24 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7957 (tp40) REVERT: L 39 SER cc_start: 0.9126 (t) cc_final: 0.8902 (t) REVERT: L 75 ASN cc_start: 0.9424 (t0) cc_final: 0.9063 (t0) REVERT: L 84 GLN cc_start: 0.7245 (mm110) cc_final: 0.6877 (mm-40) REVERT: L 85 ASP cc_start: 0.8188 (p0) cc_final: 0.7973 (p0) REVERT: L 87 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6930 (mmpt) REVERT: L 90 ASP cc_start: 0.7681 (m-30) cc_final: 0.6683 (p0) REVERT: L 92 ASP cc_start: 0.9040 (m-30) cc_final: 0.8246 (t0) REVERT: L 102 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7294 (pp20) REVERT: L 113 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8254 (pt0) REVERT: L 148 GLU cc_start: 0.8740 (tp30) cc_final: 0.8516 (tp30) REVERT: L 159 MET cc_start: 0.7327 (mmm) cc_final: 0.6886 (mtm) REVERT: M 65 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7652 (tm-30) REVERT: M 68 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8315 (tt0) REVERT: M 71 MET cc_start: 0.9215 (ttm) cc_final: 0.8922 (ttm) REVERT: M 81 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7455 (pp) REVERT: M 108 GLU cc_start: 0.7827 (mm-30) cc_final: 0.6838 (tm-30) REVERT: N 71 MET cc_start: 0.8524 (mtp) cc_final: 0.8270 (mtp) REVERT: N 132 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5765 (m-30) REVERT: N 168 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: N 173 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8047 (mptt) REVERT: O 36 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8764 (tm) REVERT: O 40 TYR cc_start: 0.8377 (m-80) cc_final: 0.8142 (m-10) REVERT: O 62 GLU cc_start: 0.8317 (mp0) cc_final: 0.8080 (mp0) REVERT: O 144 LYS cc_start: 0.8762 (mtmp) cc_final: 0.8496 (mtmp) REVERT: O 149 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8675 (tp) REVERT: P 38 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8603 (ttm) REVERT: P 43 ASP cc_start: 0.8460 (t70) cc_final: 0.7792 (t0) REVERT: P 51 ASN cc_start: 0.8813 (m110) cc_final: 0.8509 (m110) REVERT: P 64 ARG cc_start: 0.7949 (tmt170) cc_final: 0.7700 (tmt170) REVERT: P 75 ASN cc_start: 0.9043 (t0) cc_final: 0.8645 (t0) REVERT: P 76 GLN cc_start: 0.8947 (mt0) cc_final: 0.8183 (mp10) REVERT: P 132 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.7053 (t70) REVERT: P 158 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8764 (mtmt) REVERT: P 159 MET cc_start: 0.7672 (ttm) cc_final: 0.7316 (ttp) REVERT: Q 18 GLU cc_start: 0.8557 (tt0) cc_final: 0.8084 (tp30) REVERT: Q 24 GLN cc_start: 0.9103 (tp-100) cc_final: 0.8507 (tp-100) REVERT: Q 35 TYR cc_start: 0.7998 (m-10) cc_final: 0.7700 (m-10) REVERT: Q 60 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8305 (p) REVERT: Q 76 GLN cc_start: 0.8867 (mt0) cc_final: 0.8619 (mt0) REVERT: Q 127 ASP cc_start: 0.8216 (t0) cc_final: 0.7797 (t0) REVERT: Q 169 TYR cc_start: 0.8964 (t80) cc_final: 0.8564 (t80) REVERT: R 8 GLN cc_start: 0.7965 (pt0) cc_final: 0.7575 (pm20) REVERT: R 11 GLN cc_start: 0.8555 (tt0) cc_final: 0.7321 (tm-30) REVERT: R 45 ASP cc_start: 0.6523 (p0) cc_final: 0.5842 (p0) REVERT: R 51 ASN cc_start: 0.8754 (m-40) cc_final: 0.8411 (m110) REVERT: R 74 GLN cc_start: 0.7860 (tp40) cc_final: 0.7536 (tp-100) REVERT: R 75 ASN cc_start: 0.8667 (t0) cc_final: 0.8277 (t0) REVERT: R 92 ASP cc_start: 0.8459 (m-30) cc_final: 0.7895 (p0) REVERT: R 154 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7520 (t) REVERT: R 159 MET cc_start: 0.7943 (mtp) cc_final: 0.7593 (ttm) REVERT: S 11 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8321 (tm-30) REVERT: S 24 GLN cc_start: 0.7748 (tp40) cc_final: 0.7408 (tp40) REVERT: S 68 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7883 (mt-10) REVERT: S 74 GLN cc_start: 0.7567 (mm-40) cc_final: 0.6983 (tp-100) REVERT: S 80 ARG cc_start: 0.7934 (mmp80) cc_final: 0.7446 (mmp80) REVERT: S 87 LYS cc_start: 0.6308 (mmtt) cc_final: 0.5665 (pttp) REVERT: S 110 ASN cc_start: 0.7816 (m-40) cc_final: 0.7464 (t0) REVERT: T 14 HIS cc_start: 0.7179 (t-90) cc_final: 0.6824 (t-90) REVERT: T 45 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7196 (p0) REVERT: T 84 GLN cc_start: 0.7254 (mm110) cc_final: 0.7038 (mm110) REVERT: T 138 TYR cc_start: 0.8446 (m-80) cc_final: 0.8223 (m-80) REVERT: U 11 GLN cc_start: 0.7933 (mp10) cc_final: 0.7709 (mm110) REVERT: U 54 LYS cc_start: 0.8488 (mttt) cc_final: 0.8104 (mtmp) REVERT: U 144 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8420 (mttt) REVERT: V 18 GLU cc_start: 0.8188 (tt0) cc_final: 0.7567 (tp30) REVERT: V 35 TYR cc_start: 0.8331 (m-80) cc_final: 0.8054 (m-10) REVERT: V 64 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7121 (tmm-80) REVERT: V 68 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7045 (mt-10) REVERT: V 74 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7827 (tm-30) REVERT: V 80 ARG cc_start: 0.6692 (mmt-90) cc_final: 0.5949 (mmt180) REVERT: V 85 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: V 117 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7572 (mp0) REVERT: W 24 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8842 (tm-30) REVERT: W 62 GLU cc_start: 0.8384 (tt0) cc_final: 0.7987 (tp30) REVERT: W 64 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6959 (tmm-80) REVERT: W 68 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8344 (tt0) REVERT: W 74 GLN cc_start: 0.8840 (tp-100) cc_final: 0.8219 (tp-100) REVERT: W 76 GLN cc_start: 0.9241 (mt0) cc_final: 0.8900 (mt0) REVERT: W 80 ARG cc_start: 0.8904 (mmm-85) cc_final: 0.8410 (mpt180) REVERT: W 92 ASP cc_start: 0.6774 (m-30) cc_final: 0.5987 (p0) REVERT: X 70 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8380 (mm) REVERT: X 80 ARG cc_start: 0.7878 (mmt-90) cc_final: 0.7011 (pmm150) outliers start: 249 outliers final: 89 residues processed: 851 average time/residue: 0.7078 time to fit residues: 720.3310 Evaluate side-chains 712 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 585 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 106 HIS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 106 HIS Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 140 ASN Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 132 ASP Chi-restraints excluded: chain P residue 147 LYS Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 172 ASP Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 144 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 132 ASP Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain V residue 172 ASP Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 64 ARG Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 134 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 47 optimal weight: 7.9990 chunk 218 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 376 optimal weight: 8.9990 chunk 381 optimal weight: 0.8980 chunk 249 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 260 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 76 GLN A 106 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN C 22 ASN C 155 ASN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 ASN ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN I 76 GLN I 99 ASN J 12 ASN J 140 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 ASN L 106 HIS M 84 GLN ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN N 24 GLN O 22 ASN O 24 GLN O 26 ASN P 106 HIS P 126 ASN Q 75 ASN R 12 ASN R 14 HIS S 75 ASN ** S 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 GLN U 119 HIS ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN ** X 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.122569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.109417 restraints weight = 70915.593| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.96 r_work: 0.3602 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34512 Z= 0.158 Angle : 0.619 11.091 46488 Z= 0.325 Chirality : 0.039 0.174 4896 Planarity : 0.004 0.063 6120 Dihedral : 4.338 23.917 4488 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 6.58 % Allowed : 27.55 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.13), residues: 4080 helix: 2.30 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.60 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 80 TYR 0.026 0.002 TYR M 169 PHE 0.029 0.001 PHE F 133 TRP 0.007 0.001 TRP I 94 HIS 0.013 0.001 HIS L 106 Details of bonding type rmsd covalent geometry : bond 0.00342 (34512) covalent geometry : angle 0.61942 (46488) hydrogen bonds : bond 0.05662 ( 2139) hydrogen bonds : angle 4.01111 ( 6417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 650 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: A 12 ASN cc_start: 0.9243 (t0) cc_final: 0.8312 (t0) REVERT: A 22 ASN cc_start: 0.8172 (m110) cc_final: 0.7852 (m-40) REVERT: A 38 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8694 (ttp) REVERT: A 40 TYR cc_start: 0.8991 (m-10) cc_final: 0.8687 (m-10) REVERT: A 43 ASP cc_start: 0.8424 (t0) cc_final: 0.8193 (t0) REVERT: A 64 ARG cc_start: 0.8069 (ttt90) cc_final: 0.7618 (ttp-170) REVERT: A 172 ASP cc_start: 0.8986 (t70) cc_final: 0.8785 (t0) REVERT: B 24 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7393 (tm-30) REVERT: B 58 HIS cc_start: 0.7398 (t70) cc_final: 0.7008 (t70) REVERT: B 76 GLN cc_start: 0.8281 (mt0) cc_final: 0.7471 (mt0) REVERT: B 90 ASP cc_start: 0.8380 (m-30) cc_final: 0.7896 (p0) REVERT: B 148 GLU cc_start: 0.8952 (tp30) cc_final: 0.8592 (tp30) REVERT: C 43 ASP cc_start: 0.8729 (t0) cc_final: 0.8487 (t0) REVERT: C 45 ASP cc_start: 0.8400 (p0) cc_final: 0.7224 (t0) REVERT: C 62 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6875 (tp30) REVERT: C 86 ILE cc_start: 0.9197 (mt) cc_final: 0.8461 (tt) REVERT: C 90 ASP cc_start: 0.8767 (m-30) cc_final: 0.7844 (p0) REVERT: C 101 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8281 (mpp) REVERT: C 108 GLU cc_start: 0.8700 (tp30) cc_final: 0.8444 (mm-30) REVERT: C 124 ASP cc_start: 0.5892 (OUTLIER) cc_final: 0.5140 (p0) REVERT: C 127 ASP cc_start: 0.7891 (t0) cc_final: 0.7565 (t70) REVERT: C 173 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8753 (mmtp) REVERT: D 16 ASP cc_start: 0.7895 (m-30) cc_final: 0.7329 (t0) REVERT: D 62 GLU cc_start: 0.7378 (mp0) cc_final: 0.6960 (tm-30) REVERT: D 75 ASN cc_start: 0.8464 (m-40) cc_final: 0.8034 (t0) REVERT: D 80 ARG cc_start: 0.7958 (mmt-90) cc_final: 0.7543 (mmp80) REVERT: D 99 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7551 (m110) REVERT: D 127 ASP cc_start: 0.6844 (t0) cc_final: 0.5471 (p0) REVERT: D 168 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8173 (pm20) REVERT: E 11 GLN cc_start: 0.8526 (tp-100) cc_final: 0.8161 (tp-100) REVERT: E 16 ASP cc_start: 0.8623 (m-30) cc_final: 0.7980 (t0) REVERT: E 18 GLU cc_start: 0.8820 (tt0) cc_final: 0.7961 (tp30) REVERT: E 24 GLN cc_start: 0.8091 (tp40) cc_final: 0.7849 (tm-30) REVERT: E 43 ASP