Starting phenix.real_space_refine on Sat Aug 23 13:20:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5h_38935/08_2025/8y5h_38935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5h_38935/08_2025/8y5h_38935.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/8y5h_38935/08_2025/8y5h_38935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5h_38935/08_2025/8y5h_38935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y5h_38935/08_2025/8y5h_38935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5h_38935/08_2025/8y5h_38935.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= 0.002 sd= 0.035 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 69 5.16 5 C 8025 2.51 5 N 2057 2.21 5 O 2254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12405 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2876 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "B" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "C" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1936 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 9, 'TRANS': 239} Chain: "D" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2862 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 13, 'TRANS': 344} Chain: "E" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2548 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 21, 'TRANS': 300} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SPD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.38, per 1000 atoms: 0.27 Number of scatterers: 12405 At special positions: 0 Unit cell: (98.496, 89.984, 165.376, 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 69 16.00 O 2254 8.00 N 2057 7.00 C 8025 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: 1.04 Conformation dependent library (CDL) restraints added in 584.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2934 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 15 sheets defined 49.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 105 through 116 removed outlier: 4.847A pdb=" N GLY A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 123 through 134 removed outlier: 3.926A pdb=" N ARG A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 163 Processing helix chain 'A' and resid 179 through 198 removed outlier: 4.011A pdb=" N ASN A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.785A pdb=" N MET A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 241 through 248 removed outlier: 3.656A pdb=" N ILE A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 23 Processing helix chain 'B' and resid 23 through 34 removed outlier: 3.666A pdb=" N ASN B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 removed outlier: 3.850A pdb=" N LEU B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 57 " --> pdb=" O TYR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 91 removed outlier: 4.567A pdb=" N VAL B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 75 " --> pdb=" O MET B 71 " (cutoff:3.500A) Proline residue: B 85 - end of helix Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 105 through 111 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.746A pdb=" N TYR B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.724A pdb=" N LEU B 137 " --> pdb=" O PHE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 162 removed outlier: 3.886A pdb=" N VAL B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.538A pdb=" N MET B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Proline residue: B 168 - end of helix removed outlier: 3.568A pdb=" N SER B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.873A pdb=" N LEU B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 removed outlier: 3.607A pdb=" N PHE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.800A pdb=" N LEU B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 221 through 229 removed outlier: 4.385A pdb=" N SER B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 removed outlier: 3.799A pdb=" N VAL B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 277 removed outlier: 3.543A pdb=" N SER B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 28 Proline residue: C 21 - end of helix Processing helix chain 'C' and resid 44 through 53 removed outlier: 3.966A pdb=" N SER C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 