Starting phenix.real_space_refine on Sun Feb 8 10:00:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oa0_70268/02_2026/9oa0_70268.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oa0_70268/02_2026/9oa0_70268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oa0_70268/02_2026/9oa0_70268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oa0_70268/02_2026/9oa0_70268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oa0_70268/02_2026/9oa0_70268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oa0_70268/02_2026/9oa0_70268.map" } resolution = 3.1 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= 0.001 sd= 0.013 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 44 5.16 5 C 27500 2.51 5 N 7832 2.21 5 O 8283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43659 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1875 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain: "B" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1875 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain: "C" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1875 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain: "D" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1875 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain: "E" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1875 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain: "F" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1875 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain: "G" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1875 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain: "H" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1875 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain: "I" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1875 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain: "J" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1875 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain: "K" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1875 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain: "a" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "b" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "c" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "d" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "e" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "f" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "g" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "h" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "i" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "j" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "k" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Time building chain proxies: 10.04, per 1000 atoms: 0.23 Number of scatterers: 43659 At special positions: 0 Unit cell: (216.08, 216.08, 121.91, 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 44 16.00 O 8283 8.00 N 7832 7.00 C 27500 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: 4.04 Conformation dependent library (CDL) restraints added in 1.9 seconds 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10516 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 85 sheets defined 56.2% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 113 through 133 Proline residue: A 120 - end of helix removed outlier: 3.871A pdb=" N ARG A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 142 removed outlier: 3.525A pdb=" N GLN A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 162 removed outlier: 3.744A pdb=" N VAL A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 232 removed outlier: 4.451A pdb=" N ALA A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 251 removed outlier: 3.904A pdb=" N GLU A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 114 through 133 Proline residue: B 120 - end of helix removed outlier: 3.690A pdb=" N ARG B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 142 through 161 removed outlier: 3.702A pdb=" N VAL B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 232 removed outlier: 4.576A pdb=" N ALA B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 194 " --> pdb=" O GLN B 190 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 251 removed outlier: 3.821A pdb=" N GLU B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 114 through 134 Proline residue: C 120 - end of helix removed outlier: 3.618A pdb=" N ARG C 133 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE C 134 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 142 Processing helix chain 'C' and resid 142 through 161 removed outlier: 3.921A pdb=" N VAL C 146 " --> pdb=" O GLN C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 231 removed outlier: 3.628A pdb=" N ALA C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 252 removed outlier: 3.830A pdb=" N GLU C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 110 Processing helix chain 'D' and resid 113 through 134 Proline residue: D 120 - end of helix removed outlier: 3.644A pdb=" N ARG D 133 " --> pdb=" O SER D 129 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 removed outlier: 3.675A pdb=" N GLN D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 162 removed outlier: 3.720A pdb=" N VAL D 146 " --> pdb=" O GLN D 142 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE D 161 " --> pdb=" O ARG D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 232 removed outlier: 3.953A pdb=" N PHE D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR D 230 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 251 removed outlier: 4.047A pdb=" N GLU D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 114 through 134 Proline residue: E 120 - end of helix removed outlier: 4.107A pdb=" N PHE E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 142 through 162 removed outlier: 3.753A pdb=" N THR E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE E 161 " --> pdb=" O ARG E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 232 removed outlier: 3.971A pdb=" N GLU E 194 " --> pdb=" O GLN E 190 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 251 removed outlier: 3.825A pdb=" N GLU E 237 " --> pdb=" O ASP E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 110 Processing helix chain 'F' and resid 114 through 134 Proline residue: F 120 - end of helix removed outlier: 3.526A pdb=" N ARG F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE F 134 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 142 removed outlier: 3.710A pdb=" N GLN F 142 " --> pdb=" O GLU F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 162 removed outlier: 3.698A pdb=" N VAL F 146 " --> pdb=" O GLN F 142 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR F 160 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE F 161 " --> pdb=" O ARG F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 232 removed outlier: 3.524A pdb=" N ALA F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU F 194 " --> pdb=" O GLN F 190 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR F 230 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 251 removed outlier: 4.272A pdb=" N GLU F 237 " --> pdb=" O ASP F 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU F 238 " --> pdb=" O GLY F 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 118 through 134 removed outlier: 3.671A pdb=" N ARG G 133 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE G 134 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 142 removed outlier: 3.635A pdb=" N GLN G 142 " --> pdb=" O GLU G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 removed outlier: 3.719A pdb=" N VAL G 146 " --> pdb=" O GLN G 142 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR G 160 " --> pdb=" O GLU G 156 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE G 161 " --> pdb=" O ARG G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 232 removed outlier: 3.915A pdb=" N GLU G 194 " --> pdb=" O GLN G 190 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR G 230 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 251 removed outlier: 3.993A pdb=" N GLU G 237 " --> pdb=" O ASP G 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 110 Processing helix chain 'H' and resid 113 through 134 Proline residue: H 120 - end of helix removed outlier: 3.698A pdb=" N ARG H 133 " --> pdb=" O SER H 129 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE H 134 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 142 Processing helix chain 'H' and resid 142 through 162 removed outlier: 3.618A pdb=" N VAL H 146 " --> pdb=" O GLN H 142 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR H 160 " --> pdb=" O GLU H 156 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE H 161 " --> pdb=" O ARG H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 230 removed outlier: 3.679A pdb=" N GLN H 190 " --> pdb=" O LYS H 186 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE H 198 " --> pdb=" O GLU H 194 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU H 201 " --> pdb=" O ARG H 197 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR H 230 " --> pdb=" O ASN H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 251 removed outlier: 3.842A pdb=" N GLU H 237 " --> pdb=" O ASP H 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 114 through 133 Proline residue: I 120 - end of helix removed outlier: 3.898A pdb=" N ARG I 133 " --> pdb=" O SER I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 142 Processing helix chain 'I' and resid 142 through 162 removed outlier: 3.863A pdb=" N VAL I 146 " --> pdb=" O GLN I 142 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR I 160 " --> pdb=" O GLU I 156 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE I 161 " --> pdb=" O ARG I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 232 removed outlier: 3.786A pdb=" N ALA I 193 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR I 230 " --> pdb=" O ASN I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 252 removed outlier: 3.960A pdb=" N GLU I 237 " --> pdb=" O ASP I 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 113 through 134 Proline residue: J 120 - end of helix removed outlier: 3.588A pdb=" N ARG J 133 " --> pdb=" O SER J 129 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE J 134 " --> pdb=" O VAL J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 142 removed outlier: 3.759A pdb=" N GLN J 142 " --> pdb=" O GLU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 162 removed outlier: 3.661A pdb=" N VAL J 146 " --> pdb=" O GLN J 142 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR J 160 " --> pdb=" O GLU J 156 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE J 161 " --> pdb=" O ARG J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 232 removed outlier: 5.412A pdb=" N ALA J 182 " --> pdb=" O GLU J 178 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL J 183 " --> pdb=" O PHE J 179 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU J 201 " --> pdb=" O ARG J 197 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 251 removed outlier: 3.875A pdb=" N GLU J 237 " --> pdb=" O ASP J 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 114 through 134 Proline residue: K 120 - end of helix removed outlier: 3.612A pdb=" N ARG K 133 " --> pdb=" O SER K 129 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE K 134 " --> pdb=" O VAL K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 142 Processing helix chain 'K' and resid 142 through 162 removed outlier: 3.672A pdb=" N VAL K 146 " --> pdb=" O GLN K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 232 removed outlier: 3.855A pdb=" N GLU K 194 " --> pdb=" O GLN K 190 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 251 removed outlier: 3.846A pdb=" N GLU K 237 " --> pdb=" O ASP K 233 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 38 Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 128 through 146 Proline residue: a 134 - end of helix removed outlier: 3.563A pdb=" N ALA a 146 " --> pdb=" O LYS a 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 156 Processing helix chain 'a' and resid 156 through 175 removed outlier: 4.130A pdb=" N ASP a 174 " --> pdb=" O GLU a 170 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE a 175 " --> pdb=" O ARG a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 190 through 240 removed outlier: 3.703A pdb=" N GLN a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU a 215 " --> pdb=" O GLN a 211 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU a 240 " --> pdb=" O LYS a 236 " (cutoff:3.500A) Processing helix chain 'a' and resid 241 through 244 removed outlier: 3.565A pdb=" N LYS a 244 " --> pdb=" O ALA a 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 241 through 244' Processing helix chain 'a' and resid 246 through 266 removed outlier: 3.824A pdb=" N LYS a 250 " --> pdb=" O PRO a 246 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR a 266 " --> pdb=" O LYS a 262 " (cutoff:3.500A) Processing helix chain 'a' and resid 276 through 279 Processing helix chain 'a' and resid 288 through 293 Processing helix chain 'b' and resid 34 through 38 Processing helix chain 'b' and resid 116 through 124 Processing helix chain 'b' and resid 127 through 146 Proline residue: b 134 - end of helix removed outlier: 3.603A pdb=" N ALA b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 149 through 156 Processing helix chain 'b' and resid 156 through 174 removed outlier: 3.774A pdb=" N GLU b 170 " --> pdb=" O ARG b 166 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP b 174 " --> pdb=" O GLU b 170 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 240 removed outlier: 3.845A pdb=" N GLN b 211 " --> pdb=" O ALA b 207 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE b 212 " --> pdb=" O GLN b 208 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL b 214 " --> pdb=" O ALA b 210 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU b 215 " --> pdb=" O GLN b 211 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU b 240 " --> pdb=" O LYS b 236 " (cutoff:3.500A) Processing helix chain 'b' and resid 241 through 245 removed outlier: 3.561A pdb=" N LYS b 244 " --> pdb=" O ALA b 241 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN b 245 " --> pdb=" O LEU b 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 241 through 245' Processing helix chain 'b' and resid 246 through 266 removed outlier: 3.778A pdb=" N LYS b 250 " --> pdb=" O PRO b 246 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR b 266 " --> pdb=" O LYS b 262 " (cutoff:3.500A) Processing helix chain 'b' and resid 276 through 279 Processing helix chain 'b' and resid 288 through 293 removed outlier: 3.558A pdb=" N SER b 293 " --> pdb=" O ARG b 289 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 38 Processing helix chain 'c' and resid 116 through 125 Processing helix chain 'c' and resid 128 through 146 Proline residue: c 134 - end of helix removed outlier: 3.727A pdb=" N ALA c 146 " --> pdb=" O LYS c 142 " (cutoff:3.500A) Processing helix chain 'c' and resid 149 through 156 Processing helix chain 'c' and resid 156 through 174 removed outlier: 4.235A pdb=" N ASP c 174 " --> pdb=" O GLU c 170 " (cutoff:3.500A) Processing helix chain 'c' and resid 190 through 240 removed outlier: 4.492A pdb=" N GLN c 211 " --> pdb=" O ALA c 207 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE c 212 " --> pdb=" O GLN c 208 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU c 240 " --> pdb=" O LYS c 236 " (cutoff:3.500A) Processing helix chain 'c' and resid 246 through 266 removed outlier: 3.824A pdb=" N LYS c 250 " --> pdb=" O PRO c 246 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR c 266 " --> pdb=" O LYS c 262 " (cutoff:3.500A) Processing helix chain 'c' and resid 276 through 279 Processing helix chain 'c' and resid 288 through 293 Processing helix chain 'd' and resid 34 through 38 Processing helix chain 'd' and resid 116 through 125 removed outlier: 3.633A pdb=" N MET d 120 " --> pdb=" O GLU d 