cc_start: 0.8959 (t0) cc_final: 0.8718 (t0) REVERT: E 45 ASP cc_start: 0.7065 (p0) cc_final: 0.5948 (t70) REVERT: E 76 GLN cc_start: 0.8540 (tt0) cc_final: 0.8280 (tm-30) REVERT: E 91 CYS cc_start: 0.5658 (m) cc_final: 0.5093 (m) REVERT: E 92 ASP cc_start: 0.8490 (m-30) cc_final: 0.7664 (t0) REVERT: E 113 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7868 (tm-30) REVERT: E 116 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8609 (tm) REVERT: E 157 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7301 (ttp-110) REVERT: F 24 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8249 (tm-30) REVERT: F 26 ASN cc_start: 0.8028 (t0) cc_final: 0.7774 (t0) REVERT: F 38 MET cc_start: 0.8651 (mtp) cc_final: 0.8246 (ttm) REVERT: F 45 ASP cc_start: 0.7777 (p0) cc_final: 0.7252 (p0) REVERT: F 47 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8537 (m) REVERT: F 80 ARG cc_start: 0.8153 (mmm160) cc_final: 0.6823 (mmt-90) REVERT: F 85 ASP cc_start: 0.7497 (m-30) cc_final: 0.7122 (m-30) REVERT: F 90 ASP cc_start: 0.8878 (m-30) cc_final: 0.8284 (p0) REVERT: F 92 ASP cc_start: 0.8449 (m-30) cc_final: 0.7044 (t0) REVERT: F 117 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8097 (tp30) REVERT: F 144 LYS cc_start: 0.8100 (mtmt) cc_final: 0.7759 (mttp) REVERT: G 18 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7564 (mt-10) REVERT: G 38 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8170 (mmm) REVERT: G 45 ASP cc_start: 0.5130 (t0) cc_final: 0.4179 (t0) REVERT: G 54 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7689 (tmmt) REVERT: G 59 GLN cc_start: 0.9142 (tp40) cc_final: 0.8831 (tp40) REVERT: G 71 MET cc_start: 0.8955 (mtm) cc_final: 0.8723 (mtm) REVERT: G 75 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8614 (t0) REVERT: G 172 ASP cc_start: 0.8570 (m-30) cc_final: 0.8201 (m-30) REVERT: H 46 ASP cc_start: 0.8334 (p0) cc_final: 0.8122 (t0) REVERT: H 50 LYS cc_start: 0.7513 (tppt) cc_final: 0.7265 (tppt) REVERT: H 65 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: H 72 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7586 (tppt) REVERT: H 86 ILE cc_start: 0.8524 (mt) cc_final: 0.7858 (tp) REVERT: H 117 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8600 (pp20) REVERT: H 127 ASP cc_start: 0.8252 (t0) cc_final: 0.7717 (t0) REVERT: I 21 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8290 (tt) REVERT: I 74 GLN cc_start: 0.8396 (tp40) cc_final: 0.7816 (tm-30) REVERT: I 76 GLN cc_start: 0.8749 (mt0) cc_final: 0.8337 (mt0) REVERT: I 90 ASP cc_start: 0.8426 (m-30) cc_final: 0.7378 (t0) REVERT: I 108 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: J 24 GLN cc_start: 0.9264 (tp40) cc_final: 0.8451 (tm-30) REVERT: J 64 ARG cc_start: 0.8167 (ttt90) cc_final: 0.7879 (ttt90) REVERT: J 68 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8062 (tm-30) REVERT: J 102 GLU cc_start: 0.8812 (mt-10) cc_final: 0.7685 (tm-30) REVERT: J 113 GLN cc_start: 0.8427 (tp-100) cc_final: 0.8156 (tm-30) REVERT: J 132 ASP cc_start: 0.7627 (t70) cc_final: 0.7149 (m-30) REVERT: K 65 GLU cc_start: 0.9256 (tt0) cc_final: 0.8992 (tm-30) REVERT: K 68 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: K 86 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7797 (tp) REVERT: K 168 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7962 (mp0) REVERT: L 24 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7888 (tm-30) REVERT: L 75 ASN cc_start: 0.9363 (t0) cc_final: 0.9115 (t0) REVERT: L 84 GLN cc_start: 0.7226 (mm110) cc_final: 0.6856 (mm-40) REVERT: L 85 ASP cc_start: 0.8217 (p0) cc_final: 0.7846 (p0) REVERT: L 90 ASP cc_start: 0.7714 (m-30) cc_final: 0.6506 (p0) REVERT: L 102 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7241 (pp20) REVERT: L 113 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8226 (pt0) REVERT: L 148 GLU cc_start: 0.8827 (tp30) cc_final: 0.8590 (tp30) REVERT: M 65 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7786 (tm-30) REVERT: M 68 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8320 (tt0) REVERT: M 71 MET cc_start: 0.9207 (ttm) cc_final: 0.8986 (ttm) REVERT: M 75 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8197 (t0) REVERT: M 81 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7519 (pp) REVERT: M 108 GLU cc_start: 0.7857 (mm-30) cc_final: 0.6921 (tm-30) REVERT: N 43 ASP cc_start: 0.8639 (t0) cc_final: 0.8439 (t0) REVERT: N 71 MET cc_start: 0.8518 (mtp) cc_final: 0.8316 (mtp) REVERT: N 132 ASP cc_start: 0.6294 (OUTLIER) cc_final: 0.5589 (m-30) REVERT: N 173 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8068 (mptt) REVERT: O 36 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8817 (tm) REVERT: O 40 TYR cc_start: 0.8309 (m-80) cc_final: 0.8091 (m-10) REVERT: O 62 GLU cc_start: 0.8239 (mp0) cc_final: 0.7961 (mp0) REVERT: O 96 SER cc_start: 0.7077 (m) cc_final: 0.6843 (m) REVERT: O 140 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7566 (t0) REVERT: O 169 TYR cc_start: 0.8613 (t80) cc_final: 0.8197 (t80) REVERT: P 38 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8631 (ttm) REVERT: P 43 ASP cc_start: 0.8651 (t70) cc_final: 0.7911 (t0) REVERT: P 51 ASN cc_start: 0.8881 (m110) cc_final: 0.8599 (m110) REVERT: P 65 GLU cc_start: 0.9122 (tp30) cc_final: 0.8858 (tp30) REVERT: P 68 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7520 (mt-10) REVERT: P 76 GLN cc_start: 0.8873 (mt0) cc_final: 0.8149 (mp10) REVERT: P 102 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8957 (mm-30) REVERT: P 132 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6922 (t70) REVERT: Q 18 GLU cc_start: 0.8430 (tt0) cc_final: 0.8008 (tp30) REVERT: Q 24 GLN cc_start: 0.9087 (tp-100) cc_final: 0.8418 (tp-100) REVERT: Q 55 TYR cc_start: 0.7350 (t80) cc_final: 0.6984 (t80) REVERT: Q 76 GLN cc_start: 0.8832 (mt0) cc_final: 0.8592 (mt0) REVERT: Q 169 TYR cc_start: 0.8965 (t80) cc_final: 0.8616 (t80) REVERT: R 8 GLN cc_start: 0.7962 (pt0) cc_final: 0.7564 (pm20) REVERT: R 11 GLN cc_start: 0.8579 (tt0) cc_final: 0.7318 (tm130) REVERT: R 51 ASN cc_start: 0.8726 (m-40) cc_final: 0.8293 (m110) REVERT: R 74 GLN cc_start: 0.7644 (tp40) cc_final: 0.7262 (tp-100) REVERT: R 75 ASN cc_start: 0.8716 (t0) cc_final: 0.8335 (t0) REVERT: R 92 ASP cc_start: 0.8590 (m-30) cc_final: 0.7964 (p0) REVERT: R 139 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8785 (mt) REVERT: R 154 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7508 (t) REVERT: R 159 MET cc_start: 0.7855 (mtp) cc_final: 0.7634 (ttm) REVERT: S 11 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8329 (tm-30) REVERT: S 24 GLN cc_start: 0.7611 (tp40) cc_final: 0.6898 (tm-30) REVERT: S 68 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7814 (mt-10) REVERT: S 87 LYS cc_start: 0.6544 (mmtt) cc_final: 0.5987 (pttp) REVERT: S 110 ASN cc_start: 0.7824 (m-40) cc_final: 0.7495 (t0) REVERT: S 169 TYR cc_start: 0.8130 (t80) cc_final: 0.7841 (t80) REVERT: T 14 HIS cc_start: 0.7205 (t-90) cc_final: 0.6823 (t-90) REVERT: T 45 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7201 (p0) REVERT: T 84 GLN cc_start: 0.7222 (mm110) cc_final: 0.7003 (mm110) REVERT: U 11 GLN cc_start: 0.7945 (mp10) cc_final: 0.7447 (mm110) REVERT: U 18 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8000 (tp30) REVERT: U 54 LYS cc_start: 0.8425 (mttt) cc_final: 0.8022 (mtmp) REVERT: U 74 GLN cc_start: 0.7359 (tm130) cc_final: 0.6652 (tm-30) REVERT: U 80 ARG cc_start: 0.7786 (mpt-90) cc_final: 0.7480 (mpt90) REVERT: U 144 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8473 (mttt) REVERT: V 18 GLU cc_start: 0.8159 (tt0) cc_final: 0.7588 (tp30) REVERT: V 35 TYR cc_start: 0.8388 (m-80) cc_final: 0.8118 (m-10) REVERT: V 64 ARG cc_start: 0.7696 (ttm-80) cc_final: 0.7150 (tmm-80) REVERT: V 68 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: V 74 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7758 (tp40) REVERT: V 80 ARG cc_start: 0.6686 (mmt-90) cc_final: 0.5976 (mmt180) REVERT: V 85 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: V 107 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8517 (tm) REVERT: V 117 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7513 (mp0) REVERT: W 24 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8823 (tm-30) REVERT: W 62 GLU cc_start: 0.8426 (tt0) cc_final: 0.8004 (tp30) REVERT: W 68 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8337 (tt0) REVERT: W 74 GLN cc_start: 0.8839 (tp-100) cc_final: 0.8144 (tp-100) REVERT: W 76 GLN cc_start: 0.9221 (mt0) cc_final: 0.8888 (mt0) REVERT: W 80 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8361 (mpt180) REVERT: W 92 ASP cc_start: 0.6825 (m-30) cc_final: 0.5985 (p0) REVERT: X 24 GLN cc_start: 0.8565 (tp40) cc_final: 0.8321 (mm-40) REVERT: X 62 GLU cc_start: 0.7464 (tt0) cc_final: 0.7156 (tm-30) REVERT: X 80 ARG cc_start: 0.7773 (mmt-90) cc_final: 0.7094 (tpp-160) outliers start: 240 outliers final: 90 residues processed: 824 average time/residue: 0.6918 time to fit residues: 683.4350 Evaluate side-chains 723 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 598 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 76 GLN Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 106 HIS Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 140 ASN Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 132 ASP Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain V residue 172 ASP Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 134 ILE Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 254 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 339 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 311 optimal weight: 20.0000 chunk 404 optimal weight: 1.9990 chunk 320 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 292 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 106 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN C 155 ASN D 74 GLN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 ASN ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN G 126 ASN H 51 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 ASN K 74 GLN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN O 22 ASN O 24 GLN O 26 ASN O 140 ASN P 106 HIS Q 26 ASN R 12 ASN R 14 HIS R 26 ASN S 110 ASN ** S 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 GLN ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.120054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.107295 restraints weight = 72613.330| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 4.03 r_work: 0.3601 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34512 Z= 0.155 Angle : 0.622 11.562 46488 Z= 0.324 Chirality : 0.039 0.168 4896 Planarity : 0.004 0.067 6120 Dihedral : 4.306 24.037 4488 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 6.39 % Allowed : 28.29 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.13), residues: 