88 Processing helix chain 'C' and resid 92 through 105 Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 127 through 152 removed outlier: 3.620A pdb=" N LEU C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Proline residue: C 141 - end of helix Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 165 removed outlier: 4.234A pdb=" N GLU C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 176 through 198 removed outlier: 3.522A pdb=" N LEU C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Proline residue: C 183 - end of helix removed outlier: 3.931A pdb=" N ALA C 187 " --> pdb=" O PRO C 183 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 removed outlier: 3.772A pdb=" N PHE C 205 " --> pdb=" O VAL C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 removed outlier: 3.648A pdb=" N LYS C 217 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 253 removed outlier: 3.521A pdb=" N ALA C 232 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 Processing helix chain 'D' and resid 105 through 117 removed outlier: 4.986A pdb=" N GLY D 113 " --> pdb=" O ASN D 109 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 135 removed outlier: 3.921A pdb=" N VAL D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 163 Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.869A pdb=" N ASN D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.603A pdb=" N ALA D 211 " --> pdb=" O ASP D 207 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 238 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'E' and resid 41 through 51 removed outlier: 3.569A pdb=" N PHE E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 48 " --> pdb=" O GLU E 44 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 72 Processing helix chain 'E' and resid 83 through 93 removed outlier: 4.221A pdb=" N ASP E 88 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS E 89 " --> pdb=" O TYR E 85 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 removed outlier: 3.894A pdb=" N ASN E 109 " --> pdb=" O ASN E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 156 Processing helix chain 'E' and resid 168 through 174 Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 191 through 200 removed outlier: 3.549A pdb=" N ASN E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 206 Proline residue: E 204 - end of helix No H-bonds generated for 'chain 'E' and resid 201 through 206' Processing helix chain 'E' and resid 215 through 220 Processing helix chain 'E' and resid 230 through 238 Processing helix chain 'E' and resid 267 through 279 removed outlier: 3.558A pdb=" N LEU E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 292 removed outlier: 3.621A pdb=" N THR E 290 " --> pdb=" O GLN E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.797A pdb=" N LYS E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 346 removed outlier: 3.622A pdb=" N TYR E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS E 343 " --> pdb=" O GLU E 339 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA E 346 " --> pdb=" O GLN E 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 41 removed outlier: 6.470A pdb=" N VAL A 32 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N CYS A 26 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ARG A 24 " --> pdb=" O PRO A 34 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 36 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 73 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 23 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER A 71 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.551A pdb=" N ASN A 92 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASP A 172 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL A 94 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE A 45 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL A 219 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR A 47 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N MET A 221 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU A 49 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE A 218 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP A 229 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 220 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 