116 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 145 Proline residue: d 134 - end of helix Processing helix chain 'd' and resid 146 through 148 No H-bonds generated for 'chain 'd' and resid 146 through 148' Processing helix chain 'd' and resid 149 through 156 Processing helix chain 'd' and resid 156 through 174 removed outlier: 4.225A pdb=" N ASP d 174 " --> pdb=" O GLU d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 243 removed outlier: 4.430A pdb=" N GLN d 211 " --> pdb=" O ALA d 207 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE d 212 " --> pdb=" O GLN d 208 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA d 241 " --> pdb=" O MET d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 246 through 266 removed outlier: 3.808A pdb=" N LYS d 250 " --> pdb=" O PRO d 246 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR d 266 " --> pdb=" O LYS d 262 " (cutoff:3.500A) Processing helix chain 'd' and resid 276 through 279 Processing helix chain 'd' and resid 288 through 293 Processing helix chain 'e' and resid 34 through 38 Processing helix chain 'e' and resid 116 through 125 Processing helix chain 'e' and resid 128 through 145 Proline residue: e 134 - end of helix Processing helix chain 'e' and resid 146 through 148 No H-bonds generated for 'chain 'e' and resid 146 through 148' Processing helix chain 'e' and resid 149 through 156 Processing helix chain 'e' and resid 156 through 174 removed outlier: 4.060A pdb=" N ASP e 174 " --> pdb=" O GLU e 170 " (cutoff:3.500A) Processing helix chain 'e' and resid 190 through 240 removed outlier: 4.164A pdb=" N GLN e 211 " --> pdb=" O ALA e 207 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE e 212 " --> pdb=" O GLN e 208 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS e 218 " --> pdb=" O VAL e 214 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN e 219 " --> pdb=" O GLU e 215 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU e 240 " --> pdb=" O LYS e 236 " (cutoff:3.500A) Processing helix chain 'e' and resid 241 through 244 removed outlier: 3.567A pdb=" N LYS e 244 " --> pdb=" O ALA e 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 241 through 244' Processing helix chain 'e' and resid 246 through 266 removed outlier: 3.732A pdb=" N LYS e 250 " --> pdb=" O PRO e 246 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE e 254 " --> pdb=" O LYS e 250 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR e 266 " --> pdb=" O LYS e 262 " (cutoff:3.500A) Processing helix chain 'e' and resid 276 through 279 Processing helix chain 'e' and resid 288 through 295 removed outlier: 4.084A pdb=" N LEU e 294 " --> pdb=" O GLY e 290 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE e 295 " --> pdb=" O SER e 291 " (cutoff:3.500A) Processing helix chain 'f' and resid 34 through 38 Processing helix chain 'f' and resid 116 through 125 removed outlier: 3.586A pdb=" N TYR f 121 " --> pdb=" O LEU f 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 128 through 146 Proline residue: f 134 - end of helix removed outlier: 3.760A pdb=" N ALA f 146 " --> pdb=" O LYS f 142 " (cutoff:3.500A) Processing helix chain 'f' and resid 149 through 156 Processing helix chain 'f' and resid 156 through 174 removed outlier: 4.037A pdb=" N ASP f 174 " --> pdb=" O GLU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 190 through 242 removed outlier: 4.501A pdb=" N GLN f 211 " --> pdb=" O ALA f 207 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE f 212 " --> pdb=" O GLN f 208 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET f 237 " --> pdb=" O GLU f 233 " (cutoff:3.500A) Processing helix chain 'f' and resid 243 through 245 No H-bonds generated for 'chain 'f' and resid 243 through 245' Processing helix chain 'f' and resid 246 through 266 removed outlier: 3.804A pdb=" N LYS f 250 " --> pdb=" O PRO f 246 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR f 266 " --> pdb=" O LYS f 262 " (cutoff:3.500A) Processing helix chain 'f' and resid 276 through 279 Processing helix chain 'f' and resid 288 through 294 Processing helix chain 'g' and resid 34 through 38 Processing helix chain 'g' and resid 116 through 125 removed outlier: 3.556A pdb=" N MET g 120 " --> pdb=" O GLU g 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR g 121 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 128 through 146 Proline residue: g 134 - end of helix removed outlier: 3.574A pdb=" N ALA g 146 " --> pdb=" O LYS g 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 156 Processing helix chain 'g' and resid 156 through 174 removed outlier: 4.189A pdb=" N ASP g 174 " --> pdb=" O GLU g 170 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 240 removed outlier: 4.219A pdb=" N GLN g 211 " --> pdb=" O ALA g 207 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE g 212 " --> pdb=" O GLN g 208 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU g 215 " --> pdb=" O GLN g 211 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU g 240 " --> pdb=" O LYS g 236 " (cutoff:3.500A) Processing helix chain 'g' and resid 241 through 244 removed outlier: 3.608A pdb=" N LYS g 244 " --> pdb=" O ALA g 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 241 through 244' Processing helix chain 'g' and resid 246 through 266 removed outlier: 3.822A pdb=" N LYS g 250 " --> pdb=" O PRO g 246 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR g 266 " --> pdb=" O LYS g 262 " (cutoff:3.500A) Processing helix chain 'g' and resid 276 through 279 Processing helix chain 'g' and resid 288 through 293 Processing helix chain 'h' and resid 34 through 38 Processing helix chain 'h' and resid 116 through 125 Processing helix chain 'h' and resid 128 through 145 Proline residue: h 134 - end of helix Processing helix chain 'h' and resid 146 through 148 No H-bonds generated for 'chain 'h' and resid 146 through 148' Processing helix chain 'h' and resid 149 through 156 Processing helix chain 'h' and resid 156 through 174 removed outlier: 4.171A pdb=" N ASP h 174 " --> pdb=" O GLU h 170 " (cutoff:3.500A) Processing helix chain 'h' and resid 190 through 240 removed outlier: 3.629A pdb=" N GLN h 211 " --> pdb=" O ALA h 207 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU h 215 " --> pdb=" O GLN h 211 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU h 240 " --> pdb=" O LYS h 236 " (cutoff:3.500A) Processing helix chain 'h' and resid 241 through 244 removed outlier: 3.537A pdb=" N LYS h 244 " --> pdb=" O ALA h 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 241 through 244' Processing helix chain 'h' and resid 246 through 266 removed outlier: 3.830A pdb=" N LYS h 250 " --> pdb=" O PRO h 246 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR h 266 " --> pdb=" O LYS h 262 " (cutoff:3.500A) Processing helix chain 'h' and resid 276 through 279 Processing helix chain 'h' and resid 288 through 293 Processing helix chain 'i' and resid 34 through 38 Processing helix chain 'i' and resid 116 through 125 Processing helix chain 'i' and resid 128 through 145 Proline residue: i 134 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 149 through 156 Processing helix chain 'i' and resid 156 through 174 removed outlier: 4.072A pdb=" N ASP i 174 " --> pdb=" O GLU i 170 " (cutoff:3.500A) Processing helix chain 'i' and resid 190 through 240 removed outlier: 4.140A pdb=" N GLN i 211 " --> pdb=" O ALA i 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE i 212 " --> pdb=" O GLN i 208 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN i 219 " --> pdb=" O GLU i 215 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG i 222 " --> pdb=" O LYS i 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU i 240 " --> pdb=" O LYS i 236 " (cutoff:3.500A) Processing helix chain 'i' and resid 246 through 266 removed outlier: 3.831A pdb=" N LYS i 250 " --> pdb=" O PRO i 246 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR i 266 " --> pdb=" O LYS i 262 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 279 Processing helix chain 'i' and resid 288 through 293 Processing helix chain 'j' and resid 34 through 38 Processing helix chain 'j' and resid 116 through 125 Processing helix chain 'j' and resid 128 through 145 Proline residue: j 134 - end of helix Processing helix chain 'j' and resid 146 through 148 No H-bonds generated for 'chain 'j' and resid 146 through 148' Processing helix chain 'j' and resid 149 through 156 Processing helix chain 'j' and resid 156 through 174 removed outlier: 4.146A pdb=" N ASP j 174 " --> pdb=" O GLU j 170 " (cutoff:3.500A) Processing helix chain 'j' and resid 190 through 240 removed outlier: 3.725A pdb=" N GLN j 211 " --> pdb=" O ALA j 207 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN j 219 " --> pdb=" O GLU j 215 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU j 240 " --> pdb=" O LYS j 236 " (cutoff:3.500A) Processing helix chain 'j' and resid 240 through 245 removed outlier: 4.483A pdb=" N LYS j 244 " --> pdb=" O GLU j 240 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASN j 245 " --> pdb=" O ALA j 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 240 through 245' Processing helix chain 'j' and resid 246 through 266 removed outlier: 3.911A pdb=" N LYS j 250 " --> pdb=" O PRO j 246 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR j 266 " --> pdb=" O LYS j 262 " (cutoff:3.500A) Processing helix chain 'j' and resid 276 through 279 Processing helix chain 'j' and resid 288 through 293 Processing helix chain 'k' and resid 34 through 39 Processing helix chain 'k' and resid 116 through 125 Processing helix chain 'k' and resid 128 through 145 Proline residue: k 134 - end of helix Processing helix chain 'k' and resid 146 through 148 No H-bonds generated for 'chain 'k' and resid 146 through 148' Processing helix chain 'k' and resid 149 through 156 Processing helix chain 'k' and resid 156 through 174 removed outlier: 4.103A pdb=" N ASP k 174 " --> pdb=" O GLU k 170 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 240 removed outlier: 3.754A pdb=" N GLN k 211 " --> pdb=" O ALA k 207 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN k 219 " --> pdb=" O GLU k 215 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG k 222 " --> pdb=" O LYS k 218 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU k 240 " --> pdb=" O LYS k 236 " (cutoff:3.500A) Processing helix chain 'k' and resid 240 through 245 removed outlier: 4.377A pdb=" N LYS k 244 " --> pdb=" O GLU k 240 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN k 245 " --> pdb=" O ALA k 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 240 through 245' Processing helix chain 'k' and resid 246 through 266 removed outlier: 3.691A pdb=" N LYS k 250 " --> pdb=" O PRO k 246 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE k 254 " --> pdb=" O LYS k 250 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR k 266 " --> pdb=" O LYS k 262 " (cutoff:3.500A) Processing helix chain 'k' and resid 276 through 279 Processing helix chain 'k' and resid 288 through 293 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.767A pdb=" N TYR A 28 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 30 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 75 removed outlier: 6.564A pdb=" N ARG A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU A 165 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 81 Processing sheet with id=AA5, first strand: chain 'A' and resid 257 through 260 removed outlier: 7.307A pdb=" N ILE A 257 " --> pdb=" O ARG a 270 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N TYR a 272 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR A 259 " --> pdb=" O TYR a 272 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR a 274 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE G 257 " --> pdb=" O ARG g 270 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N TYR g 272 " --> pdb=" O ILE G 257 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR G 259 " --> pdb=" O TYR g 272 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N THR g 274 " --> pdb=" O TYR G 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.542A pdb=" N TYR B 28 " --> pdb=" O HIS B 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 75 removed outlier: 7.208A pdb=" N ASN B 89 " --> pdb=" O HIS B 172 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N HIS B 172 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR B 91 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 170 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG B 93 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL B 168 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 95 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 27 through 28 removed outlier: 4.252A pdb=" N TYR C 28 " --> pdb=" O HIS C 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 44 through 45 Processing sheet with id=AB3, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB4, first strand: chain 'C' and resid 72 through 75 removed outlier: 7.701A pdb=" N ASN C 87 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N THR C 174 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN C 89 " --> pdb=" O HIS C 172 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N HIS C 172 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR C 91 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU C 170 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG C 93 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL C 168 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 95 " --> pdb=" O ASP C 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 27 through 30 removed outlier: 3.732A pdb=" N TYR D 28 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 30 " --> pdb=" O GLY D 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AB7, first strand: chain 'D' and resid 72 through 75 removed outlier: 6.568A pdb=" N ARG D 97 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU D 165 " --> pdb=" O ARG D 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 78 through 81 Processing sheet with id=AB9, first strand: chain 'E' and resid 27 through 30 removed outlier: 3.768A pdb=" N TYR E 28 " --> pdb=" O HIS E 55 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 34 through 40 Processing sheet with id=AC2, first strand: chain 'E' and resid 72 through 81 removed outlier: 3.622A pdb=" N LEU E 92 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR E 91 " --> pdb=" O THR E 171 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR E 171 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG E 97 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU E 165 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 27 through 28 removed outlier: 4.156A pdb=" N TYR F 28 " --> pdb=" O HIS F 55 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 44 through 45 Processing sheet with id=AC5, first strand: chain 'F' and resid 72 through 75 Processing sheet with id=AC6, first strand: chain 'F' and resid 72 through 75 removed outlier: 7.179A pdb=" N ASN F 89 " --> pdb=" O LEU F 173 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU F 173 " --> pdb=" O ASN F 89 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR F 91 " --> pdb=" O THR F 171 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR F 171 " --> pdb=" O THR F 91 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG F 97 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU F 165 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 27 through 30 removed outlier: 3.736A pdb=" N TYR G 28 " --> pdb=" O HIS G 55 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL G 30 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 44 through 45 Processing sheet with id=AC9, first strand: chain 'G' and resid 72 through 75 Processing sheet with id=AD1, first strand: chain 'G' and resid 72 through 75 removed outlier: 7.085A pdb=" N THR G 91 " --> pdb=" O THR G 171 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR G 171 " --> pdb=" O THR G 91 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG G 97 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU G 165 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 28 through 30 removed outlier: 4.610A pdb=" N TYR H 28 " --> pdb=" O HIS H 55 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS H 55 " --> pdb=" O TYR H 28 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 44 through 45 Processing sheet with id=AD4, first strand: chain 'H' and resid 72 through 75 Processing sheet with id=AD5, first strand: chain 'H' and resid 72 through 75 removed outlier: 7.275A pdb=" N ASN H 89 " --> pdb=" O LEU H 173 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU H 173 " --> pdb=" O ASN H 89 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR H 91 " --> pdb=" O THR H 171 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR H 171 " --> pdb=" O THR H 91 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG H 97 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU H 165 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 27 through 28 removed outlier: 4.195A pdb=" N TYR I 28 " --> pdb=" O HIS I 55 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 44 through 45 Processing sheet with id=AD8, first strand: chain 'I' and resid 72 through 75 Processing sheet with id=AD9, first strand: chain 'I' and resid 72 through 75 removed outlier: 7.199A pdb=" N ASN I 89 " --> pdb=" O LEU I 173 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU I 173 " --> pdb=" O ASN I 89 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR I 91 " --> pdb=" O THR I 171 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR I 171 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG I 97 " --> pdb=" O LEU I 165 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU I 165 " --> pdb=" O ARG I 97 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 27 through 30 removed outlier: 3.762A pdb=" N TYR J 28 " --> pdb=" O HIS J 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL J 30 " --> pdb=" O GLY J 53 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 44 through 45 Processing sheet with id=AE3, first strand: chain 'J' and resid 72 through 75 Processing sheet with id=AE4, first strand: chain 'J' and resid 72 through 75 removed outlier: 7.646A pdb=" N ASN J 89 " --> pdb=" O LEU J 173 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU J 173 " --> pdb=" O ASN J 89 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR J 91 " --> pdb=" O THR J 171 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR J 171 " --> pdb=" O THR J 91 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG J 97 " --> pdb=" O LEU J 165 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU J 165 " --> pdb=" O ARG J 97 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 27 through 30 removed outlier: 3.738A pdb=" N TYR K 28 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL K 30 " --> pdb=" O GLY K 53 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 44 through 45 Processing sheet with id=AE7, first strand: chain 'K' and resid 72 through 75 removed outlier: 6.781A pdb=" N ARG K 93 " --> pdb=" O VAL K 168 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL K 168 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU K 95 " --> pdb=" O ASP K 166 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 78 through 81 Processing sheet with id=AE9, first strand: chain 'a' and resid 40 through 43 Processing sheet with id=AF1, first strand: chain 'a' and resid 57 through 58 removed outlier: 3.656A pdb=" N TYR a 77 " --> pdb=" O PHE a 52 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'a' and resid 88 through 91 removed outlier: 6.549A pdb=" N SER a 105 " --> pdb=" O THR a 185 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG a 111 " --> pdb=" O LEU a 179 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU a 179 " --> pdb=" O ARG a 111 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 94 through 95 Processing sheet with id=AF4, first strand: chain 'b' and resid 40 through 43 Processing sheet with id=AF5, first strand: chain 'b' and resid 47 through 50 Processing sheet with id=AF6, first strand: chain 'b' and resid 52 through 53 Processing sheet with id=AF7, first strand: chain 'b' and resid 88 through 91 removed outlier: 6.511A pdb=" N SER b 105 " --> pdb=" O THR b 185 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA b 183 " --> pdb=" O ARG b 107 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG b 111 " --> pdb=" O LEU b 179 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU b 179 " --> pdb=" O ARG b 111 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 94 through 95 Processing sheet with id=AF9, first strand: chain 'c' and resid 40 through 43 Processing sheet with id=AG1, first strand: chain 'c' and resid 47 through 50 Processing sheet with id=AG2, first strand: chain 'c' and resid 86 through 95 removed outlier: 3.966A pdb=" N SER c 110 " --> pdb=" O ARG c 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE c 104 " --> pdb=" O SER c 92 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET c 101 " --> pdb=" O PHE c 189 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N PHE c 189 " --> pdb=" O MET c 101 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN c 103 " --> pdb=" O LEU c 187 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU c 187 " --> pdb=" O ASN c 103 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER c 105 " --> pdb=" O THR c 185 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARG c 111 " --> pdb=" O LEU c 179 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU c 179 " --> pdb=" O ARG c 111 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'd' and resid 40 through 43 Processing sheet with id=AG4, first strand: chain 'd' and resid 57 through 58 removed outlier: 3.539A pdb=" N TYR d 77 " --> pdb=" O PHE d 52 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 86 through 91 removed outlier: 3.836A pdb=" N SER d 110 " --> pdb=" O ARG d 86 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER d 105 " --> pdb=" O THR d 185 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG d 111 " --> pdb=" O LEU d 179 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU d 179 " --> pdb=" O ARG d 111 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'd' and resid 94 through 95 Processing sheet with id=AG7, first strand: chain 'e' and resid 40 through 43 Processing sheet with id=AG8, first strand: chain 'e' and resid 57 through 58 removed outlier: 3.793A pdb=" N TYR e 77 " --> pdb=" O PHE e 52 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'e' and resid 86 through 91 removed outlier: 3.922A pdb=" N SER e 110 " --> pdb=" O ARG e 86 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER e 105 " --> pdb=" O THR e 185 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG e 111 " --> pdb=" O LEU e 179 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU e 179 " --> pdb=" O ARG e 111 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'e' and resid 94 through 95 Processing sheet with id=AH2, first strand: chain 'f' and resid 40 through 43 Processing sheet with id=AH3, first strand: chain 'f' and resid 57 through 58 removed outlier: 3.674A pdb=" N TYR f 77 " --> pdb=" O PHE f 52 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'f' and resid 86 through 91 removed outlier: 3.952A pdb=" N SER f 110 " --> pdb=" O ARG f 86 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER f 105 " --> pdb=" O ILE f 184 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE f 184 " --> pdb=" O SER f 105 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ARG f 107 " --> pdb=" O VAL f 182 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL f 182 " --> pdb=" O ARG f 107 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU f 109 " --> pdb=" O ASP f 180 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'f' and resid 94 through 95 Processing sheet with id=AH6, first strand: chain 'g' and resid 40 through 43 Processing sheet with id=AH7, first strand: chain 'g' and resid 57 through 58 removed outlier: 3.615A pdb=" N TYR g 77 " --> pdb=" O PHE g 52 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'g' and resid 86 through 90 removed outlier: 6.872A pdb=" N ARG g 111 " --> pdb=" O LEU g 179 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU g 179 " --> pdb=" O ARG g 111 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'g' and resid 93 through 95 Processing sheet with id=AI1, first strand: chain 'h' and resid 40 through 43 Processing sheet with id=AI2, first strand: chain 'h' and resid 57 through 58 Processing sheet with id=AI3, first strand: chain 'h' and resid 86 through 94 removed outlier: 3.979A pdb=" N SER h 110 " --> pdb=" O ARG h 86 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER h 92 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE h 104 " --> pdb=" O SER h 92 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER h 105 " --> pdb=" O THR h 185 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG h 111 " --> pdb=" O LEU h 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU h 179 " --> pdb=" O ARG h 111 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'i' and resid 40 through 43 Processing sheet with id=AI5, first strand: chain 'i' and resid 47 through 52 Processing sheet with id=AI6, first strand: chain 'i' and resid 86 through 91 removed outlier: 3.862A pdb=" N SER i 110 " --> pdb=" O ARG i 86 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER i 105 " --> pdb=" O ILE i 184 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE i 184 " --> pdb=" O SER i 105 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG i 107 " --> pdb=" O VAL i 182 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL i 182 " --> pdb=" O ARG i 107 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU i 109 " --> pdb=" O ASP i 180 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'i' and resid 94 through 95 Processing sheet with id=AI8, first strand: chain 'j' and resid 40 through 43 Processing sheet with id=AI9, first strand: chain 'j' and resid 57 through 58 removed outlier: 3.662A pdb=" N TYR j 77 " --> pdb=" O PHE j 52 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'j' and resid 86 through 95 removed outlier: 3.900A pdb=" N SER j 110 " --> pdb=" O ARG j 86 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE j 104 " --> pdb=" O SER j 92 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG j 107 " --> pdb=" O ILE j 184 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE j 184 " --> pdb=" O ARG j 107 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU j 109 " --> pdb=" O VAL j 182 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL j 182 " --> pdb=" O LEU j 109 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ARG j 111 " --> pdb=" O ASP j 180 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP j 180 " --> pdb=" O ARG j 111 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'k' and resid 40 through 43 Processing sheet with id=AJ3, first strand: chain 'k' and resid 57 through 58 Processing sheet with id=AJ4, first strand: chain 'k' and resid 86 through 95 removed outlier: 4.005A pdb=" N SER k 110 " --> pdb=" O ARG k 86 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER k 92 " --> pdb=" O ILE k 104 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE k 104 " --> pdb=" O SER k 92 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN k 103 " --> pdb=" O LEU k 187 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU k 187 " --> pdb=" O ASN k 103 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER k 105 " --> pdb=" O THR k 185 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG k 111 " --> pdb=" O LEU k 179 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU k 179 " --> pdb=" O ARG k 111 " (cutoff:3.500A) 2722 hydrogen bonds defined for protein. 7818 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: 10.84 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 15013 1.34 - 1.46: 8877 1.46 - 1.58: 20308 1.58 - 1.70: 0 1.70 - 1.81: 77 Bond restraints: 44275 Sorted by residual: bond pdb=" C TYR B 259 " pdb=" N LEU B 260 " ideal model delta sigma weight residual 1.331 1.292 0.039 2.83e-02 1.25e+03 1.94e+00 bond pdb=" CA LEU k 242 " pdb=" C LEU k 242 " ideal model delta sigma weight residual 1.522 1.502 0.020 1.72e-02 3.38e+03 1.34e+00 bond pdb=" C THR E 80 " pdb=" N GLY E 81 " ideal model delta sigma weight residual 1.332 1.338 -0.006 5.00e-03 4.00e+04 1.28e+00 bond pdb=" CA VAL I 78 " pdb=" CB VAL I 78 " ideal model delta sigma weight residual 1.550 1.540 0.010 1.03e-02 9.43e+03 1.02e+00 bond pdb=" CG LYS e 89 " pdb=" CD LYS e 89 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.58e-01 ... (remaining 44270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 59048 1.53 - 3.06: 652 3.06 - 4.59: 125 4.59 - 6.12: 2 6.12 - 7.65: 2 Bond angle restraints: 59829 Sorted by residual: angle pdb=" N VAL I 78 " pdb=" CA VAL I 78 " pdb=" C VAL I 78 " ideal model delta sigma weight residual 107.88 111.93 -4.05 1.38e+00 5.25e-01 8.62e+00 angle pdb=" N ILE D 110 " pdb=" CA ILE D 110 " pdb=" C ILE D 110 " ideal model delta sigma weight residual 113.71 111.18 2.53 9.50e-01 1.11e+00 7.07e+00 angle pdb=" CB MET e 101 " pdb=" CG MET e 101 " pdb=" SD MET e 101 " ideal model delta sigma weight residual 112.70 120.35 -7.65 3.00e+00 1.11e-01 6.51e+00 angle pdb=" CA ARG E 197 " pdb=" CB ARG E 197 " pdb=" CG ARG E 197 " ideal model delta sigma weight residual 114.10 118.67 -4.57 2.00e+00 2.50e-01 5.23e+00 angle pdb=" N TRP F 60 " pdb=" CA TRP F 60 " pdb=" CB TRP F 60 " ideal model delta sigma weight residual 113.65 110.35 3.30 1.47e+00 4.63e-01 5.04e+00 ... (remaining 59824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 23383 17.92 - 35.85: 2924 35.85 - 53.77: 746 53.77 - 71.69: 155 71.69 - 89.62: 116 Dihedral angle restraints: 27324 sinusoidal: 11165 harmonic: 16159 Sorted by residual: dihedral pdb=" CA PHE A 179 " pdb=" C PHE A 179 " pdb=" N THR A 180 " pdb=" CA THR A 180 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASP C 166 " pdb=" CB ASP C 166 " pdb=" CG ASP C 166 " pdb=" OD1 ASP C 166 " ideal model delta sinusoidal sigma weight residual -30.00 -89.38 59.38 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP J 166 " pdb=" CB ASP J 166 " pdb=" CG ASP J 166 " pdb=" OD1 ASP J 166 " ideal model delta sinusoidal sigma weight residual -30.00 -89.04 59.04 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 27321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4394 0.028 - 0.056: 1696 0.056 - 0.083: 439 0.083 - 0.111: 244 0.111 - 0.139: 157 Chirality restraints: 6930 Sorted by residual: chirality pdb=" CA VAL D 78 " pdb=" N VAL D 78 " pdb=" C VAL D 78 " pdb=" CB VAL D 78 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE C 65 " pdb=" N ILE C 65 " pdb=" C ILE C 65 " pdb=" CB ILE C 65 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE D 65 " pdb=" N ILE D 65 " pdb=" C ILE D 65 " pdb=" CB ILE D 65 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 6927 not shown) Planarity restraints: 7832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE f 72 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO f 73 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO f 73 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO f 73 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR j 77 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO j 78 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO j 78 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO j 78 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG g 86 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO g 87 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO g 87 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO g 87 " 0.017 5.00e-02 4.00e+02 ... (remaining 7829 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 491 2.54 - 3.13: 37152 3.13 - 3.72: 70606 3.72 - 4.31: 93795 4.31 - 4.90: 160253 Nonbonded interactions: 362297 Sorted by model distance: nonbonded pdb=" O ASN F 89 " pdb=" OG1 THR F 174 " model vdw 1.947 3.040 nonbonded pdb=" O ASN H 89 " pdb=" OG1 THR H 174 " model vdw 1.964 3.040 nonbonded pdb=" O ASN A 89 " pdb=" OG1 THR A 174 " model vdw 1.973 3.040 nonbonded pdb=" OG1 THR E 141 " pdb=" OE1 GLN E 142 " model vdw 1.997 3.040 nonbonded pdb=" OD1 ASP H 217 " pdb=" OH TYR g 248 " model vdw 2.003 3.040 ... (remaining 362292 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: 0.01 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' } 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' } 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: 8.