4080 helix: 2.45 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.58 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 80 TYR 0.024 0.002 TYR E 169 PHE 0.029 0.001 PHE R 133 TRP 0.011 0.001 TRP D 94 HIS 0.012 0.001 HIS L 106 Details of bonding type rmsd covalent geometry : bond 0.00339 (34512) covalent geometry : angle 0.62242 (46488) hydrogen bonds : bond 0.05480 ( 2139) hydrogen bonds : angle 3.93396 ( 6417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 662 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: A 12 ASN cc_start: 0.9272 (t0) cc_final: 0.8321 (t0) REVERT: A 22 ASN cc_start: 0.8220 (m110) cc_final: 0.7914 (m-40) REVERT: A 24 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.6847 (tm-30) REVERT: A 38 MET cc_start: 0.8914 (ttm) cc_final: 0.8700 (ttp) REVERT: A 64 ARG cc_start: 0.8086 (ttt90) cc_final: 0.7615 (ttp-170) REVERT: A 76 GLN cc_start: 0.8047 (mt0) cc_final: 0.7443 (mt0) REVERT: A 172 ASP cc_start: 0.8994 (t70) cc_final: 0.8789 (t0) REVERT: B 24 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 58 HIS cc_start: 0.7420 (t70) cc_final: 0.7036 (t70) REVERT: B 76 GLN cc_start: 0.8251 (mt0) cc_final: 0.7438 (mt0) REVERT: B 90 ASP cc_start: 0.8520 (m-30) cc_final: 0.8104 (p0) REVERT: B 123 THR cc_start: 0.8009 (m) cc_final: 0.7804 (p) REVERT: B 132 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7448 (m-30) REVERT: B 148 GLU cc_start: 0.8978 (tp30) cc_final: 0.8616 (tp30) REVERT: C 40 TYR cc_start: 0.8306 (m-10) cc_final: 0.8036 (m-10) REVERT: C 43 ASP cc_start: 0.8751 (t0) cc_final: 0.8483 (t0) REVERT: C 45 ASP cc_start: 0.8482 (p0) cc_final: 0.7275 (t0) REVERT: C 62 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6844 (tp30) REVERT: C 90 ASP cc_start: 0.8808 (m-30) cc_final: 0.7865 (p0) REVERT: C 101 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8276 (mpp) REVERT: C 108 GLU cc_start: 0.8701 (tp30) cc_final: 0.8447 (mm-30) REVERT: C 124 ASP cc_start: 0.5815 (OUTLIER) cc_final: 0.5024 (p0) REVERT: C 173 LYS cc_start: 0.9254 (mmtt) cc_final: 0.8691 (mmtm) REVERT: D 16 ASP cc_start: 0.7992 (m-30) cc_final: 0.7392 (t0) REVERT: D 62 GLU cc_start: 0.7380 (mp0) cc_final: 0.6972 (tm-30) REVERT: D 75 ASN cc_start: 0.8611 (m-40) cc_final: 0.8071 (t0) REVERT: D 80 ARG cc_start: 0.7703 (mmt-90) cc_final: 0.7426 (mmp80) REVERT: D 99 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7555 (m110) REVERT: D 127 ASP cc_start: 0.6833 (t0) cc_final: 0.5455 (p0) REVERT: D 168 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8031 (pm20) REVERT: E 11 GLN cc_start: 0.8445 (tp-100) cc_final: 0.8048 (tp-100) REVERT: E 18 GLU cc_start: 0.8825 (tt0) cc_final: 0.7966 (tp30) REVERT: E 43 ASP cc_start: 0.8906 (t0) cc_final: 0.8699 (t0) REVERT: E 45 ASP cc_start: 0.6992 (p0) cc_final: 0.5865 (t70) REVERT: E 62 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: E 91 CYS cc_start: 0.5641 (m) cc_final: 0.5090 (m) REVERT: E 92 ASP cc_start: 0.8466 (m-30) cc_final: 0.7741 (t0) REVERT: E 99 ASN cc_start: 0.7280 (t0) cc_final: 0.6969 (t0) REVERT: E 113 GLN cc_start: 0.8147 (tp-100) cc_final: 0.7914 (tm-30) REVERT: E 117 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: E 157 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7149 (ttp-110) REVERT: F 24 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8222 (tm-30) REVERT: F 26 ASN cc_start: 0.8037 (t0) cc_final: 0.7798 (t0) REVERT: F 38 MET cc_start: 0.8589 (mtp) cc_final: 0.8215 (ttm) REVERT: F 45 ASP cc_start: 0.7791 (p0) cc_final: 0.7374 (p0) REVERT: F 47 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8555 (m) REVERT: F 80 ARG cc_start: 0.8324 (mmm160) cc_final: 0.7154 (mmt-90) REVERT: F 85 ASP cc_start: 0.7406 (m-30) cc_final: 0.7002 (m-30) REVERT: F 90 ASP cc_start: 0.8869 (m-30) cc_final: 0.8303 (p0) REVERT: F 92 ASP cc_start: 0.8545 (m-30) cc_final: 0.7193 (t0) REVERT: F 106 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.6772 (t70) REVERT: F 113 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8784 (tm-30) REVERT: F 117 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8197 (tp30) REVERT: F 144 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7866 (mttm) REVERT: F 159 MET cc_start: 0.6774 (mtp) cc_final: 0.6284 (ttm) REVERT: G 11 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8576 (tp-100) REVERT: G 18 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7569 (mt-10) REVERT: G 38 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8184 (mmm) REVERT: G 59 GLN cc_start: 0.9145 (tp40) cc_final: 0.8823 (tp40) REVERT: G 75 ASN cc_start: 0.9096 (m-40) cc_final: 0.8658 (t0) REVERT: G 172 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8186 (m-30) REVERT: H 37 SER cc_start: 0.9245 (t) cc_final: 0.9029 (p) REVERT: H 46 ASP cc_start: 0.8256 (p0) cc_final: 0.8018 (t0) REVERT: H 50 LYS cc_start: 0.7637 (tppt) cc_final: 0.7399 (tppt) REVERT: H 65 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: H 72 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7598 (tppt) REVERT: H 127 ASP cc_start: 0.8423 (t0) cc_final: 0.7941 (t0) REVERT: H 163 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: I 21 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8293 (tt) REVERT: I 74 GLN cc_start: 0.8465 (tp40) cc_final: 0.7761 (tm-30) REVERT: I 76 GLN cc_start: 0.8666 (mt0) cc_final: 0.8400 (mt0) REVERT: I 90 ASP cc_start: 0.8410 (m-30) cc_final: 0.7365 (t0) REVERT: I 108 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: J 24 GLN cc_start: 0.9270 (tp40) cc_final: 0.8449 (tm-30) REVERT: J 64 ARG cc_start: 0.8177 (ttt90) cc_final: 0.7880 (ttt90) REVERT: J 95 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8835 (tm-30) REVERT: J 102 GLU cc_start: 0.8856 (mt-10) cc_final: 0.7723 (tm-30) REVERT: J 113 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8067 (tm-30) REVERT: J 132 ASP cc_start: 0.7540 (t70) cc_final: 0.7185 (m-30) REVERT: K 65 GLU cc_start: 0.9243 (tt0) cc_final: 0.8987 (tm-30) REVERT: K 68 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8018 (tp30) REVERT: K 76 GLN cc_start: 0.8464 (mt0) cc_final: 0.7779 (mp10) REVERT: K 86 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7859 (tp) REVERT: K 168 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7931 (mp0) REVERT: L 24 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7975 (tm-30) REVERT: L 75 ASN cc_start: 0.9334 (t0) cc_final: 0.9054 (t0) REVERT: L 84 GLN cc_start: 0.7257 (mm110) cc_final: 0.6959 (mm-40) REVERT: L 90 ASP cc_start: 0.7745 (m-30) cc_final: 0.6322 (p0) REVERT: L 102 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7236 (pp20) REVERT: L 113 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: L 148 GLU cc_start: 0.8856 (tp30) cc_final: 0.8611 (tp30) REVERT: M 65 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7806 (tm-30) REVERT: M 68 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8323 (tt0) REVERT: M 71 MET cc_start: 0.9240 (ttm) cc_final: 0.9009 (ttm) REVERT: M 75 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8390 (t0) REVERT: M 81 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7510 (pp) REVERT: M 108 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7048 (tm-30) REVERT: N 132 ASP cc_start: 0.6307 (OUTLIER) cc_final: 0.5728 (m-30) REVERT: N 159 MET cc_start: 0.7927 (ttm) cc_final: 0.7480 (ttm) REVERT: N 173 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8055 (mptt) REVERT: O 36 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8789 (tm) REVERT: O 40 TYR cc_start: 0.8290 (m-80) cc_final: 0.8061 (m-10) REVERT: O 62 GLU cc_start: 0.8242 (mp0) cc_final: 0.7950 (mp0) REVERT: O 96 SER cc_start: 0.6935 (m) cc_final: 0.6656 (m) REVERT: O 169 TYR cc_start: 0.8519 (t80) cc_final: 0.8137 (t80) REVERT: P 43 ASP cc_start: 0.8748 (t70) cc_final: 0.8003 (t0) REVERT: P 51 ASN cc_start: 0.8866 (m110) cc_final: 0.8587 (m110) REVERT: P 68 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7435 (mt-10) REVERT: P 102 GLU cc_start: 0.9374 (mm-30) cc_final: 0.8984 (mm-30) REVERT: P 132 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7153 (t70) REVERT: Q 18 GLU cc_start: 0.8395 (tt0) cc_final: 0.7907 (tp30) REVERT: Q 55 TYR cc_start: 0.7298 (t80) cc_final: 0.6980 (t80) REVERT: Q 76 GLN cc_start: 0.8640 (mt0) cc_final: 0.8422 (mt0) REVERT: Q 169 TYR cc_start: 0.8969 (t80) cc_final: 0.8628 (t80) REVERT: R 8 GLN cc_start: 0.7905 (pt0) cc_final: 0.7618 (pm20) REVERT: R 11 GLN cc_start: 0.8666 (tt0) cc_final: 0.7776 (tm-30) REVERT: R 51 ASN cc_start: 0.8736 (m-40) cc_final: 0.8361 (m110) REVERT: R 74 GLN cc_start: 0.7682 (tp40) cc_final: 0.7308 (tp-100) REVERT: R 75 ASN cc_start: 0.8760 (t0) cc_final: 0.8373 (t0) REVERT: R 77 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.6918 (tpp80) REVERT: R 92 ASP cc_start: 0.8627 (m-30) cc_final: 0.8012 (p0) REVERT: R 154 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7535 (t) REVERT: S 11 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8373 (tm-30) REVERT: S 24 GLN cc_start: 0.7768 (tp40) cc_final: 0.7560 (tp40) REVERT: S 40 TYR cc_start: 0.8911 (m-80) cc_final: 0.8350 (m-80) REVERT: S 68 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7838 (mt-10) REVERT: S 80 ARG cc_start: 0.8134 (mmp80) cc_final: 0.7900 (mmp80) REVERT: S 87 LYS cc_start: 0.6483 (mmtt) cc_final: 0.5825 (pttp) REVERT: S 110 ASN cc_start: 0.7866 (m110) cc_final: 0.7543 (t0) REVERT: T 45 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7036 (p0) REVERT: T 84 GLN cc_start: 0.7235 (mm110) cc_final: 0.6963 (mm110) REVERT: U 11 GLN cc_start: 0.7988 (mp10) cc_final: 0.7484 (mm110) REVERT: U 43 ASP cc_start: 0.8682 (t70) cc_final: 0.8398 (t0) REVERT: U 54 LYS cc_start: 0.8428 (mttt) cc_final: 0.8034 (mtmp) REVERT: U 74 GLN cc_start: 0.7632 (tm130) cc_final: 0.7355 (tm-30) REVERT: U 80 ARG cc_start: 0.7814 (mpt-90) cc_final: 0.7285 (mpt90) REVERT: U 86 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7794 (tp) REVERT: U 144 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8572 (mppt) REVERT: V 18 GLU cc_start: 0.8192 (tt0) cc_final: 0.7656 (tp30) REVERT: V 64 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7177 (tmm-80) REVERT: V 68 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7115 (mt-10) REVERT: V 74 GLN cc_start: 0.8255 (tp-100) cc_final: 0.7788 (tp40) REVERT: V 80 ARG cc_start: 0.6723 (mmt-90) cc_final: 0.6106 (mmt180) REVERT: V 85 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: V 107 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8512 (tm) REVERT: V 117 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7461 (mp0) REVERT: W 62 GLU cc_start: 0.8431 (tt0) cc_final: 0.8036 (tp30) REVERT: W 68 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8573 (tt0) REVERT: W 74 GLN cc_start: 0.8862 (tp-100) cc_final: 0.8162 (tp-100) REVERT: W 76 GLN cc_start: 0.9226 (mt0) cc_final: 0.8849 (mt0) REVERT: W 80 ARG cc_start: 