275 removed outlier: 7.745A pdb=" N ARG A 266 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG A 261 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG A 268 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 259 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 303 Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 303 Processing sheet with id=AA6, first strand: chain 'D' and resid 30 through 33 removed outlier: 3.578A pdb=" N VAL D 32 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS D 25 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 33 removed outlier: 3.578A pdb=" N VAL D 32 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS D 25 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE D 23 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER D 71 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 92 through 94 removed outlier: 3.513A pdb=" N ASN D 92 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP D 172 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE D 45 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL D 219 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR D 47 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N MET D 221 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU D 49 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE D 218 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP D 229 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL D 220 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 274 through 279 removed outlier: 3.758A pdb=" N GLU D 260 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN D 270 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL D 258 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 299 through 301 Processing sheet with id=AB2, first strand: chain 'D' and resid 319 through 322 removed outlier: 3.550A pdb=" N GLU D 319 " --> pdb=" O VAL D 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 28 through 33 Processing sheet with id=AB4, first strand: chain 'E' and resid 225 through 229 Processing sheet with id=AB5, first strand: chain 'E' and resid 225 through 229 removed outlier: 6.873A pdb=" N ASP E 257 " --> pdb=" O TYR E 129 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TRP E 131 " --> pdb=" O TRP E 255 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TRP E 255 " --> pdb=" O TRP E 131 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA E 133 " --> pdb=" O ILE E 253 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE E 253 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 164 through 165 563 hydrogen bonds defined for protein. 1617 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: 1.98 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2045 1.29 - 1.42: 3118 1.42 - 1.55: 7368 1.55 - 1.68: 4 1.68 - 1.81: 129 Bond restraints: 12664 Sorted by residual: bond pdb=" C ARG D 320 " pdb=" O ARG D 320 " ideal model delta sigma weight residual 1.234 1.161 0.073 1.22e-02 6.72e+03 3.55e+01 bond pdb=" CA ARG D 320 " pdb=" CB ARG D 320 " ideal model delta sigma weight residual 1.535 1.476 0.060 2.09e-02 2.29e+03 8.13e+00 bond pdb=" CA ASP D 353 " pdb=" C ASP D 353 " ideal model delta sigma weight residual 1.522 1.555 -0.033 1.24e-02 6.50e+03 7.22e+00 bond pdb=" CD ARG D 320 " pdb=" NE ARG D 320 " ideal model delta sigma weight residual 1.458 1.422 0.036 1.40e-02 5.10e+03 6.46e+00 bond pdb=" CA ASP D 351 " pdb=" C ASP D 351 " ideal model delta sigma weight residual 1.523 1.557 -0.033 1.34e-02 5.57e+03 6.20e+00 ... (remaining 12659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 16630 2.08 - 4.15: 467 4.15 - 6.23: 63 6.23 - 8.30: 18 8.30 - 10.38: 4 Bond angle restraints: 17182 Sorted by residual: angle pdb=" C ASP D 348 " pdb=" N ASP D 349 " pdb=" CA ASP D 349 " ideal model delta sigma weight residual 122.85 117.70 5.15 1.10e+00 8.26e-01 2.19e+01 angle pdb=" C SER A 97 " pdb=" N TYR A 98 " pdb=" CA TYR A 98 " ideal model delta sigma weight residual 121.54 129.73 -8.19 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C ILE C 213 " pdb=" N LEU C 214 " pdb=" CA LEU C 214 " ideal model delta sigma weight residual 120.09 125.41 -5.32 1.25e+00 6.40e-01 1.81e+01 angle pdb=" C GLY C 208 " pdb=" N PRO C 209 " pdb=" CA PRO C 209 " ideal model delta sigma weight residual 119.05 123.66 -4.61 1.11e+00 8.12e-01 1.72e+01 angle pdb=" N ASP D 351 " pdb=" CA ASP D 351 " pdb=" C ASP D 351 " ideal model delta sigma weight residual 110.80 119.30 -8.50 2.13e+00 2.20e-01 1.59e+01 ... (remaining 17177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 6860 18.01 - 36.03: 630 36.03 - 54.04: 103 54.04 - 72.05: 20 72.05 - 90.06: 11 Dihedral angle restraints: 7624 sinusoidal: 3080 harmonic: 4544 Sorted by residual: dihedral pdb=" CA GLU A 297 " pdb=" C GLU A 297 " pdb=" N ASP A 298 " pdb=" CA ASP A 298 " ideal model delta harmonic sigma weight residual -180.00 -151.87 -28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA TYR E 59 " pdb=" C TYR E 59 " pdb=" N GLU E 60 " pdb=" CA GLU E 60 " ideal model delta harmonic sigma weight residual 180.00 152.31 27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA TRP D 364 " pdb=" C TRP D 364 " pdb=" N VAL D 365 " pdb=" CA VAL D 365 " ideal model delta harmonic sigma weight residual -180.00 -155.99 -24.01 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 7621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1758 0.080 - 0.161: 214 0.161 - 0.241: 3 0.241 - 0.321: 2 0.321 - 0.402: 1 Chirality restraints: 1978 Sorted by residual: chirality pdb=" CA ASP D 351 " pdb=" N ASP D 351 " pdb=" C ASP D 351 " pdb=" CB ASP D 351 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA ASP D 349 " pdb=" N ASP D 349 " pdb=" C ASP D 349 " pdb=" CB ASP D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASP D 353 " pdb=" N ASP D 353 " pdb=" C ASP D 353 " pdb=" CB ASP D 353 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1975 not shown) Planarity restraints: 2183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 319 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLU D 319 " 0.063 2.00e-02 2.50e+03 pdb=" O GLU D 319 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG D 320 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 285 " -0.052 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO A 286 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 285 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO D 286 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 286 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 286 " 0.040 5.00e-02 4.00e+02 ... (remaining 2180 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1599 2.74 - 3.28: 11551 3.28 - 3.82: 18763 3.82 - 4.36: 22101 4.36 - 4.90: 39253 Nonbonded interactions: 93267 Sorted by model distance: nonbonded pdb=" NH1 ARG A 261 " pdb=" O ASP A 263 " model vdw 2.206 3.120 nonbonded pdb=" OD2 ASP B 226 " pdb=" OH TYR C 219 " model vdw 2.215 3.040 nonbonded pdb=" O GLY E 240 " pdb=" OG1 THR E 241 " model vdw 2.226 3.040 nonbonded pdb=" O PRO A 145 " pdb=" ND1 HIS A 146 " model vdw 2.241 3.120 nonbonded pdb=" O SER E 183 " pdb=" OG1 THR E 186 " model vdw 2.252 3.040 ... (remaining 93262 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 373) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.910 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 12664 Z= 0.333 Angle : 0.851 10.378 17182 Z= 0.482 Chirality : 0.053 0.402 1978 Planarity : 0.006 0.078 2183 Dihedral : 14.337 90.065 4690 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.52 % Allowed : 0.74 % Favored : 98.75 % Cbeta Deviations : 0.07 % 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 aren not related in a simple way. whole: -1.85 (0.20), residues: 1552 helix: -0.44 (0.20), residues: 685 sheet: -0.74 (0.34), residues: 239 loop : -2.26 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 320 TYR 0.036 0.003 TYR B 129 PHE 0.029 0.002 PHE B 48 TRP 0.027 0.003 TRP D 364 HIS 0.012 0.002 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00750 (12664) covalent geometry : angle 0.85142 (17182) hydrogen bonds : bond 0.26310 ( 547) hydrogen bonds : angle 7.97537 ( 1617) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 372 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8267 (mmtt) cc_final: 0.8026 (mmtt) REVERT: A 210 GLU cc_start: 0.7397 (tt0) cc_final: 0.7101 (tt0) REVERT: A 237 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6832 (mt-10) REVERT: A 265 GLN cc_start: 0.6409 (pt0) cc_final: 0.6114 (pt0) REVERT: A 303 GLU cc_start: 0.6815 (pp20) cc_final: 0.6481 (pp20) REVERT: A 343 GLU cc_start: 0.7950 (pt0) cc_final: 0.7442 (pt0) REVERT: D 79 GLU cc_start: 0.6787 (mp0) cc_final: 0.6033 (mp0) REVERT: D 129 MET cc_start: 0.7563 (mmm) cc_final: 0.7234 (mmm) REVERT: D 164 ASN cc_start: 0.8405 (m110) cc_final: 0.8111 (m110) REVERT: D 298 ASP cc_start: 0.7954 (m-30) cc_final: 0.7721 (m-30) REVERT: D 325 MET cc_start: 0.7631 (ttt) cc_final: 0.7315 (ttt) REVERT: D 359 LYS cc_start: 0.8075 (tttp) cc_final: 0.7829 (mtpp) REVERT: E 70 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7646 (mtpt) REVERT: E 72 TYR cc_start: 0.7899 (m-80) cc_final: 0.7635 (m-80) REVERT: E 109 ASN cc_start: 0.7921 (m-40) cc_final: 0.7672 (m110) REVERT: E 198 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6924 (tm-30) REVERT: E 322 LYS cc_start: 0.7220 (mtpt) cc_final: 0.7005 (mtpt) REVERT: E 328 ASN cc_start: 0.7976 (m-40) cc_final: 0.7751 (m-40) REVERT: E 339 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6889 (tm-30) outliers start: 7 outliers final: 3 residues processed: 378 average time/residue: 0.1285 time to fit residues: 67.3966 Evaluate side-chains 336 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 333 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain D residue 320 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN D 147 GLN D 291 HIS D 335 ASN E 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106063 restraints weight = 17702.392| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.06 r_work: 0.3235 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12664 Z= 0.206 Angle : 0.688 8.440 17182 Z= 0.360 Chirality : 0.047 0.152 1978 Planarity : 0.006 0.064 2183 Dihedral : 5.680 51.350 1700 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.62 % Allowed : 10.69 % Favored : 87.69 % 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 aren not related in a simple way. whole: -1.01 (0.21), residues: 1552 helix: 0.59 (0.20), residues: 696 sheet: -0.76 (0.34), residues: 250 loop : -2.12 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 261 TYR 0.020 0.002 TYR B 223 PHE 0.022 0.002 PHE C 138 TRP 0.019 0.002 TRP E 151 HIS 0.007 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00484 (12664) covalent geometry : angle 0.68764 (17182) hydrogen bonds : bond 0.06710 ( 547) hydrogen bonds : angle 5.31547 ( 1617) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 368 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7831 (mtt-85) cc_final: 0.7502 (mtt-85) REVERT: A 118 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8229 (mmtt) REVERT: A 210 GLU cc_start: 0.8248 (tt0) cc_final: 0.7999 (tt0) REVERT: A 234 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7944 (mt-10) REVERT: A 303 GLU cc_start: 0.7499 (pp20) cc_final: 0.7147 (pp20) REVERT: C 170 PHE cc_start: 0.8180 (t80) cc_final: 0.7641 (t80) REVERT: D 76 LEU cc_start: 0.7725 (tt) cc_final: 0.7069 (tt) REVERT: D 77 ASP cc_start: 0.7255 (m-30) cc_final: 0.6787 (m-30) REVERT: D 79 GLU cc_start: 0.7390 (mp0) cc_final: 0.6608 (mp0) REVERT: D 164 ASN cc_start: 0.8609 (m110) cc_final: 0.8302 (m110) REVERT: D 173 GLN cc_start: 0.8405 (mp10) cc_final: 0.7949 (mp10) REVERT: D 298 ASP cc_start: 0.8317 (m-30) cc_final: 0.8022 (m-30) REVERT: E 70 LYS cc_start: 0.8267 (mtpt) cc_final: 0.8021 (mtpt) REVERT: E 72 TYR cc_start: 0.7585 (m-80) cc_final: 0.7381 (m-80) REVERT: E 109 ASN cc_start: 0.8437 (m-40) cc_final: 0.8226 (m-40) REVERT: E 171 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7924 (mt-10) REVERT: E 193 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7735 (tm-30) REVERT: E 269 GLU cc_start: 0.7948 (mp0) cc_final: 0.7709 (mp0) REVERT: E 311 ASP cc_start: 0.7945 (t0) cc_final: 0.7693 (t0) REVERT: E 322 LYS cc_start: 0.7568 (mtpt) cc_final: 0.7271 (mtpt) REVERT: E 328 ASN cc_start: 0.8451 (m-40) cc_final: 0.8203 (m-40) REVERT: E 339 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7552 (tm-30) outliers start: 22 outliers final: 15 residues processed: 376 average time/residue: 0.1180 time to fit residues: 61.5478 Evaluate side-chains 376 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 361 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 310 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 56 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 85 optimal weight: 0.0980 chunk 34 optimal weight: 6.