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 41.820 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.190 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.003 0.048 44275 Z= 0.145 Angle : 0.455 7.653 59829 Z= 0.249 Chirality : 0.039 0.139 6930 Planarity : 0.003 0.032 7832 Dihedral : 17.692 89.616 16808 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.52 % Allowed : 22.56 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.11), residues: 5489 helix: 0.90 (0.10), residues: 2739 sheet: 0.69 (0.18), residues: 880 loop : -0.77 (0.15), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 195 TYR 0.009 0.001 TYR I 249 PHE 0.007 0.001 PHE G 179 TRP 0.003 0.000 TRP H 60 HIS 0.002 0.001 HIS d 47 Details of bonding type rmsd covalent geometry : bond 0.00303 (44275) covalent geometry : angle 0.45508 (59829) hydrogen bonds : bond 0.13091 ( 2694) hydrogen bonds : angle 6.27780 ( 7818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 391 time to evaluate : 1.796 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 60 TRP cc_start: 0.5280 (t-100) cc_final: 0.4688 (t60) REVERT: A 242 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: B 60 TRP cc_start: 0.5145 (t-100) cc_final: 0.4296 (t60) REVERT: B 177 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8032 (tppt) REVERT: B 186 LYS cc_start: 0.6914 (mptt) cc_final: 0.6694 (mptt) REVERT: C 60 TRP cc_start: 0.4944 (t-100) cc_final: 0.4485 (t60) REVERT: D 60 TRP cc_start: 0.5358 (t-100) cc_final: 0.4698 (t60) REVERT: E 117 ARG cc_start: 0.7308 (mtt180) cc_final: 0.6858 (mtt180) REVERT: F 60 TRP cc_start: 0.5375 (t-100) cc_final: 0.4557 (t60) REVERT: G 60 TRP cc_start: 0.5108 (t-100) cc_final: 0.4448 (t60) REVERT: G 87 ASN cc_start: 0.7847 (m-40) cc_final: 0.7339 (p0) REVERT: G 171 THR cc_start: 0.7212 (p) cc_final: 0.6948 (p) REVERT: H 60 TRP cc_start: 0.5536 (t-100) cc_final: 0.4938 (t60) REVERT: H 149 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6986 (mt0) REVERT: I 46 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6616 (tp-100) REVERT: I 60 TRP cc_start: 0.5208 (t-100) cc_final: 0.4592 (t60) REVERT: J 60 TRP cc_start: 0.5221 (t-100) cc_final: 0.4697 (t60) REVERT: K 60 TRP cc_start: 0.5012 (t-100) cc_final: 0.4415 (t60) REVERT: a 53 ASN cc_start: 0.7041 (t0) cc_final: 0.5977 (p0) REVERT: a 74 TRP cc_start: 0.6606 (t-100) cc_final: 0.5888 (t60) REVERT: b 74 TRP cc_start: 0.5941 (t-100) cc_final: 0.5214 (t60) REVERT: b 117 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7144 (tt) REVERT: b 120 MET cc_start: 0.8989 (ttp) cc_final: 0.8689 (tmm) REVERT: b 165 ARG cc_start: 0.7117 (ttp80) cc_final: 0.6902 (mtp-110) REVERT: c 74 TRP cc_start: 0.6152 (t-100) cc_final: 0.5338 (t60) REVERT: c 101 MET cc_start: 0.4584 (tpt) cc_final: 0.3819 (mmp) REVERT: c 168 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6439 (tp) REVERT: d 208 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8372 (tp-100) REVERT: e 74 TRP cc_start: 0.5723 (t-100) cc_final: 0.4982 (t60) REVERT: h 70 PHE cc_start: 0.5882 (m-80) cc_final: 0.4926 (p90) REVERT: h 74 TRP cc_start: 0.6461 (t-100) cc_final: 0.5379 (t60) REVERT: h 156 GLN cc_start: 0.8550 (mt0) cc_final: 0.7896 (mt0) REVERT: i 74 TRP cc_start: 0.7120 (t-100) cc_final: 0.5975 (t60) REVERT: i 92 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.7694 (t) REVERT: j 53 ASN cc_start: 0.6801 (t0) cc_final: 0.6536 (m-40) REVERT: j 59 GLN cc_start: 0.5336 (OUTLIER) cc_final: 0.5080 (pt0) REVERT: j 74 TRP cc_start: 0.5683 (t-100) cc_final: 0.4796 (t60) REVERT: k 74 TRP cc_start: 0.6183 (t-100) cc_final: 0.5203 (t60) outliers start: 118 outliers final: 88 residues processed: 497 average time/residue: 0.2477 time to fit residues: 210.3576 Evaluate side-chains 417 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 321 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 172 HIS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 149 GLN Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 149 GLN Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 211 ILE Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 103 ASN Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain b residue 103 ASN Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 181 ASP Chi-restraints excluded: chain b residue 192 GLU Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 90 ILE Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain c residue 126 LEU Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain d residue 40 VAL Chi-restraints excluded: chain d residue 59 GLN Chi-restraints excluded: chain d residue 103 ASN Chi-restraints excluded: chain d residue 168 LEU Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 208 GLN Chi-restraints excluded: chain e residue 103 ASN Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 124 LEU Chi-restraints excluded: chain f residue 168 LEU Chi-restraints excluded: chain f residue 218 LYS Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 59 GLN Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain h residue 168 LEU Chi-restraints excluded: chain h residue 192 GLU Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 92 SER Chi-restraints excluded: chain i residue 103 ASN Chi-restraints excluded: chain i residue 185 THR Chi-restraints excluded: chain j residue 59 GLN Chi-restraints excluded: chain j residue 90 ILE Chi-restraints excluded: chain j residue 91 SER Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 291 SER Chi-restraints excluded: chain k residue 59 GLN Chi-restraints excluded: chain k residue 117 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 523 optimal weight: 0.8980 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 172 HIS F 205 GLN G 34 HIS I 34 HIS c 211 GLN ** d 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 156 GLN ** f 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 76 GLN ** i 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.154125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.102495 restraints weight = 101798.117| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 4.43 r_work: 0.3204 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 44275 Z= 0.210 Angle : 0.575 7.514 59829 Z= 0.302 Chirality : 0.042 0.146 6930 Planarity : 0.004 0.063 7832 Dihedral : 6.432 89.307 6275 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.50 % Allowed : 21.53 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.11), residues: 5489 helix: 0.96 (0.10), residues: 2717 sheet: 0.33 (0.17), residues: 935 loop : -0.81 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 133 TYR 0.020 0.002 TYR g 128 PHE 0.011 0.001 PHE B 179 TRP 0.008 0.001 TRP c 74 HIS 0.004 0.001 HIS d 47 Details of bonding type rmsd covalent geometry : bond 0.00477 (44275) covalent geometry : angle 0.57536 (59829) hydrogen bonds : bond 0.05441 ( 2694) hydrogen bonds : angle 5.35329 ( 7818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 409 time to evaluate : 1.874 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 60 TRP cc_start: 0.5348 (t-100) cc_final: 0.4722 (t60) REVERT: B 60 TRP cc_start: 0.5429 (t-100) cc_final: 0.4614 (t60) REVERT: B 171 THR cc_start: 0.6032 (p) cc_final: 0.5665 (p) REVERT: B 177 LYS cc_start: 0.8374 (ttpt) cc_final: 0.7935 (tppt) REVERT: C 60 TRP cc_start: 0.5128 (t-100) cc_final: 0.4562 (t60) REVERT: C 174 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7429 (p) REVERT: D 60 TRP cc_start: 0.5303 (t-100) cc_final: 0.4684 (t60) REVERT: D 83 LYS cc_start: 0.5572 (pttp) cc_final: 0.5324 (pttt) REVERT: F 60 TRP cc_start: 0.5414 (t-100) cc_final: 0.4563 (t60) REVERT: F 143 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6683 (ttm-80) REVERT: G 52 GLU cc_start: 0.5441 (mt-10) cc_final: 0.4963 (mt-10) REVERT: G 60 TRP cc_start: 0.5106 (t-100) cc_final: 0.4425 (t60) REVERT: G 87 ASN cc_start: 0.7820 (m-40) cc_final: 0.7491 (p0) REVERT: G 171 THR cc_start: 0.6685 (p) cc_final: 0.6363 (p) REVERT: H 60 TRP cc_start: 0.5609 (t-100) cc_final: 0.4946 (t60) REVERT: I 60 TRP cc_start: 0.5359 (t-100) cc_final: 0.4723 (t60) REVERT: I 174 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8065 (p) REVERT: J 60 TRP cc_start: 0.5369 (t-100) cc_final: 0.4813 (t60) REVERT: K 60 TRP cc_start: 0.4992 (t-100) cc_final: 0.4402 (t60) REVERT: K 174 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7468 (p) REVERT: a 74 TRP cc_start: 0.6853 (t-100) cc_final: 0.6238 (t60) REVERT: a 156 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8388 (mm-40) REVERT: a 179 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.5263 (mt) REVERT: b 74 TRP cc_start: 0.6153 (t-100) cc_final: 0.5584 (t60) REVERT: b 89 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8134 (mmtm) REVERT: b 117 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.6993 (tt) REVERT: b 120 MET cc_start: 0.9105 (ttp) cc_final: 0.8821 (tmm) REVERT: c 74 TRP cc_start: 0.5842 (t-100) cc_final: 0.4981 (t60) REVERT: c 101 MET cc_start: 0.3627 (tpt) cc_final: 0.3062 (mmp) REVERT: d 53 ASN cc_start: 0.6838 (m-40) cc_final: 0.6490 (m-40) REVERT: d 59 GLN cc_start: 0.5964 (OUTLIER) cc_final: 0.5617 (pm20) REVERT: d 74 TRP cc_start: 0.5861 (t-100) cc_final: 0.4901 (t60) REVERT: d 109 LEU cc_start: 0.7521 (tp) cc_final: 0.7310 (tp) REVERT: d 208 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8687 (tp-100) REVERT: e 74 TRP cc_start: 0.5624 (t-100) cc_final: 0.4821 (t60) REVERT: h 41 PHE cc_start: 0.6210 (OUTLIER) cc_final: 0.5956 (m-80) REVERT: h 53 ASN cc_start: 0.6732 (t0) cc_final: 0.6131 (p0) REVERT: h 62 THR cc_start: 0.3672 (OUTLIER) cc_final: 0.3452 (m) REVERT: h 70 PHE cc_start: 0.5380 (m-80) cc_final: 0.4578 (p90) REVERT: h 74 TRP cc_start: 0.6798 (t-100) cc_final: 0.5958 (t60) REVERT: i 74 TRP cc_start: 0.7087 (t-100) cc_final: 0.6270 (t60) REVERT: i 92 SER cc_start: 0.8214 (p) cc_final: 0.7727 (t) REVERT: i 117 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.8004 (tp) REVERT: j 74 TRP cc_start: 0.5851 (t-100) cc_final: 0.4920 (t60) REVERT: j 92 SER cc_start: 0.8287 (OUTLIER) cc_final: 0.7976 (t) REVERT: k 70 PHE cc_start: 0.5625 (m-80) cc_final: 0.4865 (p90) REVERT: k 74 TRP cc_start: 0.6217 (t-100) cc_final: 0.5228 (t60) REVERT: k 156 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8278 (mm-40) REVERT: k 201 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7345 (tt0) outliers start: 211 outliers final: 116 residues processed: 593 average time/residue: 0.2414 time to fit residues: 247.1178 Evaluate side-chains 471 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 342 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 59 GLN Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 181 ASP Chi-restraints excluded: chain b residue 192 GLU Chi-restraints excluded: chain c residue 90 ILE Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain d residue 59 GLN Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 168 LEU Chi-restraints excluded: chain d residue 202 VAL Chi-restraints excluded: chain d residue 208 GLN Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain d residue 225 ILE Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 202 VAL Chi-restraints excluded: chain e residue 263 THR Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 137 VAL Chi-restraints excluded: chain f residue 168 LEU Chi-restraints excluded: chain f residue 192 GLU Chi-restraints excluded: chain f residue 202 VAL Chi-restraints excluded: chain f residue 214 VAL Chi-restraints excluded: chain g residue 51 PHE Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 291 SER Chi-restraints excluded: chain h residue 41 PHE Chi-restraints excluded: chain h residue 62 THR Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 168 LEU Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 192 GLU Chi-restraints excluded: chain h residue 197 VAL Chi-restraints excluded: chain h residue 237 MET Chi-restraints excluded: chain h residue 269 ASN Chi-restraints excluded: chain h residue 291 SER Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 117 LEU Chi-restraints excluded: chain i residue 127 ASP Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 167 GLU Chi-restraints excluded: chain i residue 168 LEU Chi-restraints excluded: chain j residue 59 GLN Chi-restraints excluded: chain j residue 63 ILE Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 117 LEU Chi-restraints excluded: chain j residue 137 VAL Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 59 GLN Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 137 VAL Chi-restraints excluded: chain k residue 168 LEU Chi-restraints excluded: chain k residue 179 LEU Chi-restraints excluded: chain k residue 201 GLN Chi-restraints excluded: chain k residue 202 VAL Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 432 optimal weight: 20.0000 chunk 492 optimal weight: 5.9990 chunk 98 optimal weight: 40.0000 chunk 236 optimal weight: 0.8980 chunk 336 optimal weight: 0.9980 chunk 362 optimal weight: 0.9990 chunk 444 optimal weight: 0.7980 chunk 258 optimal weight: 3.9990 chunk 445 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 chunk 524 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 HIS D 34 HIS ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN F 34 HIS F 87 ASN F 172 HIS H 34 HIS I 87 ASN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 201 GLN d 113 ASN e 152 GLN f 76 GLN ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 113 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.155447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.099256 restraints weight = 101119.045| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.27 r_work: 0.3294 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 44275 Z= 0.135 Angle : 0.506 5.515 59829 Z= 0.269 Chirality : 0.041 0.150 6930 Planarity : 0.003 0.051 7832 Dihedral : 5.456 85.844 6191 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.10 % Allowed : 22.19 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.11), residues: 5489 helix: 1.12 (0.09), residues: 2717 sheet: 0.32 (0.17), residues: 935 loop : -0.78 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 133 TYR 0.013 0.001 TYR g 128 PHE 0.011 0.001 PHE B 179 TRP 0.010 0.001 TRP i 74 HIS 0.002 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00287 (44275) covalent geometry : angle 0.50622 (59829) hydrogen bonds : bond 0.04955 ( 2694) hydrogen bonds : angle 5.05084 ( 7818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 390 time to evaluate : 1.692 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 60 TRP cc_start: 0.5320 (t-100) cc_final: 0.4701 (t60) REVERT: A 173 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5907 (mm) REVERT: B 60 TRP cc_start: 0.5548 (t-100) cc_final: 0.4755 (t60) REVERT: B 171 THR cc_start: 0.5996 (p) cc_final: 0.5633 (p) REVERT: B 177 LYS cc_start: 0.8382 (ttpt) cc_final: 0.7913 (tppt) REVERT: B 242 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: C 60 TRP cc_start: 0.5062 (t-100) cc_final: 0.4510 (t60) REVERT: C 174 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7524 (p) REVERT: C 207 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7009 (ttmt) REVERT: D 60 TRP cc_start: 0.5272 (t-100) cc_final: 0.4693 (t60) REVERT: D 83 LYS cc_start: 0.5595 (pttp) cc_final: 0.5363 (pttt) REVERT: E 83 LYS cc_start: 0.6976 (ttmt) cc_final: 0.6628 (mtpt) REVERT: E 110 ILE cc_start: 0.7617 (mm) cc_final: 0.7263 (tp) REVERT: F 60 TRP cc_start: 0.5515 (t-100) cc_final: 0.4677 (t60) REVERT: F 143 