0.8828 (mmm-85) cc_final: 0.8370 (mpt180) REVERT: W 92 ASP cc_start: 0.7199 (m-30) cc_final: 0.6021 (p0) REVERT: X 62 GLU cc_start: 0.7497 (tt0) cc_final: 0.7151 (tm-30) REVERT: X 80 ARG cc_start: 0.7818 (mmt-90) cc_final: 0.7103 (tpp-160) outliers start: 233 outliers final: 96 residues processed: 832 average time/residue: 0.6962 time to fit residues: 693.9547 Evaluate side-chains 732 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 598 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 106 HIS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 76 GLN Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain N residue 22 ASN Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 132 ASP Chi-restraints excluded: chain P residue 147 LYS Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain Q residue 35 TYR Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain V residue 172 ASP Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 38 MET Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 134 ILE Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 364 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN C 24 GLN D 24 GLN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN G 126 ASN H 75 ASN H 140 ASN J 140 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN O 22 ASN O 24 GLN O 26 ASN P 106 HIS P 155 ASN Q 26 ASN R 12 ASN S 75 ASN T 66 HIS ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.123308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.110110 restraints weight = 70933.522| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 4.00 r_work: 0.3610 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34512 Z= 0.136 Angle : 0.625 12.232 46488 Z= 0.323 Chirality : 0.038 0.185 4896 Planarity : 0.004 0.070 6120 Dihedral : 4.236 24.771 4488 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.46 % Allowed : 29.88 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.13), residues: 4080 helix: 2.68 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -0.68 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 80 TYR 0.024 0.002 TYR G 169 PHE 0.032 0.001 PHE R 133 TRP 0.012 0.001 TRP A 94 HIS 0.013 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00295 (34512) covalent geometry : angle 0.62532 (46488) hydrogen bonds : bond 0.05077 ( 2139) hydrogen bonds : angle 3.77107 ( 6417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 702 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9244 (t0) cc_final: 0.8322 (t0) REVERT: A 22 ASN cc_start: 0.8214 (m110) cc_final: 0.7927 (m-40) REVERT: A 24 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: A 64 ARG cc_start: 0.8032 (ttt90) cc_final: 0.7606 (tmm-80) REVERT: A 76 GLN cc_start: 0.7799 (mt0) cc_final: 0.7413 (mt0) REVERT: A 172 ASP cc_start: 0.8952 (t70) cc_final: 0.8741 (t0) REVERT: B 24 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7211 (tm-30) REVERT: B 58 HIS cc_start: 0.7329 (t70) cc_final: 0.6949 (t70) REVERT: B 76 GLN cc_start: 0.7912 (mt0) cc_final: 0.7201 (mt0) REVERT: B 90 ASP cc_start: 0.8539 (m-30) cc_final: 0.8193 (p0) REVERT: B 123 THR cc_start: 0.7986 (m) cc_final: 0.7782 (p) REVERT: B 132 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: B 141 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8448 (mt-10) REVERT: B 148 GLU cc_start: 0.8890 (tp30) cc_final: 0.8529 (tp30) REVERT: C 13 TYR cc_start: 0.6920 (t80) cc_final: 0.6374 (t80) REVERT: C 24 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8576 (tp40) REVERT: C 43 ASP cc_start: 0.8597 (t0) cc_final: 0.8366 (t0) REVERT: C 45 ASP cc_start: 0.8566 (p0) cc_final: 0.7498 (t0) REVERT: C 62 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6755 (tp30) REVERT: C 86 ILE cc_start: 0.9081 (mt) cc_final: 0.8449 (tt) REVERT: C 90 ASP cc_start: 0.8779 (m-30) cc_final: 0.7945 (p0) REVERT: C 101 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8381 (mpp) REVERT: C 108 GLU cc_start: 0.8642 (tp30) cc_final: 0.8406 (mm-30) REVERT: C 124 ASP cc_start: 0.5686 (OUTLIER) cc_final: 0.4972 (p0) REVERT: C 127 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.6867 (t70) REVERT: C 173 LYS cc_start: 0.9211 (mmtt) cc_final: 0.8712 (mmtp) REVERT: D 16 ASP cc_start: 0.7978 (m-30) cc_final: 0.7381 (t0) REVERT: D 62 GLU cc_start: 0.7352 (mp0) cc_final: 0.6982 (mm-30) REVERT: D 75 ASN cc_start: 0.8606 (m-40) cc_final: 0.8053 (t0) REVERT: D 80 ARG cc_start: 0.7812 (mmt-90) cc_final: 0.7569 (mmp80) REVERT: D 99 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7722 (m110) REVERT: D 127 ASP cc_start: 0.6728 (t0) cc_final: 0.5521 (p0) REVERT: E 11 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8077 (tp-100) REVERT: E 18 GLU cc_start: 0.8780 (tt0) cc_final: 0.7903 (tp30) REVERT: E 43 ASP cc_start: 0.8973 (t0) cc_final: 0.8757 (t0) REVERT: E 45 ASP cc_start: 0.6946 (p0) cc_final: 0.5635 (t70) REVERT: E 62 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6930 (tm-30) REVERT: E 91 CYS cc_start: 0.5643 (m) cc_final: 0.5104 (m) REVERT: E 92 ASP cc_start: 0.8509 (m-30) cc_final: 0.7790 (OUTLIER) REVERT: E 113 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7835 (tm-30) REVERT: E 138 TYR cc_start: 0.7963 (m-10) cc_final: 0.7760 (m-10) REVERT: E 157 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7104 (ttp-110) REVERT: F 24 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8177 (tm-30) REVERT: F 38 MET cc_start: 0.8567 (mtp) cc_final: 0.8176 (ttm) REVERT: F 43 ASP cc_start: 0.8859 (t0) cc_final: 0.8377 (t0) REVERT: F 45 ASP cc_start: 0.7736 (p0) cc_final: 0.6077 (p0) REVERT: F 47 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8277 (m) REVERT: F 70 LEU cc_start: 0.8857 (tp) cc_final: 0.8576 (tm) REVERT: F 80 ARG cc_start: 0.8332 (mmm160) cc_final: 0.7135 (mmt-90) REVERT: F 85 ASP cc_start: 0.7354 (m-30) cc_final: 0.7058 (m-30) REVERT: F 90 ASP cc_start: 0.8862 (m-30) cc_final: 0.8282 (p0) REVERT: F 92 ASP cc_start: 0.8619 (m-30) cc_final: 0.7287 (t0) REVERT: F 106 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6716 (t70) REVERT: F 113 GLN cc_start: 0.9134 (tp-100) cc_final: 0.8844 (tm-30) REVERT: F 117 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8125 (tp30) REVERT: F 144 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7820 (mttp) REVERT: G 11 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8500 (tp-100) REVERT: G 18 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7524 (mt-10) REVERT: G 38 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8165 (mmm) REVERT: G 59 GLN cc_start: 0.9116 (tp40) cc_final: 0.8791 (tp40) REVERT: G 75 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8488 (t0) REVERT: G 106 HIS cc_start: 0.6650 (t-90) cc_final: 0.6001 (m-70) REVERT: G 146 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7672 (mm) REVERT: G 172 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8114 (m-30) REVERT: H 37 SER cc_start: 0.9247 (t) cc_final: 0.9043 (p) REVERT: H 46 ASP cc_start: 0.8262 (p0) cc_final: 0.8039 (t0) REVERT: H 50 LYS cc_start: 0.7530 (tppt) cc_final: 0.7284 (tppt) REVERT: H 65 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7925 (mm-30) REVERT: H 72 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7511 (tppt) REVERT: H 101 MET cc_start: 0.8826 (mtp) cc_final: 0.8571 (mtp) REVERT: H 127 ASP cc_start: 0.8370 (t0) cc_final: 0.7834 (t0) REVERT: I 21 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8211 (tt) REVERT: I 74 GLN cc_start: 0.8379 (tp40) cc_final: 0.7688 (tm-30) REVERT: I 76 GLN cc_start: 0.8534 (mt0) cc_final: 0.8311 (mt0) REVERT: I 90 ASP cc_start: 0.8378 (m-30) cc_final: 0.7330 (t0) REVERT: I 108 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: J 23 ARG cc_start: 0.8876 (mpp80) cc_final: 0.8575 (mpp80) REVERT: J 24 GLN cc_start: 0.9287 (tp40) cc_final: 0.8473 (tm-30) REVERT: J 64 ARG cc_start: 0.8182 (ttt90) cc_final: 0.7939 (ttt90) REVERT: J 71 MET cc_start: 0.9050 (ttm) cc_final: 0.8832 (ttm) REVERT: J 92 ASP cc_start: 0.7798 (m-30) cc_final: 0.7250 (p0) REVERT: J 95 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8843 (tm-30) REVERT: J 102 GLU cc_start: 0.8871 (mt-10) cc_final: 0.7767 (tm-30) REVERT: J 113 GLN cc_start: 0.8342 (tp-100) cc_final: 0.8054 (tm-30) REVERT: J 132 ASP cc_start: 0.7473 (t70) cc_final: 0.7109 (m-30) REVERT: J 169 TYR cc_start: 0.7521 (t80) cc_final: 0.7224 (t80) REVERT: K 38 MET cc_start: 0.8992 (tpp) cc_final: 0.8580 (mmm) REVERT: K 65 GLU cc_start: 0.9184 (tt0) cc_final: 0.8955 (tm-30) REVERT: K 68 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7953 (tp30) REVERT: K 86 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7975 (tp) REVERT: K 148 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7542 (mt-10) REVERT: K 168 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7825 (mp0) REVERT: L 24 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7915 (tm-30) REVERT: L 75 ASN cc_start: 0.9246 (t0) cc_final: 0.8979 (t0) REVERT: L 84 GLN cc_start: 0.7359 (mm110) cc_final: 0.7070 (mm-40) REVERT: L 87 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7290 (mmpt) REVERT: L 90 ASP cc_start: 0.7880 (m-30) cc_final: 0.6339 (p0) REVERT: L 102 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7142 (pp20) REVERT: L 113 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: L 148 GLU cc_start: 0.8829 (tp30) cc_final: 0.8561 (tp30) REVERT: M 63 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6409 (mm-30) REVERT: M 65 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7761 (tm-30) REVERT: M 68 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8284 (tt0) REVERT: M 71 MET cc_start: 0.9240 (ttm) cc_final: 0.8991 (ttm) REVERT: M 81 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7364 (pp) REVERT: M 108 GLU cc_start: 0.7820 (mm-30) cc_final: 0.6921 (tm-30) REVERT: N 132 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.5683 (m-30) REVERT: N 159 MET cc_start: 0.7952 (ttm) cc_final: 0.7623 (ttm) REVERT: N 168 GLU cc_start: 0.8553 (tt0) cc_final: 0.8285 (tm-30) REVERT: N 173 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7797 (mptm) REVERT: O 36 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8693 (tm) REVERT: O 40 TYR cc_start: 0.8216 (m-80) cc_final: 0.7998 (m-10) REVERT: O 62 GLU cc_start: 0.8286 (mp0) cc_final: 0.7985 (mp0) REVERT: O 96 SER cc_start: 0.6939 (m) cc_final: 0.6184 (p) REVERT: P 38 MET cc_start: 0.8642 (ttp) cc_final: 0.8004 (tmm) REVERT: P 43 ASP cc_start: 0.8738 (t70) cc_final: 0.7913 (t0) REVERT: P 51 ASN cc_start: 0.8823 (m110) cc_final: 0.8552 (m110) REVERT: P 64 ARG cc_start: 0.7867 (tmt170) cc_final: 0.7601 (tmt170) REVERT: P 68 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7439 (mt-10) REVERT: P 84 GLN cc_start: 0.7794 (mm110) cc_final: 0.7580 (mm110) REVERT: P 94 TRP cc_start: 0.8699 (m100) cc_final: 0.8331 (m-90) REVERT: P 102 GLU cc_start: 0.9365 (mm-30) cc_final: 0.8973 (mm-30) REVERT: Q 18 GLU cc_start: 0.8364 (tt0) cc_final: 0.8013 (tp30) REVERT: Q 55 TYR cc_start: 0.7261 (t80) cc_final: 0.6958 (t80) REVERT: Q 76 GLN cc_start: 0.8637 (mt0) cc_final: 0.8431 (mt0) REVERT: Q 169 TYR cc_start: 0.8826 (t80) cc_final: 0.8490 (t80) REVERT: R 8 GLN cc_start: 0.7866 (pt0) cc_final: 0.7554 (pm20) REVERT: R 11 GLN cc_start: 0.8653 (tt0) cc_final: 0.7683 (tm130) REVERT: R 51 ASN cc_start: 0.8823 (m-40) cc_final: 0.8334 (m110) REVERT: R 74 GLN cc_start: 0.7437 (tp40) cc_final: 0.7218 (tp-100) REVERT: R 75 ASN cc_start: 0.8695 (t0) cc_final: 0.8192 (t0) REVERT: R 77 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6884 (tpp80) REVERT: R 92 ASP cc_start: 0.8625 (m-30) cc_final: 0.8098 (p0) REVERT: R 154 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.7206 (t) REVERT: S 24 GLN cc_start: 0.7658 (tp40) cc_final: 0.7430 (tp40) REVERT: S 40 TYR cc_start: 0.8915 (m-80) cc_final: 0.8439 (m-80) REVERT: S 43 ASP cc_start: 0.8623 (t0) cc_final: 0.8346 (t0) REVERT: S 68 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7862 (mt-10) REVERT: S 87 LYS cc_start: 0.6432 (mmtt) cc_final: 0.5788 (pttp) REVERT: S 110 ASN cc_start: 0.7982 (m110) cc_final: 0.7675 (t0) REVERT: S 169 TYR cc_start: 0.8070 (t80) cc_final: 0.7837 (t80) REVERT: T 45 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7121 (p0) REVERT: T 84 GLN cc_start: 0.7195 (mm110) cc_final: 0.6942 (mm110) REVERT: T 92 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8183 (m-30) REVERT: U 11 GLN cc_start: 0.7977 (mp10) cc_final: 0.7475 (mm110) REVERT: U 18 GLU cc_start: 0.8661 (tm-30) cc_final: 0.7938 (tp30) REVERT: U 43 ASP cc_start: 0.8647 (t70) cc_final: 0.8306 (t0) REVERT: U 74 GLN cc_start: 0.7614 (tm130) cc_final: 0.6910 (tm-30) REVERT: U 80 ARG cc_start: 0.7910 (mpt-90) cc_final: 0.7569 (mpt90) REVERT: U 86 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7765 (tp) REVERT: U 144 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8527 (mppt) REVERT: V 18 GLU cc_start: 0.8115 (tt0) cc_final: 0.7558 (tp30) REVERT: V 64 ARG cc_start: 0.7633 (ttm-80) cc_final: 0.7095 (tmm-80) REVERT: V 68 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7064 (mt-10) REVERT: V 71 MET cc_start: 0.8111 (ttm) cc_final: 0.7481 (tmm) REVERT: V 74 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7872 (tp40) REVERT: V 80 ARG cc_start: 0.6705 (mmt-90) cc_final: 0.6124 (mmt180) REVERT: V 85 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: V 117 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7558 (mp0) REVERT: W 62 GLU cc_start: 0.8411 (tt0) cc_final: 0.8005 (tp30) REVERT: W 68 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8523 (tt0) REVERT: W 74 GLN cc_start: 0.8878 (tp-100) cc_final: 0.8211 (tp-100) REVERT: W 76 GLN cc_start: 0.9197 (mt0) cc_final: 0.8850 (mt0) REVERT: W 80 ARG cc_start: 0.8865 (mmm-85) cc_final: 0.8397 (mpt180) REVERT: W 92 ASP cc_start: 0.6787 (m-30) cc_final: 0.5985 (p0) REVERT: X 62 GLU cc_start: 0.7485 (tt0) cc_final: 0.7133 (tm-30) REVERT: X 80 ARG cc_start: 0.7705 (mmt-90) cc_final: 0.6964 (tpp-160) REVERT: X 84 GLN cc_start: 0.8580 (mp10) cc_final: 0.8336 (mm-40) outliers start: 199 outliers final: 83 residues processed: 849 average time/residue: 0.6669 time to fit residues: 683.1484 Evaluate side-chains 754 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 634 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 106 HIS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain Q residue 13 TYR Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 172 ASP Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 38 MET Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 279 optimal weight: 2.9990 chunk 288 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 239 optimal weight: 8.9990 chunk 370 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN C 24 GLN C 155 ASN D 24 GLN D 75 ASN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN G 51 ASN G 75 ASN G 126 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN N 24 GLN O 22 ASN O 24 GLN O 26 ASN P 74 GLN P 106 HIS Q 26 ASN R 12 ASN ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 155 ASN ** W 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.125172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.112295 restraints weight = 74558.718| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 4.06 r_work: 0.3572 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34512 Z= 0.175 Angle : 0.674 11.341 46488 Z= 0.348 Chirality : 0.040 0.194 4896 Planarity : 0.004 0.073 6120 Dihedral : 4.338 27.085 4488 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.32 % Allowed : 30.98 % Favored : 63.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.13), residues: 4080 helix: 2.54 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -0.79 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 80 TYR 0.030 0.002 TYR I 169 PHE 0.030 0.001 PHE R 133 TRP 0.022 0.002 TRP K 94 HIS 0.014 0.001 HIS R 152 Details of bonding type rmsd covalent geometry : bond 0.00392 (34512) covalent geometry : angle 0.67391 (46488) hydrogen bonds : bond 0.05464 ( 2139) hydrogen bonds : angle 4.00833 ( 6417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 649 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8267 (m110) cc_final: 0.7979 (m-40) REVERT: A 24 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: A 45 ASP cc_start: 0.6801 (p0) cc_final: 0.6405 (p0) REVERT: A 64 ARG cc_start: 0.8025 (ttt90) cc_final: 0.7711 (tmm-80) REVERT: A 172 ASP cc_start: 0.9046 (t70) cc_final: 0.8843 (t0) REVERT: B 24 GLN cc_start: 0.8427 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 40 TYR cc_start: 0.8796 (m-10) cc_final: 0.8328 (m-10) REVERT: B 58 HIS cc_start: 0.7512 (t70) cc_final: 0.7122 (t70) REVERT: B 76 GLN cc_start: 0.8223 (mt0) cc_final: 0.7427 (mt0) REVERT: B 90 ASP cc_start: 0.8670 (m-30) cc_final: 0.8389 (t0) REVERT: B 123 THR cc_start: 0.8035 (m) cc_final: 0.7820 (p) REVERT: B 141 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8468 (mt-10) REVERT: B 148 GLU cc_start: 0.8963 (tp30) cc_final: 0.8618 (tp30) REVERT: C 13 TYR cc_start: 0.7489 (t80) cc_final: 0.6921 (t80) REVERT: C 24 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8637 (tp40) REVERT: C 40 TYR cc_start: 0.8339 (m-10) cc_final: 0.8138 (m-10) REVERT: C 43 ASP cc_start: 0.8707 (t0) cc_final: 0.8407 (t0) REVERT: C 45 ASP cc_start: 0.8598 (p0) cc_final: 0.7730 (t0) REVERT: C 62 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6833 (tp30) REVERT: C 86 ILE cc_start: 0.9093 (mt) cc_final: 0.8520 (tt) REVERT: C 90 ASP cc_start: 0.8790 (m-30) cc_final: 0.7924 (p0) REVERT: C 101 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8307 (mpp) REVERT: C 108 GLU cc_start: 0.8707 (tp30) cc_final: 0.8433 (mm-30) REVERT: C 124 ASP cc_start: 0.5882 (OUTLIER) cc_final: 0.5105 (p0) REVERT: C 173 LYS cc_start: 0.9281 (mmtt) cc_final: 0.8703 (mmtm) REVERT: D 16 ASP cc_start: 0.7968 (m-30) cc_final: 0.7420 (t0) REVERT: D 27 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8113 (tm) REVERT: D 43 ASP cc_start: 0.9364 (t70) cc_final: 0.8722 (t0) REVERT: D 62 GLU cc_start: 0.7430 (mp0) cc_final: 0.6989 (tm-30) REVERT: D 75 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8362 (t0) REVERT: D 99 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7596 (m110) REVERT: D 127 ASP cc_start: 0.6723 (t0) cc_final: 0.5501 (p0) REVERT: E 11 GLN cc_start: 0.8603 (tp-100) cc_final: 0.8183 (tp-100) REVERT: E 18 GLU cc_start: 0.8843 (tt0) cc_final: 0.7999 (tp30) REVERT: E 43 ASP cc_start: 0.9052 (t0) cc_final: 0.8841 (t0) REVERT: E 45 ASP cc_start: 0.7230 (p0) cc_final: 0.5770 (t0) REVERT: E 62 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: E 91 CYS cc_start: 0.5275 (m) cc_final: 0.4653 (m) REVERT: E 92 ASP cc_start: 0.8590 (m-30) cc_final: 0.7894 (OUTLIER) REVERT: E 113 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7924 (tm-30) REVERT: E 117 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: E 157 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7264 (ttp-110) REVERT: F 24 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8246 (tm-30) REVERT: F 38 MET cc_start: 0.8567 (mtp) cc_final: 0.8150 (ttm) REVERT: F 45 ASP cc_start: 0.7811 (p0) cc_final: 0.6217 (p0) REVERT: F 47 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8326 (m) REVERT: F 80 ARG cc_start: 0.8379 (mmm160) cc_final: 0.7230 (mmt-90) REVERT: F 85 ASP cc_start: 0.7409 (m-30) cc_final: 0.7150 (m-30) REVERT: F 90 ASP cc_start: 0.8653 (m-30) cc_final: 0.8115 (p0) REVERT: F 92 ASP cc_start: 0.8534 (m-30) cc_final: 0.7245 (t0) REVERT: F 106 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.6683 (t70) REVERT: F 113 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8835 (tm-30) REVERT: F 144 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7913 (mttm) REVERT: G 18 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7618 (mt-10) REVERT: G 38 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8614 (mmm) REVERT: G 59 GLN cc_start: 0.9216 (tp40) cc_final: 0.8909 (tp40) REVERT: G 75 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8562 (t0) REVERT: G 172 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: H 18 GLU cc_start: 0.8180 (tt0) cc_final: 0.7418 (tm-30) REVERT: H 37 SER cc_start: 0.9292 (t) cc_final: 0.9088 (p) REVERT: H 46 ASP cc_start: 0.8214 (p0) cc_final: 0.7980 (t70) REVERT: H 50 LYS cc_start: 0.7871 (tppt) cc_final: 0.7639 (tppt) REVERT: H 65 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7957 (mm-30) REVERT: H 101 MET cc_start: 0.8878 (mtp) cc_final: 0.8614 (mtp) REVERT: H 127 ASP cc_start: 0.8369 (t0) cc_final: 0.7931 (t0) REVERT: I 21 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8337 (tt) REVERT: I 74 GLN cc_start: 0.8470 (tp40) cc_final: 0.7820 (tm-30) REVERT: I 90 ASP cc_start: 0.8423 (m-30) cc_final: 0.7472 (t0) REVERT: I 108 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: J 24 GLN cc_start: 0.9327 (tp40) cc_final: 0.8543 (tm-30) REVERT: J 68 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8259 (tm-30) REVERT: J 71 MET cc_start: 0.9002 (ttm) cc_final: 0.8767 (ttm) REVERT: J 95 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8882 (tm-30) REVERT: J 102 GLU cc_start: 0.8896 (mt-10) cc_final: 0.7771 (tm-30) REVERT: J 113 GLN cc_start: 0.8343 (tp-100) cc_final: 0.8017 (tm-30) REVERT: J 132 ASP cc_start: 0.7556 (t70) cc_final: 0.7196 (m-30) REVERT: K 30 TYR cc_start: 0.7609 (t80) cc_final: 0.7331 (t80) REVERT: K 45 ASP cc_start: 0.8087 (p0) cc_final: 0.7347 (t0) REVERT: K 65 GLU cc_start: 0.9192 (tt0) cc_final: 0.8973 (tm-30) REVERT: K 68 GLU cc_start: 0.8405 (tt0) cc_final: 0.8111 (tp30) REVERT: K 168 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7927 (mp0) REVERT: L 24 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7978 (tm-30) REVERT: L 75 ASN cc_start: 0.9288 (t0) cc_final: 