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN D 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.105023 restraints weight = 17891.683| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.07 r_work: 0.3225 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12664 Z= 0.211 Angle : 0.647 7.537 17182 Z= 0.338 Chirality : 0.047 0.155 1978 Planarity : 0.006 0.062 2183 Dihedral : 5.261 51.795 1694 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.17 % Allowed : 13.26 % Favored : 83.57 % 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 aren not related in a simple way. whole: -0.73 (0.22), residues: 1552 helix: 0.88 (0.20), residues: 699 sheet: -0.68 (0.34), residues: 251 loop : -2.04 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 261 TYR 0.021 0.002 TYR B 223 PHE 0.018 0.002 PHE C 138 TRP 0.022 0.002 TRP D 364 HIS 0.008 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00505 (12664) covalent geometry : angle 0.64651 (17182) hydrogen bonds : bond 0.06198 ( 547) hydrogen bonds : angle 4.96117 ( 1617) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 369 time to evaluate : 0.498 Fit side-chains REVERT: A 61 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7583 (mtt-85) REVERT: A 118 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8259 (mmtt) REVERT: A 210 GLU cc_start: 0.8225 (tt0) cc_final: 0.7976 (tt0) REVERT: A 234 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 303 GLU cc_start: 0.7514 (pp20) cc_final: 0.7113 (pp20) REVERT: A 320 ARG cc_start: 0.8422 (ptt90) cc_final: 0.8168 (ptt90) REVERT: C 49 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7766 (tp) REVERT: C 170 PHE cc_start: 0.8156 (t80) cc_final: 0.7619 (t80) REVERT: D 76 LEU cc_start: 0.7741 (tt) cc_final: 0.7099 (tt) REVERT: D 77 ASP cc_start: 0.7113 (m-30) cc_final: 0.6204 (m-30) REVERT: D 79 GLU cc_start: 0.7403 (mp0) cc_final: 0.6737 (mp0) REVERT: D 116 MET cc_start: 0.8673 (mmm) cc_final: 0.8379 (mmm) REVERT: D 164 ASN cc_start: 0.8632 (m110) cc_final: 0.8386 (m110) REVERT: D 173 GLN cc_start: 0.8488 (mp10) cc_final: 0.7895 (mp10) REVERT: D 248 ILE cc_start: 0.7811 (pt) cc_final: 0.7596 (pt) REVERT: D 298 ASP cc_start: 0.8339 (m-30) cc_final: 0.8048 (m-30) REVERT: E 59 TYR cc_start: 0.7184 (m-10) cc_final: 0.6761 (m-80) REVERT: E 72 TYR cc_start: 0.7646 (m-80) cc_final: 0.7415 (m-80) REVERT: E 109 ASN cc_start: 0.8414 (m-40) cc_final: 0.8204 (m-40) REVERT: E 171 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8015 (mt-10) REVERT: E 193 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7750 (tm-30) REVERT: E 238 GLN cc_start: 0.8291 (tt0) cc_final: 0.7999 (tp40) REVERT: E 311 ASP cc_start: 0.8084 (t0) cc_final: 0.7785 (t0) REVERT: E 328 ASN cc_start: 0.8387 (m-40) cc_final: 0.8146 (m-40) REVERT: E 339 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7503 (tm-30) outliers start: 43 outliers final: 32 residues processed: 385 average time/residue: 0.1185 time to fit residues: 63.0205 Evaluate side-chains 391 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 358 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 246 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN E 97 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103971 restraints weight = 17952.770| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.06 r_work: 0.3204 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 12664 Z= 0.266 Angle : 0.680 8.448 17182 Z= 0.355 Chirality : 0.049 0.169 1978 Planarity : 0.006 0.060 2183 Dihedral : 5.368 50.811 1694 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.76 % Allowed : 15.33 % Favored : 80.91 % 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 aren not related in a simple way. whole: -0.75 (0.22), residues: 1552 helix: 0.87 (0.20), residues: 703 sheet: -0.71 (0.35), residues: 250 loop : -2.08 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 261 TYR 0.025 0.002 TYR B 223 PHE 0.020 0.002 PHE C 128 TRP 0.025 0.002 TRP D 364 HIS 0.007 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00641 (12664) covalent geometry : angle 0.68007 (17182) hydrogen bonds : bond 0.06459 ( 547) hydrogen bonds : angle 4.95175 ( 1617) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 360 