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6720 (ttm-80) REVERT: G 52 GLU cc_start: 0.5573 (mt-10) cc_final: 0.5056 (mt-10) REVERT: G 60 TRP cc_start: 0.5125 (t-100) cc_final: 0.4462 (t60) REVERT: G 87 ASN cc_start: 0.7878 (m-40) cc_final: 0.7550 (p0) REVERT: G 171 THR cc_start: 0.6534 (p) cc_final: 0.6273 (p) REVERT: H 60 TRP cc_start: 0.5696 (t-100) cc_final: 0.5032 (t60) REVERT: I 60 TRP cc_start: 0.5406 (t-100) cc_final: 0.4779 (t60) REVERT: I 174 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7849 (p) REVERT: J 60 TRP cc_start: 0.5368 (t-100) cc_final: 0.4838 (t60) REVERT: K 60 TRP cc_start: 0.4993 (t-100) cc_final: 0.4384 (t60) REVERT: a 74 TRP cc_start: 0.6796 (t-100) cc_final: 0.6222 (t60) REVERT: a 113 ASN cc_start: 0.7376 (t0) cc_final: 0.7148 (t0) REVERT: a 156 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8672 (mm-40) REVERT: a 179 LEU cc_start: 0.5751 (OUTLIER) cc_final: 0.5404 (mt) REVERT: b 74 TRP cc_start: 0.6057 (t-100) cc_final: 0.5594 (t60) REVERT: b 89 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8114 (mmtm) REVERT: c 74 TRP cc_start: 0.5885 (t-100) cc_final: 0.5060 (t60) REVERT: c 101 MET cc_start: 0.3422 (tpt) cc_final: 0.2963 (mmp) REVERT: d 74 TRP cc_start: 0.5560 (t-100) cc_final: 0.4601 (t60) REVERT: d 109 LEU cc_start: 0.7591 (tp) cc_final: 0.7385 (tp) REVERT: d 208 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8662 (tp-100) REVERT: e 74 TRP cc_start: 0.5561 (t-100) cc_final: 0.4742 (t60) REVERT: e 117 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7625 (mt) REVERT: e 179 LEU cc_start: 0.4851 (OUTLIER) cc_final: 0.4628 (mt) REVERT: g 109 LEU cc_start: 0.7793 (tp) cc_final: 0.7590 (tp) REVERT: h 41 PHE cc_start: 0.6200 (OUTLIER) cc_final: 0.5964 (m-80) REVERT: h 53 ASN cc_start: 0.6623 (t0) cc_final: 0.5954 (p0) REVERT: h 70 PHE cc_start: 0.5371 (m-80) cc_final: 0.4526 (p90) REVERT: h 74 TRP cc_start: 0.6731 (t-100) cc_final: 0.5957 (t-100) REVERT: i 74 TRP cc_start: 0.6899 (t-100) cc_final: 0.6175 (t-100) REVERT: i 92 SER cc_start: 0.8192 (p) cc_final: 0.7722 (t) REVERT: j 74 TRP cc_start: 0.5826 (t-100) cc_final: 0.4891 (t60) REVERT: j 156 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8559 (mp10) REVERT: k 41 PHE cc_start: 0.6090 (OUTLIER) cc_final: 0.5695 (m-80) REVERT: k 62 THR cc_start: 0.4124 (OUTLIER) cc_final: 0.3875 (m) REVERT: k 70 PHE cc_start: 0.5589 (m-80) cc_final: 0.4787 (p90) REVERT: k 74 TRP cc_start: 0.6102 (t-100) cc_final: 0.5148 (t60) REVERT: k 156 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8695 (mm-40) outliers start: 192 outliers final: 111 residues processed: 565 average time/residue: 0.2385 time to fit residues: 234.3247 Evaluate side-chains 463 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 339 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 181 ASP Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 201 GLN Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain d residue 50 ILE Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 145 VAL Chi-restraints excluded: chain d residue 168 LEU Chi-restraints excluded: chain d residue 202 VAL Chi-restraints excluded: chain d residue 208 GLN Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 179 LEU Chi-restraints excluded: chain e residue 202 VAL Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 168 LEU Chi-restraints excluded: chain f residue 192 GLU Chi-restraints excluded: chain f residue 202 VAL Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 41 PHE Chi-restraints excluded: chain h residue 63 ILE Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 168 LEU Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 192 GLU Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 291 SER Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 113 ASN Chi-restraints excluded: chain i residue 127 ASP Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 145 VAL Chi-restraints excluded: chain i residue 167 GLU Chi-restraints excluded: chain i residue 168 LEU Chi-restraints excluded: chain i residue 223 GLN Chi-restraints excluded: chain j residue 117 LEU Chi-restraints excluded: chain j residue 137 VAL Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 41 PHE Chi-restraints excluded: chain k residue 62 THR Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 145 VAL Chi-restraints excluded: chain k residue 168 LEU Chi-restraints excluded: chain k residue 179 LEU Chi-restraints excluded: chain k residue 202 VAL Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 59 optimal weight: 20.0000 chunk 476 optimal weight: 0.3980 chunk 180 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 402 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 310 optimal weight: 0.6980 chunk 360 optimal weight: 0.6980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN B 34 HIS D 87 ASN E 34 HIS E 86 GLN E 142 GLN F 87 ASN I 87 ASN J 34 HIS J 87 ASN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** c 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 152 GLN ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 152 GLN ** k 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.155094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.098543 restraints weight = 101464.269| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.30 r_work: 0.3278 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44275 Z= 0.157 Angle : 0.514 6.167 59829 Z= 0.271 Chirality : 0.041 0.144 6930 Planarity : 0.003 0.048 7832 Dihedral : 5.153 85.200 6159 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.59 % Allowed : 22.09 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.11), residues: 5489 helix: 1.06 (0.10), residues: 2783 sheet: 0.35 (0.17), residues: 935 loop : -0.73 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 133 TYR 0.013 0.001 TYR k 121 PHE 0.010 0.001 PHE B 179 TRP 0.008 0.001 TRP i 74 HIS 0.002 0.001 HIS e 47 Details of bonding type rmsd covalent geometry : bond 0.00346 (44275) covalent geometry : angle 0.51391 (59829) hydrogen bonds : bond 0.04953 ( 2694) hydrogen bonds : angle 4.94028 ( 7818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 375 time to evaluate : 1.604 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 60 TRP cc_start: 0.5355 (t-100) cc_final: 0.4742 (t60) REVERT: A 173 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5968 (mm) REVERT: B 60 TRP cc_start: 0.5527 (t-100) cc_final: 0.4773 (t60) REVERT: B 125 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7771 (pp20) REVERT: B 171 THR cc_start: 0.6152 (p) cc_final: 0.5808 (p) REVERT: B 242 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8473 (mt-10) REVERT: C 60 TRP cc_start: 0.5079 (t-100) cc_final: 0.4541 (t60) REVERT: C 174 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7543 (p) REVERT: C 207 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7067 (ttmt) REVERT: D 60 TRP cc_start: 0.5297 (t-100) cc_final: 0.4748 (t60) REVERT: E 83 LYS cc_start: 0.6987 (ttmt) cc_final: 0.6622 (mtpt) REVERT: E 110 ILE cc_start: 0.7707 (mm) cc_final: 0.7357 (tp) REVERT: E 143 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7520 (ttt90) REVERT: F 60 TRP cc_start: 0.5517 (t-100) cc_final: 0.4725 (t60) REVERT: F 143 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6717 (ttm-80) REVERT: G 60 TRP cc_start: 0.5100 (t-100) cc_final: 0.4453 (t60) REVERT: G 87 ASN cc_start: 0.7777 (m-40) cc_final: 0.7495 (p0) REVERT: H 60 TRP cc_start: 0.5726 (t-100) cc_final: 0.5043 (t60) REVERT: I 60 TRP cc_start: 0.5379 (t-100) cc_final: 0.4759 (t60) REVERT: J 60 TRP cc_start: 0.5334 (t-100) cc_final: 0.4833 (t60) REVERT: J 142 GLN cc_start: 0.8174 (pm20) cc_final: 0.7928 (mp10) REVERT: K 60 TRP cc_start: 0.4962 (t-100) cc_final: 0.4377 (t60) REVERT: a 41 PHE cc_start: 0.6058 (OUTLIER) cc_final: 0.5840 (m-80) REVERT: a 74 TRP cc_start: 0.6763 (t-100) cc_final: 0.6192 (t60) REVERT: b 74 TRP cc_start: 0.6128 (t-100) cc_final: 0.5515 (t60) REVERT: b 117 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7353 (tt) REVERT: c 74 TRP cc_start: 0.5906 (t-100) cc_final: 0.5080 (t60) REVERT: c 101 MET cc_start: 0.3747 (tpt) cc_final: 0.3102 (mmp) REVERT: d 74 TRP cc_start: 0.5503 (t-100) cc_final: 0.4562 (t60) REVERT: d 208 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8665 (tp-100) REVERT: e 74 TRP cc_start: 0.5560 (t-100) cc_final: 0.4735 (t60) REVERT: f 156 GLN cc_start: 0.8536 (mt0) cc_final: 0.8301 (mm110) REVERT: g 41 PHE cc_start: 0.6397 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: h 41 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5943 (m-80) REVERT: h 53 ASN cc_start: 0.6551 (t0) cc_final: 0.5901 (p0) REVERT: h 70 PHE cc_start: 0.5373 (m-80) cc_final: 0.4502 (p90) REVERT: h 74 TRP cc_start: 0.6768 (t-100) cc_final: 0.6027 (t-100) REVERT: i 74 TRP cc_start: 0.6759 (t-100) cc_final: 0.6161 (t60) REVERT: i 92 SER cc_start: 0.8162 (p) cc_final: 0.7676 (t) REVERT: j 41 PHE cc_start: 0.6059 (OUTLIER) cc_final: 0.5779 (m-80) REVERT: j 74 TRP cc_start: 0.5812 (t-100) cc_final: 0.4899 (t60) REVERT: j 92 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7893 (t) REVERT: j 109 LEU cc_start: 0.7633 (tp) cc_final: 0.7429 (tp) REVERT: j 117 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8106 (tp) REVERT: k 41 PHE cc_start: 0.6148 (OUTLIER) cc_final: 0.5766 (m-80) REVERT: k 70 PHE cc_start: 0.5546 (m-80) cc_final: 0.4781 (p90) REVERT: k 74 TRP cc_start: 0.6105 (t-100) cc_final: 0.5188 (t60) REVERT: k 156 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8668 (mm-40) REVERT: k 201 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7049 (tt0) outliers start: 215 outliers final: 140 residues processed: 569 average time/residue: 0.2390 time to fit residues: 235.3051 Evaluate side-chains 503 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 346 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 41 PHE Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 181 ASP Chi-restraints excluded: chain c residue 90 ILE Chi-restraints excluded: chain c residue 91 SER Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain d residue 50 ILE Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 145 VAL Chi-restraints excluded: chain d residue 168 LEU Chi-restraints excluded: chain d residue 202 VAL Chi-restraints excluded: chain d residue 208 GLN Chi-restraints excluded: chain d residue 214 VAL Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 179 LEU Chi-restraints excluded: chain e residue 202 VAL Chi-restraints excluded: chain e residue 284 ASP Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 168 LEU Chi-restraints excluded: chain f residue 192 GLU Chi-restraints excluded: chain f residue 202 VAL Chi-restraints excluded: chain f residue 224 LYS Chi-restraints excluded: chain g residue 41 PHE Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 218 LYS Chi-restraints excluded: chain h residue 41 PHE Chi-restraints excluded: chain h residue 63 ILE Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 168 LEU Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 197 VAL Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 LYS Chi-restraints excluded: chain h residue 237 MET Chi-restraints excluded: chain h residue 291 SER Chi-restraints excluded: chain i residue 59 GLN Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 127 ASP Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 145 VAL Chi-restraints excluded: chain i residue 156 GLN Chi-restraints excluded: chain i residue 167 GLU Chi-restraints excluded: chain i residue 168 LEU Chi-restraints excluded: chain i residue 223 GLN Chi-restraints excluded: chain j residue 41 PHE Chi-restraints excluded: chain j residue 63 ILE Chi-restraints excluded: chain j residue 90 ILE Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 117 LEU Chi-restraints excluded: chain j residue 137 VAL Chi-restraints excluded: chain j residue 145 VAL Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 41 PHE Chi-restraints excluded: chain k residue 90 ILE Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 137 VAL Chi-restraints excluded: chain k residue 145 VAL Chi-restraints excluded: chain k residue 168 LEU Chi-restraints excluded: chain k residue 179 LEU Chi-restraints excluded: chain k residue 201 GLN Chi-restraints excluded: chain k residue 202 VAL Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 392 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 431 optimal weight: 20.0000 chunk 344 optimal weight: 3.9990 chunk 542 optimal weight: 0.8980 chunk 313 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 288 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 89 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN D 87 ASN F 87 ASN G 206 GLN I 87 ASN J 87 ASN J 206 GLN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 201 GLN ** g 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 201 GLN ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.155146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.098714 restraints weight = 100917.530| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.28 r_work: 0.3283 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 44275 Z= 0.154 Angle : 0.512 6.201 59829 Z= 0.269 Chirality : 0.040 0.142 6930 Planarity : 0.003 0.068 7832 Dihedral : 5.045 84.465 6154 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.57 % Allowed : 22.30 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.11), residues: 5489 helix: 1.10 (0.10), residues: 2783 sheet: 0.37 (0.17), residues: 935 loop : -0.73 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 157 TYR 0.012 0.001 TYR k 121 PHE 0.010 0.001 PHE B 179 TRP 0.007 0.001 TRP i 74 HIS 0.002 0.001 HIS h 47 Details of bonding type rmsd covalent geometry : bond 0.00340 (44275) covalent geometry : angle 0.51172 (59829) hydrogen bonds : bond 0.04879 ( 2694) hydrogen bonds : angle 4.84407 ( 7818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 372 time to evaluate : 1.225 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 60 TRP cc_start: 0.5326 (t-100) cc_final: 0.4739 (t60) REVERT: A 142 GLN cc_start: 0.8204 (pm20) cc_final: 0.7978 (mp10) REVERT: A 173 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5905 (mm) REVERT: A 197 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7162 (ptp-110) REVERT: A 242 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8522 (mt-10) REVERT: B 60 TRP cc_start: 0.5505 (t-100) cc_final: 0.4772 (t60) REVERT: B 171 THR cc_start: 0.6267 (p) cc_final: 0.5944 (p) REVERT: B 177 LYS cc_start: 0.8435 (ptmt) cc_final: 0.8067 (tppt) REVERT: B 242 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8479 (mt-10) REVERT: C 60 TRP cc_start: 0.5010 (t-100) cc_final: 0.4502 (t60) REVERT: C 174 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7501 (p) REVERT: C 186 LYS cc_start: 0.7399 (mptt) cc_final: 0.7156 (mptt) REVERT: C 207 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7091 (ttmt) REVERT: D 60 TRP cc_start: 0.5288 (t-100) cc_final: 0.4728 (t60) REVERT: D 83 LYS cc_start: 0.5632 (pttm) cc_final: 0.5278 (pttt) REVERT: D 171 THR cc_start: 0.4961 (p) cc_final: 0.4647 (p) REVERT: E 52 GLU cc_start: 0.5285 (mt-10) cc_final: 0.3963 (tt0) REVERT: E 83 LYS cc_start: 0.6994 (ttmt) cc_final: 0.6628 (mtpt) REVERT: E 110 ILE cc_start: 0.7691 (mm) cc_final: 0.7341 (tp) REVERT: F 60 TRP cc_start: 0.5551 (t-100) cc_final: 0.4795 (t60) REVERT: F 125 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7750 (pp20) REVERT: F 143 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6747 (ttm-80) REVERT: G 52 GLU cc_start: 0.5705 (mt-10) cc_final: 0.5221 (mt-10) REVERT: G 60 TRP cc_start: 0.5034 (t-100) cc_final: 0.4427 (t60) REVERT: G 87 ASN cc_start: 0.7761 (m-40) cc_final: 0.7527 (p0) REVERT: H 60 TRP cc_start: 0.5747 (t-100) cc_final: 0.5053 (t60) REVERT: I 60 TRP cc_start: 0.5435 (t-100) cc_final: 0.4825 (t60) REVERT: I 174 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7775 (p) REVERT: I 233 ASP cc_start: 0.8673 (p0) cc_final: 0.8259 (p0) REVERT: J 60 TRP cc_start: 0.5277 (t-100) cc_final: 0.4801 (t60) REVERT: K 60 TRP cc_start: 0.5007 (t-100) cc_final: 0.4421 (t60) REVERT: a 41 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.5897 (m-80) REVERT: a 74 TRP cc_start: 0.6857 (t-100) cc_final: 0.6200 (t-100) REVERT: a 179 LEU cc_start: 0.5427 (OUTLIER) cc_final: 0.5035 (mt) REVERT: b 74 TRP cc_start: 0.6087 (t-100) cc_final: 0.5512 (t60) REVERT: b 117 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7169 (tt) REVERT: c 74 TRP cc_start: 0.5799 (t-100) cc_final: 0.4966 (t60) REVERT: c 101 MET cc_start: 0.3774 (tpt) cc_final: 0.3116 (mmp) REVERT: c 117 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7713 (mt) REVERT: d 74 TRP cc_start: 0.5526 (t-100) cc_final: 0.4560 (t60) REVERT: d 109 LEU cc_start: 0.7535 (tp) cc_final: 0.7324 (tp) REVERT: d 208 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8626 (tp-100) REVERT: e 74 TRP cc_start: 0.5593 (t-100) cc_final: 0.4743 (t60) REVERT: f 218 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8569 (ttpp) REVERT: g 41 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.6114 (m-80) REVERT: h 41 PHE cc_start: 0.6121 (OUTLIER) cc_final: 0.5870 (m-80) REVERT: h 53 ASN cc_start: 0.6467 (t0) cc_final: 0.5827 (p0) REVERT: h 74 TRP cc_start: 0.6674 (t-100) cc_final: 0.5865 (t-100) REVERT: i 74 TRP cc_start: 0.6816 (t-100) cc_final: 0.6220 (t60) REVERT: i 92 SER cc_start: 0.8158 (p) cc_final: 0.7673 (t) REVERT: j 41 PHE cc_start: 0.6004 (OUTLIER) cc_final: 0.5722 (m-80) REVERT: j 74 TRP cc_start: 0.5787 (t-100) cc_final: 0.4856 (t60) REVERT: j 92 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7833 (t) REVERT: j 109 LEU cc_start: 0.7629 (tp) cc_final: 0.7419 (tp) REVERT: j 117 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8030 (tp) REVERT: j 156 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8717 (mp10) REVERT: k 41 PHE cc_start: 0.6044 (OUTLIER) cc_final: 0.5681 (m-80) REVERT: k 53 ASN cc_start: 0.6989 (m-40) cc_final: 0.6071 (p0) REVERT: k 62 THR cc_start: 0.4084 (OUTLIER) cc_final: 0.3852 (m) REVERT: k 70 PHE cc_start: 0.5506 (m-80) cc_final: 0.4770 (p90) REVERT: k 74 TRP cc_start: 0.6048 (t-100) cc_final: 0.5135 (t60) REVERT: k 156 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8659 (mm-40) REVERT: k 201 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7008 (tt0) outliers start: 214 outliers final: 155 residues processed: 569 average time/residue: 0.2160 time to fit residues: 210.3239 Evaluate side-chains 522 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 344 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain a residue 41 PHE Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 181 ASP Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 223 GLN Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 90 ILE Chi-restraints excluded: chain c residue 91 SER Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain c residue 201 GLN Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain d residue 50 ILE Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 145 VAL Chi-restraints excluded: chain d residue 168 LEU Chi-restraints excluded: chain d residue 202 VAL Chi-restraints excluded: chain d residue 208 GLN Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 179 LEU Chi-restraints excluded: chain e residue 202 VAL Chi-restraints excluded: chain e residue 263 THR Chi-restraints excluded: chain e residue 284 ASP Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 137 VAL Chi-restraints excluded: chain f residue 168 LEU Chi-restraints excluded: chain f residue 192 GLU Chi-restraints excluded: chain f residue 202 VAL Chi-restraints excluded: chain f residue 214 VAL Chi-restraints excluded: chain f residue 218 LYS Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 41 PHE Chi-restraints excluded: chain g residue 59 GLN Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 218 LYS Chi-restraints excluded: chain h residue 40 VAL Chi-restraints excluded: chain h residue 41 PHE Chi-restraints excluded: chain h residue 63 ILE Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 168 LEU Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 192 GLU Chi-restraints excluded: chain h residue 197 VAL Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 LYS Chi-restraints excluded: chain h residue 237 MET Chi-restraints excluded: chain h residue 284 ASP Chi-restraints excluded: chain h residue 291 SER Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 127 ASP Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 145 VAL Chi-restraints excluded: chain i residue 156 GLN Chi-restraints excluded: chain i residue 167 GLU Chi-restraints excluded: chain i residue 168 LEU Chi-restraints excluded: chain i residue 223 GLN Chi-restraints excluded: chain i residue 284 ASP Chi-restraints excluded: chain j residue 41 PHE Chi-restraints excluded: chain j residue 63 ILE Chi-restraints excluded: chain j residue 90 ILE Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 117 LEU Chi-restraints excluded: chain j residue 137 VAL Chi-restraints excluded: chain j residue 145 VAL Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 41 PHE Chi-restraints excluded: chain k residue 62 THR Chi-restraints excluded: chain k residue 90 ILE Chi-restraints excluded: chain k residue 137 VAL Chi-restraints excluded: chain k residue 145 VAL Chi-restraints excluded: chain k residue 168 LEU Chi-restraints excluded: chain k residue 179 LEU Chi-restraints excluded: chain k residue 201 GLN Chi-restraints excluded: chain k residue 202 VAL Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 547 optimal weight: 0.9980 chunk 521 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 459 optimal weight: 4.9990 chunk 203 optimal weight: 20.0000 chunk 346 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 402 optimal weight: 5.9990 chunk 515 optimal weight: 10.0000 chunk 246 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN C 87 ASN D 87 ASN F 87 ASN I 87 ASN I 206 GLN J 87 ASN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 GLN ** c 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 152 GLN ** g 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 156 GLN ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 156 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.154160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.103233 restraints weight = 100994.099| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 4.82 r_work: 0.3198 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 44275 Z= 0.204 Angle : 0.539 6.841 59829 Z= 0.282 Chirality : 0.041 0.147 6930 Planarity : 0.004 0.059 7832 Dihedral : 5.022 86.627 6149 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.67 % Allowed : 22.56 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.11), residues: 5489 helix: 0.96 (0.10), residues: 2816 sheet: 0.37 (0.17), residues: 935 loop : -0.86 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 133 TYR 0.013 0.002 TYR F 259 PHE 0.021 0.001 PHE B 179 TRP 0.003 0.001 TRP i 74 HIS 0.003 0.001 HIS e 47 Details of bonding type rmsd covalent geometry : bond 0.00465 (44275) covalent geometry : angle 0.53897 (59829) hydrogen bonds : bond 0.05077 ( 2694) hydrogen bonds : angle 4.88506 ( 7818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 364 time to evaluate : 1.657 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 60 TRP cc_start: 0.5314 (t-100) cc_final: 0.4725 (t60) REVERT: A 142 GLN cc_start: 0.8204 (pm20) cc_final: 0.8002 (mp10) REVERT: A 197 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7145 (ptp-110) REVERT: A 242 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8478 (mt-10) REVERT: B 60 TRP cc_start: 0.5481 (t-100) cc_final: 0.4812 (t60) REVERT: B 171 THR cc_start: 0.6310 (p) cc_final: 0.6006 (p) REVERT: B 242 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8423 (mt-10) REVERT: C 60 TRP cc_start: 0.4966 (t-100) cc_final: 0.4466 (t60) REVERT: C 174 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7545 (p) REVERT: C 207 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7047 (ttmt) REVERT: D 60 TRP cc_start: 0.5248 (t-100) cc_final: 0.4716 (t60) REVERT: D 83 LYS cc_start: 0.5709 (pttm) cc_final: 0.5327 (pttt) REVERT: D 171 THR cc_start: 0.5136 (p) cc_final: 0.4821 (p) REVERT: D 175 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6900 (m-80) REVERT: D 242 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8399 (mt-10) REVERT: E 52 GLU cc_start: 0.5332 (mt-10) cc_final: 0.4057 (tt0) REVERT: E 83 LYS cc_start: 0.6937 (ttmt) cc_final: 0.6575 (mtpt) REVERT: E 110 ILE cc_start: 0.7689 (mm) cc_final: 0.7300 (tp) REVERT: F 60 TRP cc_start: 0.5573 (t-100) cc_final: 0.4850 (t60) REVERT: F 125 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7725 (pp20) REVERT: F 143 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6738 (ttm-80) REVERT: G 52 GLU cc_start: 0.5634 (mt-10) cc_final: 0.5177 (mt-10) REVERT: G 60 TRP cc_start: 0.5010 (t-100) cc_final: 0.4426 (t60) REVERT: G 87 ASN cc_start: 0.7776 (m-40) cc_final: 0.7547 (p0) REVERT: G 174 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7939 (p) REVERT: H 60 TRP cc_start: 0.5743 (t-100) cc_final: 0.5068 (t60) REVERT: I 60 TRP cc_start: 0.5456 (t-100) cc_final: 0.4862 (t60) REVERT: I 174 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7758 (p) REVERT: J 60 TRP cc_start: 0.5265 (t-100) cc_final: 0.4800 (t60) REVERT: K 60 TRP cc_start: 0.5048 (t-100) cc_final: 0.4477 (t60) REVERT: a 41 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.5770 (m-80) REVERT: a 59 GLN cc_start: 0.5637 (OUTLIER) cc_final: 0.5435 (mm-40) REVERT: a 74 TRP cc_start: 0.6854 (t-100) cc_final: 0.6209 (t-100) REVERT: a 179 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.4998 (mt) REVERT: b 74 TRP cc_start: 0.6100 (t-100) cc_final: 0.5489 (t60) REVERT: b 117 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7167 (tt) REVERT: c 74 TRP cc_start: 0.5872 (t-100) cc_final: 0.5009 (t60) REVERT: c 101 MET cc_start: 0.3821 (tpt) cc_final: 0.3411 (mmp) REVERT: c 117 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7618 (mt) REVERT: d 74 TRP cc_start: 0.5524 (t-100) cc_final: 0.4579 (t60) REVERT: d 109 LEU cc_start: 0.7589 (tp) cc_final: 0.7360 (tp) REVERT: d 208 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8644 (tp-100) REVERT: e 74 TRP cc_start: 0.5602 (t-100) cc_final: 0.4744 (t60) REVERT: f 218 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8489 (ttpp) REVERT: h 53 ASN cc_start: 0.6495 (t0) cc_final: 0.5807 (p0) REVERT: h 70 PHE cc_start: 0.5397 (m-80) cc_final: 0.4173 (p90) REVERT: h 74 TRP cc_start: 0.6754 (t-100) cc_final: 0.5938 (t-100) REVERT: h 100 GLN cc_start: 0.5193 (OUTLIER) cc_final: 0.4839 (pt0) REVERT: i 74 TRP cc_start: 0.6939 (t-100) cc_final: 0.6348 (t60) REVERT: i 92 SER cc_start: 0.8136 (p) cc_final: 0.7670 (t) REVERT: j 41 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.5707 (m-80) REVERT: j 74 TRP cc_start: 0.5839 (t-100) cc_final: 0.4932 (t60) REVERT: j 109 LEU cc_start: 0.7661 (tp) cc_final: 0.7443 (tp) REVERT: j 156 GLN cc_start: 0.9059 (mm110) cc_final: 0.8784 (mp10) REVERT: k 41 PHE cc_start: 0.6014 (OUTLIER) cc_final: 0.5679 (m-80) REVERT: k 53 ASN cc_start: 0.6993 (m-40) cc_final: 0.6077 (p0) REVERT: k 74 TRP cc_start: 0.6053 (t-100) cc_final: 0.5148 (t60) REVERT: k 156 GLN cc_start: 0.9100 (mm110) cc_final: 0.8689 (mm-40) outliers start: 219 outliers final: 170 residues processed: 568 average time/residue: 0.2080 time to fit residues: 203.3291 Evaluate side-chains 536 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 345 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 PHE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 211 ILE Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 41 PHE Chi-restraints excluded: chain a residue 59 GLN Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain a residue 192 GLU Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 181 ASP Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 223 GLN Chi-restraints excluded: chain b residue 291 SER Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 90 ILE Chi-restraints excluded: chain c residue 91 SER Chi-restraints excluded: chain c residue 100 GLN Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 295 ILE Chi-restraints excluded: chain d residue 40 VAL Chi-restraints excluded: chain d residue 50 ILE Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 145 VAL Chi-restraints excluded: chain d residue 168 LEU Chi-restraints excluded: chain d residue 202 VAL Chi-restraints excluded: chain d residue 208 GLN Chi-restraints excluded: chain d residue 214 VAL Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain e residue 90 ILE Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 179 LEU Chi-restraints excluded: chain e residue 202 VAL Chi-restraints excluded: chain e residue 263 THR Chi-restraints excluded: chain e residue 284 ASP Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 90 ILE Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 137 VAL Chi-restraints excluded: chain f residue 168 LEU Chi-restraints excluded: chain f residue 192 GLU Chi-restraints excluded: chain f residue 202 VAL Chi-restraints excluded: chain f residue 214 VAL Chi-restraints excluded: chain f residue 218 LYS Chi-restraints excluded: chain f residue 224 LYS Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 90 ILE Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 218 LYS Chi-restraints excluded: chain h residue 63 ILE Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain h residue 100 GLN Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 168 LEU Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 192 GLU Chi-restraints excluded: chain h residue 197 VAL Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 LYS Chi-restraints excluded: chain h residue 284 ASP Chi-restraints excluded: chain h residue 291 SER Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 127 ASP Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 145 VAL Chi-restraints excluded: chain i residue 156 GLN Chi-restraints excluded: chain i residue 167 GLU Chi-restraints excluded: chain i residue 168 LEU Chi-restraints excluded: chain i residue 284 ASP Chi-restraints excluded: chain i residue 291 SER Chi-restraints excluded: chain j residue 41 PHE Chi-restraints excluded: chain j residue 63 ILE Chi-restraints excluded: chain j residue 90 ILE Chi-restraints excluded: chain j residue 137 VAL Chi-restraints excluded: chain j residue 145 VAL Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 179 LEU Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 41 PHE Chi-restraints excluded: chain k residue 90 ILE Chi-restraints excluded: chain k residue 137 VAL Chi-restraints excluded: chain k residue 145 VAL Chi-restraints excluded: chain k residue 168 LEU Chi-restraints excluded: chain k residue 179 LEU Chi-restraints excluded: chain k residue 201 GLN Chi-restraints excluded: chain k residue 202 VAL Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 255 optimal weight: 9.9990 chunk 506 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 352 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 332 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 378 optimal weight: 5.9990 chunk 454 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN D 87 ASN D 205 GLN F 87 ASN H 205 GLN J 86 GLN J 87 ASN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 201 GLN d 211 GLN e 152 GLN ** g 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.151405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.098884 restraints weight = 100262.695| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 4.51 r_work: 0.3158 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.088 44275 Z= 0.412 Angle : 0.698 11.023 59829 Z= 0.363 Chirality : 0.046 0.262 6930 Planarity : 0.005 0.052 7832 Dihedral : 5.471 84.963 6149 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.91 % Allowed : 23.22 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.11), residues: 5489 helix: 0.69 (0.10), residues: 2618 sheet: 0.24 (0.17), residues: 935 loop : -1.25 