0.9035 (t0) REVERT: L 84 GLN cc_start: 0.7523 (mm110) cc_final: 0.7265 (mm-40) REVERT: L 87 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7380 (mmpt) REVERT: L 90 ASP cc_start: 0.7920 (m-30) cc_final: 0.6302 (p0) REVERT: L 102 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7238 (pp20) REVERT: L 113 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: L 148 GLU cc_start: 0.8885 (tp30) cc_final: 0.8660 (tp30) REVERT: M 8 GLN cc_start: 0.7166 (pp30) cc_final: 0.6849 (pp30) REVERT: M 65 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7814 (tm-30) REVERT: M 68 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8317 (tt0) REVERT: M 71 MET cc_start: 0.9302 (ttm) cc_final: 0.9084 (ttm) REVERT: M 75 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8465 (t0) REVERT: M 81 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7356 (pp) REVERT: M 108 GLU cc_start: 0.7832 (mm-30) cc_final: 0.6942 (tm-30) REVERT: N 71 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8459 (ptp) REVERT: N 101 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8539 (mpp) REVERT: N 132 ASP cc_start: 0.6358 (OUTLIER) cc_final: 0.5766 (m-30) REVERT: N 159 MET cc_start: 0.8061 (ttm) cc_final: 0.7726 (ttm) REVERT: N 168 GLU cc_start: 0.8606 (tt0) cc_final: 0.8376 (pp20) REVERT: O 36 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8786 (tm) REVERT: O 62 GLU cc_start: 0.8328 (mp0) cc_final: 0.8029 (mp0) REVERT: O 96 SER cc_start: 0.7174 (m) cc_final: 0.6897 (m) REVERT: P 38 MET cc_start: 0.8761 (ttp) cc_final: 0.8126 (tmm) REVERT: P 43 ASP cc_start: 0.8808 (t70) cc_final: 0.8093 (t0) REVERT: P 51 ASN cc_start: 0.8882 (m110) cc_final: 0.8562 (m110) REVERT: P 68 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7418 (mp0) REVERT: P 94 TRP cc_start: 0.8686 (m100) cc_final: 0.8333 (m-90) REVERT: P 102 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9031 (mm-30) REVERT: Q 18 GLU cc_start: 0.8416 (tt0) cc_final: 0.8118 (tp30) REVERT: Q 55 TYR cc_start: 0.7376 (t80) cc_final: 0.7035 (t80) REVERT: Q 76 GLN cc_start: 0.8760 (mt0) cc_final: 0.8513 (mt0) REVERT: Q 92 ASP cc_start: 0.8039 (m-30) cc_final: 0.7634 (t0) REVERT: Q 169 TYR cc_start: 0.8987 (t80) cc_final: 0.8581 (t80) REVERT: R 8 GLN cc_start: 0.7988 (pt0) cc_final: 0.7640 (pm20) REVERT: R 51 ASN cc_start: 0.8860 (m-40) cc_final: 0.8452 (m110) REVERT: R 74 GLN cc_start: 0.7678 (tp40) cc_final: 0.7406 (tp-100) REVERT: R 75 ASN cc_start: 0.8890 (t0) cc_final: 0.8536 (t0) REVERT: R 77 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7034 (tpp80) REVERT: R 92 ASP cc_start: 0.8563 (m-30) cc_final: 0.8045 (p0) REVERT: R 154 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7646 (t) REVERT: S 24 GLN cc_start: 0.7909 (tp40) cc_final: 0.7700 (tp40) REVERT: S 40 TYR cc_start: 0.8886 (m-80) cc_final: 0.8354 (m-80) REVERT: S 43 ASP cc_start: 0.8690 (t0) cc_final: 0.8396 (t0) REVERT: S 68 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7952 (mt-10) REVERT: S 86 ILE cc_start: 0.8163 (mm) cc_final: 0.7604 (tp) REVERT: S 87 LYS cc_start: 0.6569 (mmtt) cc_final: 0.5846 (pttp) REVERT: T 38 MET cc_start: 0.8539 (tpp) cc_final: 0.8115 (mmm) REVERT: T 45 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7164 (p0) REVERT: T 84 GLN cc_start: 0.7297 (mm110) cc_final: 0.7061 (mm110) REVERT: T 139 LEU cc_start: 0.8412 (mt) cc_final: 0.7893 (tm) REVERT: U 11 GLN cc_start: 0.8014 (mp10) cc_final: 0.7535 (mm110) REVERT: U 43 ASP cc_start: 0.8737 (t70) cc_final: 0.8460 (t0) REVERT: U 54 LYS cc_start: 0.8465 (mttt) cc_final: 0.8013 (mtmp) REVERT: U 74 GLN cc_start: 0.7624 (tm130) cc_final: 0.7317 (tm-30) REVERT: U 80 ARG cc_start: 0.7890 (mpt-90) cc_final: 0.7390 (mpt90) REVERT: U 86 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7958 (tp) REVERT: U 144 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8516 (mppt) REVERT: V 18 GLU cc_start: 0.8203 (tt0) cc_final: 0.7709 (tp30) REVERT: V 64 ARG cc_start: 0.7793 (ttm-80) cc_final: 0.7264 (tmm-80) REVERT: V 68 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: V 74 GLN cc_start: 0.8346 (tp-100) cc_final: 0.7977 (tp40) REVERT: V 80 ARG cc_start: 0.7004 (mmt-90) cc_final: 0.6239 (mmt180) REVERT: V 85 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7799 (m-30) REVERT: W 24 GLN cc_start: 0.9216 (tm-30) cc_final: 0.8710 (tp-100) REVERT: W 38 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8085 (tpp) REVERT: W 62 GLU cc_start: 0.8480 (tt0) cc_final: 0.8084 (tp30) REVERT: W 68 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8632 (tt0) REVERT: W 74 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8243 (tp-100) REVERT: W 76 GLN cc_start: 0.9191 (mt0) cc_final: 0.8805 (mt0) REVERT: W 80 ARG cc_start: 0.8885 (mmm-85) cc_final: 0.8450 (mpt180) REVERT: W 92 ASP cc_start: 0.7239 (m-30) cc_final: 0.6054 (p0) REVERT: X 62 GLU cc_start: 0.7567 (tt0) cc_final: 0.7128 (tm-30) REVERT: X 80 ARG cc_start: 0.7782 (mmt-90) cc_final: 0.7079 (tpp-160) REVERT: X 84 GLN cc_start: 0.8584 (mp10) cc_final: 0.8331 (mm110) outliers start: 194 outliers final: 95 residues processed: 792 average time/residue: 0.6839 time to fit residues: 649.4390 Evaluate side-chains 742 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 612 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 106 HIS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 71 MET Chi-restraints excluded: chain N residue 101 MET Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain Q residue 35 TYR Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 75 ASN Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain V residue 172 ASP Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 38 MET Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 134 ILE Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 217 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 384 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 211 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN D 24 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN G 75 ASN G 126 ASN H 24 GLN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN I 76 GLN J 140 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS M 11 GLN M 84 GLN ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN O 22 ASN O 24 GLN ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 HIS Q 26 ASN R 12 ASN ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.119708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.106987 restraints weight = 73242.980| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 4.03 r_work: 0.3597 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.6810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34512 Z= 0.151 Angle : 0.664 13.039 46488 Z= 0.344 Chirality : 0.039 0.176 4896 Planarity : 0.004 0.075 6120 Dihedral : 4.291 27.039 4488 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.52 % Allowed : 32.15 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.13), residues: 4080 helix: 2.62 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -0.77 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG P 77 TYR 0.026 0.002 TYR G 169 PHE 0.031 0.001 PHE R 133 TRP 0.019 0.001 TRP K 94 HIS 0.013 0.001 HIS P 106 Details of bonding type rmsd covalent geometry : bond 0.00332 (34512) covalent geometry : angle 0.66401 (46488) hydrogen bonds : bond 0.05215 ( 2139) hydrogen bonds : angle 3.88903 ( 6417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 672 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9275 (t0) cc_final: 0.8320 (t0) REVERT: A 22 ASN cc_start: 0.8292 (m110) cc_final: 0.8017 (m-40) REVERT: A 24 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: A 45 ASP cc_start: 0.6856 (p0) cc_final: 0.6460 (p0) REVERT: A 64 ARG cc_start: 0.7959 (ttt90) cc_final: 0.7629 (tmm-80) REVERT: B 24 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7320 (tm-30) REVERT: B 40 TYR cc_start: 0.8752 (m-10) cc_final: 0.8417 (m-10) REVERT: B 58 HIS cc_start: 0.7401 (t70) cc_final: 0.7014 (t70) REVERT: B 76 GLN cc_start: 0.7920 (mt0) cc_final: 0.7128 (mt0) REVERT: B 123 THR cc_start: 0.8076 (m) cc_final: 0.7871 (p) REVERT: B 141 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8485 (mt-10) REVERT: B 148 GLU cc_start: 0.8955 (tp30) cc_final: 0.8608 (tp30) REVERT: C 13 TYR cc_start: 0.7397 (t80) cc_final: 0.6772 (t80) REVERT: C 43 ASP cc_start: 0.8659 (t0) cc_final: 0.8141 (t0) REVERT: C 45 ASP cc_start: 0.8586 (p0) cc_final: 0.7804 (t0) REVERT: C 62 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6781 (tp30) REVERT: C 86 ILE cc_start: 0.9140 (mt) cc_final: 0.8544 (tt) REVERT: C 90 ASP cc_start: 0.8907 (m-30) cc_final: 0.7991 (p0) REVERT: C 101 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8357 (mpp) REVERT: C 108 GLU cc_start: 0.8697 (tp30) cc_final: 0.8451 (mm-30) REVERT: C 124 ASP cc_start: 0.5775 (OUTLIER) cc_final: 0.5043 (p0) REVERT: C 127 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7545 (t70) REVERT: C 173 LYS cc_start: 0.9259 (mmtt) cc_final: 0.8687 (mmtm) REVERT: D 16 ASP cc_start: 0.8010 (m-30) cc_final: 0.7433 (t0) REVERT: D 27 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8031 (tm) REVERT: D 43 ASP cc_start: 0.9295 (t70) cc_final: 0.8671 (t0) REVERT: D 62 GLU cc_start: 0.7363 (mp0) cc_final: 0.6952 (tm-30) REVERT: D 75 ASN cc_start: 0.8816 (m-40) cc_final: 0.8289 (t0) REVERT: D 80 ARG cc_start: 0.7966 (mmt-90) cc_final: 0.7217 (mmp80) REVERT: D 99 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7542 (m110) REVERT: D 127 ASP cc_start: 0.6862 (t0) cc_final: 0.5623 (p0) REVERT: E 11 GLN cc_start: 0.8520 (tp-100) cc_final: 0.8125 (tp-100) REVERT: E 18 GLU cc_start: 0.8791 (tt0) cc_final: 0.8154 (tp30) REVERT: E 43 ASP cc_start: 0.8984 (t0) cc_final: 0.8750 (t0) REVERT: E 45 ASP cc_start: 0.7159 (p0) cc_final: 0.5836 (t0) REVERT: E 91 CYS cc_start: 0.5547 (m) cc_final: 0.5107 (p) REVERT: E 92 ASP cc_start: 0.8616 (m-30) cc_final: 0.7934 (t0) REVERT: E 113 GLN cc_start: 0.8138 (tp-100) cc_final: 0.7889 (tm-30) REVERT: E 117 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: E 144 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8285 (mmtp) REVERT: E 157 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7129 (ttp-110) REVERT: F 24 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8134 (tm-30) REVERT: F 38 MET cc_start: 0.8541 (mtp) cc_final: 0.8133 (ttm) REVERT: F 45 ASP cc_start: 0.7757 (p0) cc_final: 0.6054 (p0) REVERT: F 47 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8200 (m) REVERT: F 70 LEU cc_start: 0.8691 (tp) cc_final: 0.8484 (tm) REVERT: F 80 ARG cc_start: 0.8193 (mmm160) cc_final: 0.7232 (mmt90) REVERT: F 85 ASP cc_start: 0.7371 (m-30) cc_final: 0.6978 (m-30) REVERT: F 90 ASP cc_start: 0.8667 (m-30) cc_final: 0.8131 (p0) REVERT: F 92 ASP cc_start: 0.8566 (m-30) cc_final: 0.7278 (t0) REVERT: F 106 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6723 (t70) REVERT: F 113 GLN cc_start: 0.9156 (tp-100) cc_final: 0.8538 (tm-30) REVERT: F 144 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7856 (mttp) REVERT: F 169 TYR cc_start: 0.8434 (t80) cc_final: 0.7973 (t80) REVERT: G 18 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7330 (mt-10) REVERT: G 38 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8590 (mmm) REVERT: G 59 GLN cc_start: 0.9185 (tp40) cc_final: 0.8872 (tp40) REVERT: G 71 MET cc_start: 0.8863 (mtm) cc_final: 0.8629 (mtm) REVERT: G 75 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8534 (t0) REVERT: G 172 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8194 (m-30) REVERT: H 18 GLU cc_start: 0.8136 (tt0) cc_final: 0.7361 (tm-30) REVERT: H 37 SER cc_start: 0.9260 (t) cc_final: 0.9056 (p) REVERT: H 46 ASP cc_start: 0.8211 (p0) cc_final: 0.7998 (t0) REVERT: H 50 LYS cc_start: 0.7640 (tppt) cc_final: 0.7392 (tppt) REVERT: H 65 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: H 101 MET cc_start: 0.8819 (mtp) cc_final: 0.8553 (mtp) REVERT: H 127 ASP cc_start: 0.8378 (t0) cc_final: 0.8024 (t0) REVERT: I 21 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8247 (tt) REVERT: I 74 GLN cc_start: 0.8333 (tp40) cc_final: 0.7785 (tm-30) REVERT: I 90 ASP cc_start: 0.8487 (m-30) cc_final: 0.7554 (t0) REVERT: I 108 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: J 23 ARG cc_start: 0.8881 (mpp80) cc_final: 0.8576 (mpp80) REVERT: J 24 GLN cc_start: 0.9304 (tp40) cc_final: 0.8504 (tm-30) REVERT: J 71 MET cc_start: 0.8853 (ttm) cc_final: 0.8513 (ttm) REVERT: J 95 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8858 (tm-30) REVERT: J 102 GLU cc_start: 0.8881 (mt-10) cc_final: 0.7754 (tm-30) REVERT: J 113 GLN cc_start: 0.8262 (tp-100) cc_final: 0.7968 (tm-30) REVERT: J 132 ASP cc_start: 0.7465 (t70) cc_final: 0.7098 (m-30) REVERT: K 65 GLU cc_start: 0.9140 (tt0) cc_final: 0.8914 (tm-30) REVERT: K 68 GLU cc_start: 0.8547 (tt0) cc_final: 0.8132 (tp30) REVERT: K 168 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7940 (mp0) REVERT: L 24 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7873 (tm-30) REVERT: L 75 ASN cc_start: 0.9256 (t0) cc_final: 0.8998 (t0) REVERT: L 84 GLN cc_start: 0.7445 (mm110) cc_final: 0.7187 (mm-40) REVERT: L 87 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7427 (mmpt) REVERT: L 90 ASP cc_start: 0.7969 (m-30) cc_final: 0.6307 (p0) REVERT: L 102 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7167 (pp20) REVERT: L 113 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8045 (pt0) REVERT: L 148 GLU cc_start: 0.8846 (tp30) cc_final: 0.8624 (tp30) REVERT: M 8 GLN cc_start: 0.7173 (pp30) cc_final: 0.6849 (pp30) REVERT: M 65 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7757 (tm-30) REVERT: M 74 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7485 (tm-30) REVERT: M 81 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7296 (pp) REVERT: M 108 GLU cc_start: 0.7901 (mm-30) cc_final: 0.6856 (tm-30) REVERT: M 133 PHE cc_start: 0.7811 (t80) cc_final: 0.7571 (t80) REVERT: N 71 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8515 (ptp) REVERT: N 101 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8492 (mpp) REVERT: N 132 ASP cc_start: 0.6249 (OUTLIER) cc_final: 0.5577 (m-30) REVERT: N 159 MET cc_start: 0.7985 (ttm) cc_final: 0.7661 (ttm) REVERT: N 168 GLU cc_start: 0.8551 (tt0) cc_final: 0.8322 (pp20) REVERT: O 62 GLU cc_start: 0.8298 (mp0) cc_final: 0.7986 (mp0) REVERT: O 75 ASN cc_start: 0.8711 (m110) cc_final: 0.8362 (t160) REVERT: O 96 SER cc_start: 0.6975 (m) cc_final: 0.6210 (p) REVERT: P 38 MET cc_start: 0.8776 (ttp) cc_final: 0.8125 (tmm) REVERT: P 43 ASP cc_start: 0.8846 (t70) cc_final: 0.8135 (t0) REVERT: P 51 ASN cc_start: 0.8843 (m110) cc_final: 0.8548 (m110) REVERT: P 68 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7469 (mt-10) REVERT: P 94 TRP cc_start: 0.8607 (m100) cc_final: 0.8318 (m-90) REVERT: P 98 LEU cc_start: 0.8463 (tp) cc_final: 0.7905 (tm) REVERT: P 102 GLU cc_start: 0.9347 (mm-30) cc_final: 0.8926 (mm-30) REVERT: P 133 PHE cc_start: 0.9018 (t80) cc_final: 0.8555 (t80) REVERT: Q 18 GLU cc_start: 0.8393 (tt0) cc_final: 0.8071 (tp30) REVERT: Q 55 TYR cc_start: 0.7232 (t80) cc_final: 0.6964 (t80) REVERT: Q 76 GLN cc_start: 0.8759 (mt0) cc_final: 0.8510 (mt0) REVERT: Q 92 ASP cc_start: 0.8068 (m-30) cc_final: 0.7609 (t0) REVERT: Q 169 TYR cc_start: 0.8848 (t80) cc_final: 0.8494 (t80) REVERT: R 8 GLN cc_start: 0.7937 (pt0) cc_final: 0.7587 (pm20) REVERT: R 51 ASN cc_start: 0.8897 (m-40) cc_final: 0.8420 (m110) REVERT: R 75 ASN cc_start: 0.8834 (t0) cc_final: 0.8533 (t0) REVERT: R 77 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6914 (tpp80) REVERT: R 85 ASP cc_start: 0.8120 (m-30) cc_final: 0.7635 (t0) REVERT: R 92 ASP cc_start: 0.8439 (m-30) cc_final: 0.8031 (p0) REVERT: R 154 THR cc_start: 0.7763 (OUTLIER) cc_final: 0.7193 (t) REVERT: S 40 TYR cc_start: 0.8931 (m-80) cc_final: 0.8377 (m-80) REVERT: S 68 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7978 (mt-10) REVERT: S 87 LYS cc_start: 0.6477 (mmtt) cc_final: 0.5777 (pttp) REVERT: T 38 MET cc_start: 0.8467 (tpp) cc_final: 0.8055 (mmt) REVERT: T 45 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7200 (p0) REVERT: T 84 GLN cc_start: 0.7246 (mm110) cc_final: 0.7013 (mm110) REVERT: T 92 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: T 139 LEU cc_start: 0.8437 (mt) cc_final: 0.7950 (tm) REVERT: U 11 GLN cc_start: 0.7976 (mp10) cc_final: 0.7532 (mm110) REVERT: U 18 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7563 (tp30) REVERT: U 43 ASP cc_start: 0.8691 (t70) cc_final: 0.8410 (t0) REVERT: U 74 GLN cc_start: 0.7551 (tm130) cc_final: 0.6598 (tm130) REVERT: U 80 ARG cc_start: 0.7954 (mpt-90) cc_final: 0.7519 (mpt90) REVERT: U 86 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7933 (tp) REVERT: V 64 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.7159 (tmm-80) REVERT: V 68 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7208 (mt-10) REVERT: V 71 MET cc_start: 0.8115 (ttm) cc_final: 0.7550 (tmm) REVERT: V 80 ARG cc_start: 0.6990 (mmt-90) cc_final: 0.6713 (mmt180) REVERT: V 85 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: W 24 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8660 (tp-100) REVERT: W 62 GLU cc_start: 0.8428 (tt0) cc_final: 0.8020 (tp30) REVERT: W 68 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8507 (tt0) REVERT: W 74 GLN cc_start: 0.8897 (tp-100) cc_final: 0.8237 (tp-100) REVERT: W 76 GLN cc_start: 0.9184 (mt0) cc_final: 0.8828 (mt0) REVERT: W 80 ARG cc_start: 0.8857 (mmm-85) cc_final: 0.8396 (mpt180) REVERT: W 92 ASP cc_start: 0.7217 (m-30) cc_final: 0.6052 (p0) REVERT: X 62 GLU cc_start: 0.7522 (tt0) cc_final: 0.7160 (tm-30) REVERT: X 80 ARG cc_start: 0.7732 (mmt-90) cc_final: 0.7005 (tpp-160) REVERT: X 84 GLN cc_start: 0.8601 (mp10) cc_final: 0.8368 (mm-40) outliers start: 165 outliers final: 81 residues processed: 791 average time/residue: 0.6804 time to fit residues: 646.2442 Evaluate side-chains 737 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 624 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 106 HIS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 71 MET Chi-restraints excluded: chain N residue 101 MET Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain Q residue 35 TYR Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain R residue 12 ASN Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain V residue 172 ASP Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 38 MET Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 86 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 48 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 406 optimal weight: 0.2980 chunk 85 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 302 optimal weight: 0.9990 chunk 277 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 391 optimal weight: 0.9980 chunk 375 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN C 24 GLN D 24 GLN E 74 GLN E 75 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 HIS G 51 ASN G 75 ASN G 126 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 HIS I 76 GLN J 140 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS L 129 HIS M 11 GLN M 84 GLN ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 ASN O 24 GLN O 26 ASN P 106 HIS Q 26 ASN R 12 ASN ** R 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 GLN U 26 ASN V 75 ASN V 137 HIS ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.126070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.112853 restraints weight = 70526.662| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 4.00 r_work: 0.3646 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.7061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34512 Z= 0.131 Angle : 0.673 13.807 46488 Z= 0.343 Chirality : 0.038 0.197 4896 Planarity : 0.004 0.080 6120 Dihedral : 4.220 29.395 4488 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.99 % Allowed : 34.16 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.13), residues: 4080 helix: 2.80 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -0.69 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG N 80 TYR 0.033 0.002 TYR R 13 PHE 0.031 0.001 PHE R 133 TRP 0.016 0.001 TRP K 94 HIS 0.013 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00284 (34512) covalent geometry : angle 0.67292 (46488) hydrogen bonds : bond 0.04522 ( 2139) hydrogen bonds : angle 3.63806 ( 6417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 745 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9286 (t0) cc_final: 0.8327 (t0) REVERT: A 22 ASN cc_start: 0.8311 (m110) cc_final: 0.7993 (m-40) REVERT: A 64 ARG cc_start: 0.8005 (ttt90) cc_final: 0.7675 (tmm-80) REVERT: A 133 PHE cc_start: 0.8436 (t80) cc_final: 0.8164 (t80) REVERT: B 24 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7124 (tm-30) REVERT: B 40 TYR cc_start: 0.8744 (m-10) cc_final: 0.8414 (m-10) REVERT: B 58 HIS cc_start: 0.7267 (t70) cc_final: 0.6892 (t70) REVERT: B 76 GLN cc_start: 0.7900 (mt0) cc_final: 0.7215 (mt0) REVERT: B 80 ARG cc_start: 0.8290 (mmt180) cc_final: 0.7966 (mmt180) REVERT: B 141 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8491 (mt-10) REVERT: B 148 GLU cc_start: 0.8895 (tp30) cc_final: 0.8570 (tp30) REVERT: C 43 ASP cc_start: 0.8513 (t0) cc_final: 0.8064 (t0) REVERT: C 45 ASP cc_start: 0.8505 (p0) cc_final: 0.7761 (t0) REVERT: C 62 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6934 (tp30) REVERT: C 86 ILE cc_start: 0.9063 (mt) cc_final: 0.8442 (tt) REVERT: C 90 ASP cc_start: 0.8875 (m-30) cc_final: 0.8011 (p0) REVERT: C 108 GLU cc_start: 0.8629 (tp30) cc_final: 0.8383 (mm-30) REVERT: C 124 ASP cc_start: 0.5508 (OUTLIER) cc_final: 0.4837 (p0) REVERT: C 127 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7409 (t70) REVERT: C 173 LYS cc_start: 0.9219 (mmtt) cc_final: 0.8670 (mmtp) REVERT: D 16 ASP cc_start: 0.7974 (m-30) cc_final: 0.7399 (t0) REVERT: D 43 ASP cc_start: 0.9249 (t70) cc_final: 0.8571 (t0) REVERT: D 62 GLU cc_start: 0.7353 (mp0) cc_final: 0.7031 (mm-30) REVERT: D 75 ASN cc_start: 0.8685 (m-40) cc_final: 0.8226 (t0) REVERT: D 127 ASP cc_start: 0.6845 (t0) cc_final: 0.5746 (p0) REVERT: E 11 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8068 (tp-100) REVERT: E 18 GLU cc_start: 0.8768 (tt0) cc_final: 0.8224 (tp30) REVERT: E 43 ASP cc_start: 0.8887 (t0) cc_final: 0.8641 (t0) REVERT: E 45 ASP cc_start: 0.7135 (p0) cc_final: 0.5739 (t0) REVERT: E 91 CYS cc_start: 0.5537 (m) cc_final: 0.5153 (p) REVERT: E 92 ASP cc_start: 0.8623 (m-30) cc_final: 0.7986 (t0) REVERT: E 113 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7920 (tm-30) REVERT: E 117 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: E 157 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7140 (ttp-110) REVERT: F 24 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8112 (tm-30) REVERT: F 38 MET cc_start: 0.8389 (mtp) cc_final: 0.8036 (ttm) REVERT: F 43 ASP cc_start: 0.9093 (t0) cc_final: 0.8583 (t0) REVERT: F 45 ASP cc_start: 0.7725 (p0) cc_final: 0.6443 (p0) REVERT: F 47 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8378 (m) REVERT: F 80 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7080 (mmt90) REVERT: F 85 ASP cc_start: 0.7450 (m-30) cc_final: 0.6743 (m-30) REVERT: F 90 ASP cc_start: 0.8658 (m-30) cc_final: 0.8132 (p0) REVERT: F 92 ASP cc_start: 0.8570 (m-30) cc_final: 0.7244 (t0) REVERT: F 113 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8554 (tm-30) REVERT: F 144 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7873 (mttp) REVERT: F 169 TYR cc_start: 0.8317 (t80) cc_final: 0.7835 (t80) REVERT: G 18 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7538 (mt-10) REVERT: G 38 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8163 (mmt) REVERT: G 59 GLN cc_start: 0.9141 (tp40) cc_final: 0.8814 (tp40) REVERT: G 72 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7416 (tmmm) REVERT: G 75 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8623 (t0) REVERT: H 18 GLU cc_start: 0.7966 (tt0) cc_final: 0.7254 (tm-30) REVERT: H 37 SER cc_start: 0.9229 (t) cc_final: 0.9005 (p) REVERT: H 46 ASP cc_start: 0.8206 (p0) cc_final: 0.7792 (t0) REVERT: H 65 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: H 101 MET cc_start: 0.8839 (mtp) cc_final: 0.8548 (mtp) REVERT: H 127 ASP cc_start: 0.8409 (t0) cc_final: 0.7739 (t70) REVERT: H 134 ILE cc_start: 0.8862 (mm) cc_final: 0.8625 (tt) REVERT: I 21 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8236 (tt) REVERT: I 74 GLN cc_start: 0.8330 (tp40) cc_final: 0.7806 (tm-30) REVERT: I 90 ASP cc_start: 0.8433 (m-30) cc_final: 0.7521 (t0) REVERT: I 108 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: I 159 MET cc_start: 0.7411 (mtp) cc_final: 0.7117 (mmm) REVERT: J 23 ARG cc_start: 0.8899 (mpp80) cc_final: 0.8409 (ptt-90) REVERT: J 24 GLN cc_start: 0.9271 (tp40) cc_final: 0.8543 (tm-30) REVERT: J 71 MET cc_start: 0.8891 (ttm) cc_final: 0.8656 (ttm) REVERT: J 95 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8783 (tm-30) REVERT: J 102 GLU cc_start: 0.8616 (mt-10) cc_final: 0.7642 (tm-30) REVERT: J 113 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7871 (tm-30) REVERT: J 132 ASP cc_start: 0.7653 (t70) cc_final: 0.7083 (m-30) REVERT: K 45 ASP cc_start: 0.7925 (p0) cc_final: 0.7287 (t0) REVERT: K 68 GLU cc_start: 0.8583 (tt0) cc_final: 0.8128 (tp30) REVERT: K 76 GLN cc_start: 0.8261 (mt0) cc_final: 0.7695 (mt0) REVERT: K 168 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7848 (mp0) REVERT: L 24 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7819 (tm-30) REVERT: L 75 ASN cc_start: 0.9178 (t0) cc_final: 0.8959 (t0) REVERT: L 84 GLN cc_start: 0.7433 (mm110) cc_final: 0.7193 (mm-40) REVERT: L 87 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7484 (mmpt) REVERT: L 90 ASP cc_start: 0.7999 (m-30) cc_final: 0.6320 (p0) REVERT: L 102 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7126 (pp20) REVERT: L 113 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: M 63 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6407 (mm-30) REVERT: M 65 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7742 (tm-30) REVERT: M 73 LEU cc_start: 0.8258 (tt) cc_final: 0.8017 (tp) REVERT: M 75 ASN cc_start: 0.8586 (t0) cc_final: 0.8351 (t0) REVERT: M 108 GLU cc_start: 0.7856 (mm-30) cc_final: 0.6796 (tm-30) REVERT: N 71 MET cc_start: 0.8751 (ptp) cc_final: 0.8507 (ptp) REVERT: N 101 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8612 (mpp) REVERT: N 132 ASP cc_start: 0.6362 (OUTLIER) cc_final: 0.5753 (m-30) REVERT: N 159 MET cc_start: 0.7906 (ttm) cc_final: 0.7593 (ttm) REVERT: N 168 GLU cc_start: 0.8508 (tt0) cc_final: 0.8308 (pp20) REVERT: O 62 GLU cc_start: 0.8251 (mp0) cc_final: 0.7928 (mp0) REVERT: O 96 SER cc_start: 0.6831 (m) cc_final: 0.6071 (p) REVERT: P 38 MET cc_start: 0.8848 (ttp) cc_final: 0.8261 (tmm) REVERT: P 43 ASP cc_start: 0.8604 (t70) cc_final: 0.7736 (t0) REVERT: P 51 ASN cc_start: 0.8846 (m110) cc_final: 0.8559 (m110) REVERT: P 64 ARG cc_start: 0.7994 (tmt170) cc_final: 0.7763 (tmt170) REVERT: P 77 ARG cc_start: 0.8173 (mmm160) cc_final: 0.7855 (tpp80) REVERT: P 102 GLU cc_start: 0.9342 (mm-30) cc_final: 0.9036 (mm-30) REVERT: P 133 PHE cc_start: 0.8927 (t80) cc_final: 0.8539 (t80) REVERT: Q 18 GLU cc_start: 0.8278 (tt0) cc_final: 0.8049 (tp30) REVERT: Q 55 TYR cc_start: 0.7238 (t80) cc_final: 0.6674 (t80) REVERT: Q 76 GLN cc_start: 0.8714 (mt0) cc_final: 0.8415 (mt0) REVERT: Q 169 TYR cc_start: 0.8803 (t80) cc_final: 0.8518 (t80) REVERT: R 8 GLN cc_start: 0.7928 (pt0) cc_final: 0.7642 (pm20) REVERT: R 51 ASN cc_start: 0.8825 (m-40) cc_final: 0.8362 (m110) REVERT: R 75 ASN cc_start: 0.8796 (t0) cc_final: 0.8519 (t0) REVERT: R 77 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6949 (tpp80) REVERT: R 85 ASP cc_start: 0.8084 (m-30) cc_final: 0.7473 (t0) REVERT: R 92 ASP cc_start: 0.8480 (m-30) cc_final: 0.8096 (p0) REVERT: R 154 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7180 (t) REVERT: S 40 TYR cc_start: 0.8913 (m-80) cc_final: 0.8470 (m-80) REVERT: S 68 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7978 (mt-10) REVERT: S 80 ARG cc_start: 0.8034 (mmp-170) cc_final: 0.7619 (mmp80) REVERT: S 86 ILE cc_start: 0.8137 (mm) cc_final: 0.7622 (tp) REVERT: S 87 LYS cc_start: 0.6514 (mmtt) cc_final: 0.5798 (pttp) REVERT: S 132 ASP cc_start: 0.8063 (t70) cc_final: 0.7825 (t70) REVERT: T 38 MET cc_start: 0.8485 (tpp) cc_final: 0.8093 (mmt) REVERT: T 84 GLN cc_start: 0.7223 (mm110) cc_final: 0.6968 (mm110) REVERT: T 92 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8250 (m-30) REVERT: T 139 LEU cc_start: 0.8450 (mt) cc_final: 0.7918 (tm) REVERT: U 11 GLN cc_start: 0.8004 (mp10) cc_final: 0.7539 (mm110) REVERT: U 18 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7611 (tp30) REVERT: U 43 ASP cc_start: 0.8608 (t70) cc_final: 0.8354 (t0) REVERT: U 74 GLN cc_start: 0.7310 (tm130) cc_final: 0.6375 (tm130) REVERT: U 86 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7886 (tp) REVERT: V 64 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7058 (tmm-80) REVERT: V 68 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6848 (mt-10) REVERT: V 71 MET cc_start: 0.8126 (ttm) cc_final: 0.7464 (tmm) REVERT: V 85 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: W 24 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8631 (tp-100) REVERT: W 62 GLU cc_start: 0.8500 (tt0) cc_final: 0.8055 (tp30) REVERT: W 68 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8467 (tt0) REVERT: W 74 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8442 (tp-100) REVERT: W 76 GLN cc_start: 0.9042 (mt0) cc_final: 0.8753 (mt0) REVERT: W 80 ARG cc_start: 0.8881 (mmm-85) cc_final: 0.8457 (mpt180) REVERT: W 92 ASP cc_start: 0.6792 (m-30) cc_final: 0.5977 (p0) REVERT: X 54 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7198 (tppt) REVERT: X 62 GLU cc_start: 0.7441 (tt0) cc_final: 0.7073 (tm-30) REVERT: X 80 ARG cc_start: 0.7750 (mmt-90) cc_final: 0.7047 (tpp-160) outliers start: 109 outliers final: 56 residues processed: 825 average time/residue: 0.6558 time to fit residues: 653.7256 Evaluate side-chains 722 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 643 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 LYS Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 101 MET Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 151 ASP Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain V residue 172 ASP Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 38 MET Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 293 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 238 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 341 optimal weight: 7.9990 chunk 344 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN B 112 ASN D 24 GLN D 75 ASN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN G 66 HIS G 75 ASN G 126 ASN H 24 GLN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN I 76 GLN J 140 ASN K 24 GLN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 GLN L 106 HIS L 129 HIS M 11 GLN M 74 GLN M 99 ASN ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 ASN O 24 GLN ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 HIS P 140 ASN Q 26 ASN R 11 GLN ** R 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN S 75 ASN S 84 GLN ** U 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 74 GLN ** W 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 84 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.119670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.106843 restraints weight = 71907.546| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.94 r_work: 0.3569 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34512 Z= 0.193 Angle : 0.730 12.359 46488 Z= 0.378 Chirality : 0.042 0.191 4896 Planarity : 0.004 0.075 6120 Dihedral : 4.374 26.854 4488 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.34 % Allowed : 35.03 % Favored : 61.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.13), residues: 4080 helix: 2.52 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -0.84 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG N 80 TYR 0.028 0.002 TYR G 169 PHE 0.040 0.002 PHE F 133 TRP 0.024 0.002 TRP A 94 HIS 0.013 0.001 HIS L 106 Details of bonding type rmsd covalent geometry : bond 0.00435 (34512) covalent geometry : angle 0.73029 (46488) hydrogen bonds : bond 0.05462 ( 2139) hydrogen bonds : angle 4.06619 ( 6417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13425.62 seconds wall clock time: 229 minutes 22.97 seconds (13762.97 seconds total)