time to evaluate : 0.467 Fit side-chains REVERT: A 61 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.7618 (mtt-85) REVERT: A 118 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8246 (mmtt) REVERT: A 210 GLU cc_start: 0.8185 (tt0) cc_final: 0.7910 (tt0) REVERT: A 234 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7831 (mt-10) REVERT: A 272 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7992 (mm-30) REVERT: A 303 GLU cc_start: 0.7588 (pp20) cc_final: 0.7134 (pp20) REVERT: A 320 ARG cc_start: 0.8422 (ptt90) cc_final: 0.8158 (ptt90) REVERT: B 196 ILE cc_start: 0.8167 (mt) cc_final: 0.7958 (mm) REVERT: C 52 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7735 (t0) REVERT: C 170 PHE cc_start: 0.8132 (t80) cc_final: 0.7617 (t80) REVERT: D 76 LEU cc_start: 0.7674 (tt) cc_final: 0.6906 (tt) REVERT: D 77 ASP cc_start: 0.7072 (m-30) cc_final: 0.5712 (m-30) REVERT: D 79 GLU cc_start: 0.7413 (mp0) cc_final: 0.6724 (mp0) REVERT: D 98 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: D 116 MET cc_start: 0.8697 (mmm) cc_final: 0.8419 (mmm) REVERT: D 173 GLN cc_start: 0.8482 (mp10) cc_final: 0.8074 (mt0) REVERT: D 208 GLN cc_start: 0.8463 (mp10) cc_final: 0.8253 (mp10) REVERT: D 242 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7730 (tt) REVERT: D 248 ILE cc_start: 0.7819 (pt) cc_final: 0.7583 (pt) REVERT: D 298 ASP cc_start: 0.8383 (m-30) cc_final: 0.8056 (m-30) REVERT: E 59 TYR cc_start: 0.7333 (m-10) cc_final: 0.6761 (m-10) REVERT: E 72 TYR cc_start: 0.7721 (m-80) cc_final: 0.7455 (m-80) REVERT: E 109 ASN cc_start: 0.8410 (m-40) cc_final: 0.8191 (m-40) REVERT: E 171 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7956 (mt-10) REVERT: E 193 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7651 (tm-30) REVERT: E 247 TRP cc_start: 0.8092 (m100) cc_final: 0.7645 (m100) REVERT: E 311 ASP cc_start: 0.8144 (t0) cc_final: 0.7866 (t0) REVERT: E 328 ASN cc_start: 0.8357 (m-40) cc_final: 0.8154 (m-40) REVERT: E 339 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7567 (tm-30) REVERT: E 341 TYR cc_start: 0.8425 (t80) cc_final: 0.8223 (t80) outliers start: 51 outliers final: 38 residues processed: 380 average time/residue: 0.1205 time to fit residues: 62.7657 Evaluate side-chains 392 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 351 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 310 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 90 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 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 154 GLN A 252 ASN A 354 HIS A 363 ASN B 52 ASN D 88 ASN D 281 ASN E 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106826 restraints weight = 17936.222| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.10 r_work: 0.3245 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12664 Z= 0.137 Angle : 0.580 6.814 17182 Z= 0.303 Chirality : 0.044 0.177 1978 Planarity : 0.005 0.057 2183 Dihedral : 4.975 52.025 1694 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.32 % Allowed : 17.17 % Favored : 79.51 % 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 aren not related in a simple way. whole: -0.35 (0.22), residues: 1552 helix: 1.23 (0.20), residues: 711 sheet: -0.64 (0.35), residues: 250 loop : -1.90 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.015 0.001 TYR B 223 PHE 0.026 0.001 PHE C 35 TRP 0.018 0.001 TRP D 364 HIS 0.004 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00316 (12664) covalent geometry : angle 0.57993 (17182) hydrogen bonds : bond 0.04868 ( 547) hydrogen bonds : angle 4.60243 ( 1617) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 360 time to evaluate : 0.487 Fit side-chains REVERT: A 61 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7546 (mtt-85) REVERT: A 118 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8224 (mmtt) REVERT: A 210 GLU cc_start: 0.8162 (tt0) cc_final: 0.7877 (tt0) REVERT: A 234 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7779 (mt-10) REVERT: A 272 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8020 (mm-30) REVERT: A 320 ARG cc_start: 0.8444 (ptt90) cc_final: 0.8187 (ptt90) REVERT: C 49 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7685 (tp) REVERT: C 170 PHE cc_start: 0.8079 (t80) cc_final: 0.7580 (t80) REVERT: D 