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 133 TYR 0.017 0.003 TYR D 259 PHE 0.018 0.002 PHE H 161 TRP 0.010 0.001 TRP a 74 HIS 0.005 0.001 HIS a 47 Details of bonding type rmsd covalent geometry : bond 0.00951 (44275) covalent geometry : angle 0.69788 (59829) hydrogen bonds : bond 0.05895 ( 2694) hydrogen bonds : angle 5.30072 ( 7818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 352 time to evaluate : 1.263 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 60 TRP cc_start: 0.5350 (t-100) cc_final: 0.4773 (t60) REVERT: A 242 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8782 (mt-10) REVERT: B 60 TRP cc_start: 0.5608 (t-100) cc_final: 0.4937 (t60) REVERT: B 242 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8704 (mt-10) REVERT: C 60 TRP cc_start: 0.5084 (t-100) cc_final: 0.4570 (t60) REVERT: C 207 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7346 (ttmt) REVERT: D 60 TRP cc_start: 0.5208 (t-100) cc_final: 0.4718 (t60) REVERT: D 83 LYS cc_start: 0.5752 (pttm) cc_final: 0.5350 (pttt) REVERT: D 171 THR cc_start: 0.5235 (p) cc_final: 0.4925 (p) REVERT: D 175 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: D 242 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8743 (mt-10) REVERT: E 52 GLU cc_start: 0.5404 (mt-10) cc_final: 0.4997 (mt-10) REVERT: F 60 TRP cc_start: 0.5603 (t-100) cc_final: 0.4875 (t60) REVERT: F 143 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6810 (ttm-80) REVERT: F 242 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8703 (mt-10) REVERT: G 60 TRP cc_start: 0.5059 (t-100) cc_final: 0.4462 (t60) REVERT: G 87 ASN cc_start: 0.7735 (m-40) cc_final: 0.7442 (p0) REVERT: H 60 TRP cc_start: 0.5703 (t-100) cc_final: 0.5028 (t60) REVERT: H 83 LYS cc_start: 0.5229 (OUTLIER) cc_final: 0.4897 (pttt) REVERT: I 60 TRP cc_start: 0.5508 (t-100) cc_final: 0.4893 (t60) REVERT: I 174 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7699 (p) REVERT: J 60 TRP cc_start: 0.5304 (t-100) cc_final: 0.4818 (t60) REVERT: K 60 TRP cc_start: 0.5050 (t-100) cc_final: 0.4473 (t60) REVERT: a 41 PHE cc_start: 0.6009 (OUTLIER) cc_final: 0.5520 (t80) REVERT: a 59 GLN cc_start: 0.5647 (OUTLIER) cc_final: 0.5417 (mm-40) REVERT: a 74 TRP cc_start: 0.6998 (t-100) cc_final: 0.6246 (t-100) REVERT: a 156 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8554 (mm-40) REVERT: b 74 TRP cc_start: 0.6073 (t-100) cc_final: 0.5410 (t60) REVERT: b 89 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8222 (mmtm) REVERT: b 117 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7259 (tt) REVERT: c 74 TRP cc_start: 0.5953 (t-100) cc_final: 0.4985 (t60) REVERT: c 100 GLN cc_start: 0.4113 (OUTLIER) cc_final: 0.3852 (pm20) REVERT: c 101 MET cc_start: 0.4142 (tpt) cc_final: 0.3569 (mmp) REVERT: d 74 TRP cc_start: 0.5563 (t-100) cc_final: 0.4595 (t60) REVERT: d 100 GLN cc_start: 0.4668 (OUTLIER) cc_final: 0.4461 (pt0) REVERT: d 208 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8748 (tp-100) REVERT: f 238 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8681 (tt) REVERT: h 74 TRP cc_start: 0.6807 (t-100) cc_final: 0.6139 (t60) REVERT: h 100 GLN cc_start: 0.5226 (OUTLIER) cc_final: 0.4865 (pt0) REVERT: i 74 TRP cc_start: 0.6990 (t-100) cc_final: 0.6126 (t-100) REVERT: j 74 TRP cc_start: 0.5808 (t-100) cc_final: 0.4874 (t60) REVERT: j 156 GLN cc_start: 0.8991 (mm110) cc_final: 0.8708 (mp10) REVERT: k 74 TRP cc_start: 0.6225 (t-100) cc_final: 0.5285 (t60) REVERT: k 156 GLN cc_start: 0.9050 (mm110) cc_final: 0.8669 (mm-40) outliers start: 230 outliers final: 177 residues processed: 566 average time/residue: 0.1887 time to fit residues: 184.9698 Evaluate side-chains 524 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 330 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 PHE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 134 PHE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 179 PHE Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 211 ILE Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 41 PHE Chi-restraints excluded: chain a residue 59 GLN Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 192 GLU Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 223 GLN Chi-restraints excluded: chain b residue 291 SER Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 90 ILE Chi-restraints excluded: chain c residue 91 SER Chi-restraints excluded: chain c residue 100 GLN Chi-restraints excluded: chain c residue 104 ILE Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 295 ILE Chi-restraints excluded: chain d residue 40 VAL Chi-restraints excluded: chain d residue 50 ILE Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 100 GLN Chi-restraints excluded: chain d residue 113 ASN Chi-restraints excluded: chain d residue 126 LEU Chi-restraints excluded: chain d residue 145 VAL Chi-restraints excluded: chain d residue 168 LEU Chi-restraints excluded: chain d residue 202 VAL Chi-restraints excluded: chain d residue 208 GLN Chi-restraints excluded: chain d residue 214 VAL Chi-restraints excluded: chain e residue 90 ILE Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 179 LEU Chi-restraints excluded: chain e residue 202 VAL Chi-restraints excluded: chain e residue 263 THR Chi-restraints excluded: chain e residue 284 ASP Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 90 ILE Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 137 VAL Chi-restraints excluded: chain f residue 168 LEU Chi-restraints excluded: chain f residue 192 GLU Chi-restraints excluded: chain f residue 202 VAL Chi-restraints excluded: chain f residue 214 VAL Chi-restraints excluded: chain f residue 218 LYS Chi-restraints excluded: chain f residue 224 LYS Chi-restraints excluded: chain f residue 238 LEU Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 59 GLN Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 90 ILE Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 218 LYS Chi-restraints excluded: chain g residue 291 SER Chi-restraints excluded: chain h residue 63 ILE Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain h residue 100 GLN Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 168 LEU Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 192 GLU Chi-restraints excluded: chain h residue 197 VAL Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 LYS Chi-restraints excluded: chain h residue 269 ASN Chi-restraints excluded: chain h residue 284 ASP Chi-restraints excluded: chain h residue 291 SER Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 127 ASP Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 145 VAL Chi-restraints excluded: chain i residue 156 GLN Chi-restraints excluded: chain i residue 167 GLU Chi-restraints excluded: chain i residue 168 LEU Chi-restraints excluded: chain i residue 263 THR Chi-restraints excluded: chain i residue 284 ASP Chi-restraints excluded: chain i residue 291 SER Chi-restraints excluded: chain j residue 63 ILE Chi-restraints excluded: chain j residue 90 ILE Chi-restraints excluded: chain j residue 137 VAL Chi-restraints excluded: chain j residue 145 VAL Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 59 GLN Chi-restraints excluded: chain k residue 90 ILE Chi-restraints excluded: chain k residue 137 VAL Chi-restraints excluded: chain k residue 145 VAL Chi-restraints excluded: chain k residue 168 LEU Chi-restraints excluded: chain k residue 179 LEU Chi-restraints excluded: chain k residue 201 GLN Chi-restraints excluded: chain k residue 202 VAL Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 487 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 399 optimal weight: 9.9990 chunk 410 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 549 optimal weight: 0.5980 chunk 456 optimal weight: 9.9990 chunk 302 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN D 87 ASN E 206 GLN I 86 GLN ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 ASN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 GLN c 201 GLN d 159 GLN e 152 GLN ** g 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 152 GLN ** j 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.155487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.100017 restraints weight = 101341.869| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.58 r_work: 0.3291 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 44275 Z= 0.124 Angle : 0.513 7.353 59829 Z= 0.272 Chirality : 0.041 0.156 6930 Planarity : 0.003 0.053 7832 Dihedral : 4.941 85.148 6142 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.33 % Allowed : 24.95 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.11), residues: 5489 helix: 0.98 (0.10), residues: 2750 sheet: 0.20 (0.16), residues: 957 loop : -1.07 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.013 0.001 TYR h 121 PHE 0.024 0.001 PHE A 179 TRP 0.006 0.001 TRP h 74 HIS 0.002 0.001 HIS a 69 Details of bonding type rmsd covalent geometry : bond 0.00250 (44275) covalent geometry : angle 0.51317 (59829) hydrogen bonds : bond 0.04755 ( 2694) hydrogen bonds : angle 4.82613 ( 7818) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 382 time to evaluate : 1.024 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: A 60 TRP cc_start: 0.5394 (t-100) cc_final: 0.4786 (t60) REVERT: B 60 TRP cc_start: 0.5566 (t-100) cc_final: 0.4907 (t60) REVERT: B 177 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8476 (tppt) REVERT: B 242 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8513 (mt-10) REVERT: C 60 TRP cc_start: 0.5082 (t-100) cc_final: 0.4550 (t60) REVERT: C 207 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7288 (tttt) REVERT: D 60 TRP cc_start: 0.5073 (t-100) cc_final: 0.4637 (t60) REVERT: D 83 LYS cc_start: 0.5716 (pttm) cc_final: 0.5309 (pttt) REVERT: D 171 THR cc_start: 0.4891 (p) cc_final: 0.4583 (p) REVERT: D 175 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6870 (m-80) REVERT: D 242 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8493 (mt-10) REVERT: E 52 GLU cc_start: 0.5294 (mt-10) cc_final: 0.4079 (tt0) REVERT: E 110 ILE cc_start: 0.7668 (mm) cc_final: 0.7257 (tp) REVERT: F 60 TRP cc_start: 0.5614 (t-100) cc_final: 0.4905 (t60) REVERT: F 83 LYS cc_start: 0.5531 (ptpp) cc_final: 0.5294 (pttt) REVERT: F 117 ARG cc_start: 0.7309 (mmm-85) cc_final: 0.6885 (mmm-85) REVERT: F 125 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7684 (pp20) REVERT: F 242 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8455 (mt-10) REVERT: G 60 TRP cc_start: 0.5045 (t-100) cc_final: 0.4457 (t60) REVERT: G 87 ASN cc_start: 0.7750 (m-40) cc_final: 0.7468 (p0) REVERT: H 60 TRP cc_start: 0.5715 (t-100) cc_final: 0.5018 (t60) REVERT: H 106 ILE cc_start: 0.8488 (tp) cc_final: 0.8141 (mt) REVERT: I 60 TRP cc_start: 0.5466 (t-100) cc_final: 0.4878 (t60) REVERT: I 110 ILE cc_start: 0.7188 (mm) cc_final: 0.6764 (pt) REVERT: I 174 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7708 (p) REVERT: J 60 TRP cc_start: 0.5295 (t-100) cc_final: 0.4817 (t60) REVERT: K 60 TRP cc_start: 0.5084 (t-100) cc_final: 0.4496 (t60) REVERT: K 83 LYS cc_start: 0.5511 (ptpp) cc_final: 0.5177 (pttt) REVERT: a 74 TRP cc_start: 0.6929 (t-100) cc_final: 0.6153 (t-100) REVERT: b 74 TRP cc_start: 0.6097 (t-100) cc_final: 0.5459 (t60) REVERT: b 89 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8175 (mmtm) REVERT: b 117 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7208 (tt) REVERT: c 74 TRP cc_start: 0.5757 (t-100) cc_final: 0.4972 (t60) REVERT: c 100 GLN cc_start: 0.4002 (OUTLIER) cc_final: 0.3728 (pm20) REVERT: c 101 MET cc_start: 0.3663 (tpt) cc_final: 0.2854 (mmp) REVERT: d 74 TRP cc_start: 0.5513 (t-100) cc_final: 0.4420 (t60) REVERT: d 208 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8606 (tp-100) REVERT: e 74 TRP cc_start: 0.5547 (t-100) cc_final: 0.4612 (t60) REVERT: f 165 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7182 (ttp-110) REVERT: f 218 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8569 (ttpp) REVERT: h 70 PHE cc_start: 0.5420 (m-80) cc_final: 0.4268 (p90) REVERT: h 74 TRP cc_start: 0.6686 (t-100) cc_final: 0.5903 (t-100) REVERT: i 53 ASN cc_start: 0.6731 (m-40) cc_final: 0.6506 (p0) REVERT: i 74 TRP cc_start: 0.7023 (t-100) cc_final: 0.6208 (t60) REVERT: j 41 PHE cc_start: 0.5829 (OUTLIER) cc_final: 0.5546 (m-80) REVERT: j 74 TRP cc_start: 0.5695 (t-100) cc_final: 0.4717 (t60) REVERT: k 53 ASN cc_start: 0.6927 (m-40) cc_final: 0.6065 (p0) REVERT: k 70 PHE cc_start: 0.5363 (m-80) cc_final: 0.4661 (p90) REVERT: k 74 TRP cc_start: 0.6079 (t-100) cc_final: 0.5176 (t60) REVERT: k 156 GLN cc_start: 0.9118 (mm110) cc_final: 0.8720 (mm-40) outliers start: 156 outliers final: 115 residues processed: 526 average time/residue: 0.1515 time to fit residues: 137.2592 Evaluate side-chains 475 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 348 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 PHE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 179 PHE Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 192 GLU Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 223 GLN Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 91 SER Chi-restraints excluded: chain c residue 100 GLN Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain c residue 201 GLN Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 284 ASP Chi-restraints excluded: chain d residue 40 VAL Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 168 LEU Chi-restraints excluded: chain d residue 208 GLN Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 179 LEU Chi-restraints excluded: chain e residue 263 THR Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 168 LEU Chi-restraints excluded: chain f residue 192 GLU Chi-restraints excluded: chain f residue 218 LYS Chi-restraints excluded: chain f residue 224 LYS Chi-restraints excluded: chain g residue 59 GLN Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 218 LYS Chi-restraints excluded: chain h residue 63 ILE Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain h residue 168 LEU Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 192 GLU Chi-restraints excluded: chain h residue 197 VAL Chi-restraints excluded: chain h residue 218 LYS Chi-restraints excluded: chain h residue 284 ASP Chi-restraints excluded: chain h residue 291 SER Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 117 LEU Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 145 VAL Chi-restraints excluded: chain i residue 156 GLN Chi-restraints excluded: chain i residue 167 GLU Chi-restraints excluded: chain i residue 168 LEU Chi-restraints excluded: chain i residue 284 ASP Chi-restraints excluded: chain j residue 41 PHE Chi-restraints excluded: chain j residue 63 ILE Chi-restraints excluded: chain j residue 145 VAL Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 179 LEU Chi-restraints excluded: chain k residue 145 VAL Chi-restraints excluded: chain k residue 168 LEU Chi-restraints excluded: chain k residue 179 LEU Chi-restraints excluded: chain k residue 201 GLN Chi-restraints excluded: chain k residue 202 VAL Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 396 optimal weight: 20.0000 chunk 268 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 459 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 509 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 469 optimal weight: 5.9990 chunk 333 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN E 206 GLN J 87 ASN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 159 GLN g 103 ASN ** g 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 201 GLN ** j 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.151890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.098962 restraints weight = 100441.314| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 4.93 r_work: 0.3151 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 44275 Z= 0.358 Angle : 0.674 10.595 59829 Z= 0.350 Chirality : 0.045 0.162 6930 Planarity : 0.005 0.052 7832 Dihedral : 5.287 86.514 6142 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.48 % Allowed : 25.10 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.11), residues: 5489 helix: 0.55 (0.10), residues: 2750 sheet: 0.18 (0.17), residues: 935 loop : -1.14 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG i 191 TYR 0.018 0.002 TYR B 259 PHE 0.017 0.002 PHE H 161 TRP 0.011 0.001 TRP a 74 HIS 0.005 0.001 HIS d 47 Details of bonding type rmsd covalent geometry : bond 0.00831 (44275) covalent geometry : angle 0.67361 (59829) hydrogen bonds : bond 0.05697 ( 2694) hydrogen bonds : angle 5.17607 ( 7818) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 353 time to evaluate : 1.046 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: A 60 TRP cc_start: 0.5372 (t-100) cc_final: 0.4798 (t60) REVERT: A 242 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8551 (mt-10) REVERT: B 60 TRP cc_start: 0.5566 (t-100) cc_final: 0.4939 (t60) REVERT: B 242 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8450 (mt-10) REVERT: C 60 TRP cc_start: 0.5066 (t-100) cc_final: 0.4568 (t60) REVERT: C 207 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.6972 (ttmt) REVERT: C 233 ASP cc_start: 0.8885 (p0) cc_final: 0.8657 (p0) REVERT: D 60 TRP cc_start: 0.5067 (t-100) cc_final: 0.4644 (t60) REVERT: D 83 LYS cc_start: 0.5726 (pttm) cc_final: 0.5316 (pttt) REVERT: D 171 THR cc_start: 0.4944 (p) cc_final: 0.4601 (p) REVERT: D 175 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: D 242 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8475 (mt-10) REVERT: E 52 GLU cc_start: 0.5497 (mt-10) cc_final: 0.5150 (mt-10) REVERT: F 60 TRP cc_start: 0.5604 (t-100) cc_final: 0.4938 (t60) REVERT: F 83 LYS cc_start: 0.5415 (ptpp) cc_final: 0.5108 (pttt) REVERT: F 117 ARG cc_start: 0.7335 (mmm-85) cc_final: 0.6726 (mmm-85) REVERT: F 125 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7723 (pp20) REVERT: F 242 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8451 (mt-10) REVERT: G 60 TRP cc_start: 0.5071 (t-100) cc_final: 0.4495 (t60) REVERT: G 87 ASN cc_start: 0.7743 (m-40) cc_final: 0.7404 (p0) REVERT: H 60 TRP cc_start: 0.5660 (t-100) cc_final: 0.5013 (t60) REVERT: H 83 LYS cc_start: 0.5094 (OUTLIER) cc_final: 0.4762 (pttt) REVERT: I 60 TRP cc_start: 0.5475 (t-100) cc_final: 0.4888 (t60) REVERT: I 117 ARG cc_start: 0.7466 (mmm-85) cc_final: 0.6792 (mmm-85) REVERT: I 174 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7714 (p) REVERT: I 233 ASP cc_start: 0.8926 (p0) cc_final: 0.8711 (p0) REVERT: J 60 TRP cc_start: 0.5320 (t-100) cc_final: 0.4831 (t60) REVERT: K 60 TRP cc_start: 0.5022 (t-100) cc_final: 0.4468 (t60) REVERT: K 83 LYS cc_start: 0.5521 (ptpp) cc_final: 0.5117 (pttt) REVERT: a 41 PHE cc_start: 0.5800 (OUTLIER) cc_final: 0.5466 (t80) REVERT: a 74 TRP cc_start: 0.7073 (t-100) cc_final: 0.6306 (t-100) REVERT: a 156 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8582 (mm-40) REVERT: a 168 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6220 (tm) REVERT: b 74 TRP cc_start: 0.6176 (t-100) cc_final: 0.5429 (t60) REVERT: b 89 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8138 (mmtm) REVERT: c 74 TRP cc_start: 0.5707 (t-100) cc_final: 0.4903 (t60) REVERT: c 101 MET cc_start: 0.3830 (tpt) cc_final: 0.3503 (mmp) REVERT: d 74 TRP cc_start: 0.5465 (t-100) cc_final: 0.4510 (t60) REVERT: d 100 GLN cc_start: 0.4649 (OUTLIER) cc_final: 0.4428 (pt0) REVERT: d 208 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8763 (tp-100) REVERT: f 238 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8454 (tt) REVERT: g 53 ASN cc_start: 0.6472 (m-40) cc_final: 0.5641 (p0) REVERT: h 70 PHE cc_start: 0.5269 (m-80) cc_final: 0.4326 (p90) REVERT: h 74 TRP cc_start: 0.6841 (t-100) cc_final: 0.6094 (t60) REVERT: h 100 GLN cc_start: 0.5182 (OUTLIER) cc_final: 0.4825 (pt0) REVERT: i 74 TRP cc_start: 0.7085 (t-100) cc_final: 0.6187 (t-100) REVERT: j 74 TRP cc_start: 0.5564 (t-100) cc_final: 0.4692 (t60) REVERT: j 156 GLN cc_start: 0.9052 (mm110) cc_final: 0.8741 (mp10) REVERT: k 74 TRP cc_start: 0.6187 (t-100) cc_final: 0.5283 (t60) REVERT: k 156 GLN cc_start: 0.9040 (mm110) cc_final: 0.8656 (mm-40) outliers start: 163 outliers final: 128 residues processed: 502 average time/residue: 0.1549 time to fit residues: 134.0814 Evaluate side-chains 483 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 340 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 PHE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 179 PHE Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 41 PHE Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 192 GLU Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 91 SER Chi-restraints excluded: chain c residue 104 ILE Chi-restraints excluded: chain c residue 126 LEU Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain d residue 40 VAL Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 100 GLN Chi-restraints excluded: chain d residue 168 LEU Chi-restraints excluded: chain d residue 208 GLN Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 179 LEU Chi-restraints excluded: chain e residue 263 THR Chi-restraints excluded: chain e residue 284 ASP Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 137 VAL Chi-restraints excluded: chain f residue 168 LEU Chi-restraints excluded: chain f residue 192 GLU Chi-restraints excluded: chain f residue 202 VAL Chi-restraints excluded: chain f residue 218 LYS Chi-restraints excluded: chain f residue 224 LYS Chi-restraints excluded: chain f residue 238 LEU Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 218 LYS Chi-restraints excluded: chain h residue 63 ILE Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain h residue 100 GLN Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 168 LEU Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 192 GLU Chi-restraints excluded: chain h residue 197 VAL Chi-restraints excluded: chain h residue 218 LYS Chi-restraints excluded: chain h residue 284 ASP Chi-restraints excluded: chain h residue 291 SER Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 117 LEU Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 145 VAL Chi-restraints excluded: chain i residue 156 GLN Chi-restraints excluded: chain i residue 167 GLU Chi-restraints excluded: chain i residue 168 LEU Chi-restraints excluded: chain i residue 263 THR Chi-restraints excluded: chain j residue 63 ILE Chi-restraints excluded: chain j residue 90 ILE Chi-restraints excluded: chain j residue 145 VAL Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain k residue 137 VAL Chi-restraints excluded: chain k residue 145 VAL Chi-restraints excluded: chain k residue 168 LEU Chi-restraints excluded: chain k residue 179 LEU Chi-restraints excluded: chain k residue 201 GLN Chi-restraints excluded: chain k residue 202 VAL Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 525 optimal weight: 20.0000 chunk 430 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 530 optimal weight: 9.9990 chunk 354 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 342 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 277 optimal weight: 20.0000 chunk 545 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN D 87 ASN D 89 ASN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 103 ASN ** g 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.152625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.099303 restraints weight = 100557.672| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.99 r_work: 0.3174 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 44275 Z= 0.275 Angle : 0.612 8.842 59829 Z= 0.320 Chirality : 0.043 0.166 6930 Planarity : 0.004 0.051 7832 Dihedral : 5.201 87.400 6140 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.41 % Allowed : 25.14 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.11), residues: 5489 helix: 0.57 (0.10), residues: 2750 sheet: 0.02 (0.16), residues: 957 loop : -1.15 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG i 191 TYR 0.017 0.002 TYR j 77 PHE 0.018 0.001 PHE A 179 TRP 0.012 0.001 TRP i 74 HIS 0.004 0.001 HIS h 69 Details of bonding type rmsd covalent geometry : bond 0.00633 (44275) covalent geometry : angle 0.61239 (59829) hydrogen bonds : bond 0.05401 ( 2694) hydrogen bonds : angle 5.11283 ( 7818) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10978 Ramachandran restraints generated. 5489 Oldfield, 0 Emsley, 5489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 348 time to evaluate : 1.050 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 60 TRP cc_start: 0.5333 (t-100) cc_final: 0.4792 (t60) REVERT: A 242 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8541 (mt-10) REVERT: B 60 TRP cc_start: 0.5541 (t-100) cc_final: 0.4929 (t60) REVERT: B 83 LYS cc_start: 0.5399 (ptpp) cc_final: 0.4914 (pttt) REVERT: B 242 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8443 (mt-10) REVERT: C 60 TRP cc_start: 0.5037 (t-100) cc_final: 0.4556 (t60) REVERT: C 106 ILE cc_start: 0.8358 (tp) cc_final: 0.8019 (mt) REVERT: C 207 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.6916 (ttmt) REVERT: D 60 TRP cc_start: 0.5052 (t-100) cc_final: 0.4632 (t60) REVERT: D 79 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7402 (tp) REVERT: D 83 LYS cc_start: 0.5675 (pttm) cc_final: 0.5284 (pttt) REVERT: D 171 THR cc_start: 0.4791 (p) cc_final: 0.4488 (p) REVERT: D 242 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: E 52 GLU cc_start: 0.5644 (mt-10) cc_final: 0.5399 (mt-10) REVERT: F 60 TRP cc_start: 0.5562 (t-100) cc_final: 0.4910 (t60) REVERT: F 83 LYS cc_start: 0.5460 (ptpp) cc_final: 0.5152 (pttt) REVERT: F 117 ARG cc_start: 0.7316 (mmm-85) cc_final: 0.6703 (mmm-85) REVERT: F 125 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7701 (pp20) REVERT: F 242 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8421 (mt-10) REVERT: G 60 TRP cc_start: 0.5069 (t-100) cc_final: 0.4496 (t60) REVERT: G 87 ASN cc_start: 0.7698 (m-40) cc_final: 0.7347 (p0) REVERT: H 60 TRP cc_start: 0.5685 (t-100) cc_final: 0.5027 (t60) REVERT: I 60 TRP cc_start: 0.5451 (t-100) cc_final: 0.4894 (t60) REVERT: I 174 THR cc_start: 0.7978 (OUTLIER) cc_final: 0.7717 (p) REVERT: J 60 TRP cc_start: 0.5277 (t-100) cc_final: 0.4813 (t60) REVERT: K 60 TRP cc_start: 0.5036 (t-100) cc_final: 0.4467 (t60) REVERT: K 83 LYS cc_start: 0.5526 (ptpp) cc_final: 0.5126 (pttt) REVERT: a 41 PHE cc_start: 0.5796 (OUTLIER) cc_final: 0.5464 (t80) REVERT: a 74 TRP cc_start: 0.7086 (t-100) cc_final: 0.6455 (t-100) REVERT: a 168 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6177 (tm) REVERT: b 89 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8133 (mmtm) REVERT: c 74 TRP cc_start: 0.5669 (t-100) cc_final: 0.4827 (t60) REVERT: c 101 MET cc_start: 0.3839 (tpt) cc_final: 0.3422 (mmp) REVERT: d 74 TRP cc_start: 0.5479 (t-100) cc_final: 0.4470 (t60) REVERT: d 100 GLN cc_start: 0.4675 (OUTLIER) cc_final: 0.4449 (pt0) REVERT: d 208 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8765 (tp-100) REVERT: e 179 LEU cc_start: 0.4502 (OUTLIER) cc_final: 0.4269 (mt) REVERT: f 238 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8450 (tt) REVERT: h 70 PHE cc_start: 0.5270 (m-80) cc_final: 0.4299 (p90) REVERT: h 74 TRP cc_start: 0.6703 (t-100) cc_final: 0.5901 (t-100) REVERT: i 74 TRP cc_start: 0.7137 (t-100) cc_final: 0.6139 (t-100) REVERT: j 74 TRP cc_start: 0.5452 (t-100) cc_final: 0.4589 (t60) REVERT: k 74 TRP cc_start: 0.6076 (t-100) cc_final: 0.5292 (t60) REVERT: k 156 GLN cc_start: 0.9071 (mm110) cc_final: 0.8698 (mm-40) outliers start: 160 outliers final: 132 residues processed: 495 average time/residue: 0.1529 time to fit residues: 131.3516 Evaluate side-chains 486 residues out of total 4686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 340 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 179 PHE Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 41 PHE Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 192 GLU Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 91 SER Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 91 SER Chi-restraints excluded: chain c residue 104 ILE Chi-restraints excluded: chain c residue 126 LEU Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 284 ASP Chi-restraints excluded: chain d residue 40 VAL Chi-restraints excluded: chain d residue 100 GLN Chi-restraints excluded: chain d residue 145 VAL Chi-restraints excluded: chain d residue 168 LEU Chi-restraints excluded: chain d residue 202 VAL Chi-restraints excluded: chain d residue 208 GLN Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 179 LEU Chi-restraints excluded: chain e residue 202 VAL Chi-restraints excluded: chain e residue 263 THR Chi-restraints excluded: chain e residue 284 ASP Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 137 VAL Chi-restraints excluded: chain f residue 168 LEU Chi-restraints excluded: chain f residue 192 GLU Chi-restraints excluded: chain f residue 202 VAL Chi-restraints excluded: chain f residue 218 LYS Chi-restraints excluded: chain f residue 224 LYS Chi-restraints excluded: chain f residue 238 LEU Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 63 ILE Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 103 ASN Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 218 LYS Chi-restraints excluded: chain h residue 63 ILE Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 168 LEU Chi-restraints excluded: chain h residue 179 LEU Chi-restraints excluded: chain h residue 192 GLU Chi-restraints excluded: chain h residue 197 VAL Chi-restraints excluded: chain h residue 218 LYS Chi-restraints excluded: chain h residue 284 ASP Chi-restraints excluded: chain h residue 291 SER Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 117 LEU Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 145 VAL Chi-restraints excluded: chain i residue 156 GLN Chi-restraints excluded: chain i residue 167 GLU Chi-restraints excluded: chain i residue 168 LEU Chi-restraints excluded: chain i residue 263 THR Chi-restraints excluded: chain i residue 291 SER Chi-restraints excluded: chain j residue 63 ILE Chi-restraints excluded: chain j residue 90 ILE Chi-restraints excluded: chain j residue 145 VAL Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain k residue 137 VAL Chi-restraints excluded: chain k residue 145 VAL Chi-restraints excluded: chain k residue 168 LEU Chi-restraints excluded: chain k residue 179 LEU Chi-restraints excluded: chain k residue 201 GLN Chi-restraints excluded: chain k residue 202 VAL Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 260 optimal weight: 0.8980 chunk 370 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 308 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 373 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 318 optimal weight: 1.9990 chunk 504 optimal weight: 0.3980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN F 89 ASN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 159 GLN ** g 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 103 ASN ** g 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.152791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.101237 restraints weight = 101082.431| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 4.50 r_work: 0.3191 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 44275 Z= 0.254 Angle : 0.693 59.198 59829 Z= 0.378 Chirality : 0.043 0.345 6930 Planarity : 0.004 0.052 7832 Dihedral : 5.209 87.448 6140 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.80 % Allowed : 24.90 % Favored : 71.30 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.11), residues: 5489 helix: 0.59 (0.10), residues: 2750 sheet: 0.02 (0.16), residues: 957 loop : -1.15 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 195 TYR 0.015 0.002 TYR D 259 PHE 0.018 0.001 PHE A 179 TRP 0.025 0.002 TRP a 74 HIS 0.004 0.001 HIS h 69 Details of bonding type rmsd covalent geometry : bond 0.00583 (44275) covalent geometry : angle 0.69320 (59829) hydrogen bonds : bond 0.05342 ( 2694) hydrogen bonds : angle 5.10986 ( 7818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15704.38 seconds wall clock time: 267 minutes 20.28 seconds (16040.28 seconds total)