17 LEU cc_start: 0.8242 (tp) cc_final: 0.7948 (tp) REVERT: D 75 MET cc_start: 0.7907 (mtp) cc_final: 0.7640 (mmm) REVERT: D 79 GLU cc_start: 0.7479 (mp0) cc_final: 0.6696 (mp0) REVERT: D 98 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6947 (m-80) REVERT: D 173 GLN cc_start: 0.8464 (mp10) cc_final: 0.8096 (mt0) REVERT: D 248 ILE cc_start: 0.7747 (pt) cc_final: 0.4912 (mt) REVERT: D 325 MET cc_start: 0.8508 (ttm) cc_final: 0.8205 (mtm) REVERT: D 365 VAL cc_start: 0.8784 (p) cc_final: 0.8509 (t) REVERT: E 109 ASN cc_start: 0.8395 (m-40) cc_final: 0.8169 (m-40) REVERT: E 171 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7989 (mt-10) REVERT: E 193 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7634 (tm-30) REVERT: E 311 ASP cc_start: 0.8154 (t0) cc_final: 0.7850 (t0) REVERT: E 328 ASN cc_start: 0.8496 (m-40) cc_final: 0.8262 (m-40) REVERT: E 339 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7560 (tm-30) outliers start: 45 outliers final: 31 residues processed: 376 average time/residue: 0.1220 time to fit residues: 62.5876 Evaluate side-chains 385 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 352 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 310 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN D 281 ASN E 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.105165 restraints weight = 17894.606| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.06 r_work: 0.3224 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12664 Z= 0.195 Angle : 0.617 7.806 17182 Z= 0.322 Chirality : 0.046 0.168 1978 Planarity : 0.005 0.056 2183 Dihedral : 5.023 51.599 1694 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.61 % Allowed : 17.83 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.22), residues: 1552 helix: 1.23 (0.20), residues: 712 sheet: -0.65 (0.35), residues: 250 loop : -1.91 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 261 TYR 0.018 0.002 TYR B 223 PHE 0.026 0.002 PHE C 35 TRP 0.022 0.002 TRP D 364 HIS 0.005 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00470 (12664) covalent geometry : angle 0.61713 (17182) hydrogen bonds : bond 0.05486 ( 547) hydrogen bonds : angle 4.64558 ( 1617) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 365 time to evaluate : 0.321 Fit side-chains REVERT: A 61 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7606 (mtt-85) REVERT: A 118 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8259 (mmtt) REVERT: A 210 GLU cc_start: 0.8122 (tt0) cc_final: 0.7851 (tt0) REVERT: A 238 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7456 (tm-30) REVERT: A 271 VAL cc_start: 0.5776 (OUTLIER) cc_final: 0.5572 (m) REVERT: A 274 ARG cc_start: 0.6561 (ttp80) cc_final: 0.6333 (ttp80) REVERT: A 320 ARG cc_start: 0.8398 (ptt90) cc_final: 0.8157 (ptt90) REVERT: A 349 ASP cc_start: 0.6940 (m-30) cc_final: 0.6681 (m-30) REVERT: C 49 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7768 (tp) REVERT: C 170 PHE cc_start: 0.8111 (t80) cc_final: 0.7703 (t80) REVERT: C 174 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7722 (mtp-110) REVERT: D 17 LEU cc_start: 0.8221 (tp) cc_final: 0.7913 (tp) REVERT: D 20 LEU cc_start: 0.8256 (mt) cc_final: 0.7985 (mp) REVERT: D 76 LEU cc_start: 0.7717 (tt) cc_final: 0.7013 (tt) REVERT: D 77 ASP cc_start: 0.6984 (m-30) cc_final: 0.5577 (m-30) REVERT: D 79 GLU cc_start: 0.7451 (mp0) cc_final: 0.6703 (mp0) REVERT: D 98 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.7087 (m-80) REVERT: D 173 GLN cc_start: 0.8412 (mp10) cc_final: 0.8182 (mt0) REVERT: D 242 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7765 (tt) REVERT: D 248 ILE cc_start: 0.7854 (pt) cc_final: 0.7614 (pt) REVERT: D 263 ASP cc_start: 0.7419 (p0) cc_final: 0.7019 (p0) REVERT: D 298 ASP cc_start: 0.8366 (m-30) cc_final: 0.8069 (m-30) REVERT: D 365 VAL cc_start: 0.8789 (p) cc_final: 0.8446 (t) REVERT: E 59 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6811 (m-10) REVERT: E 98 LYS cc_start: 0.7886 (mmpt) cc_final: 0.7632 (mmtt) REVERT: E 109 ASN cc_start: 0.8404 (m-40) cc_final: 0.8172 (m110) REVERT: E 171 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8016 (mt-10) REVERT: E 193 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7823 (tm-30) REVERT: E 196 TYR cc_start: 0.8290 (t80) cc_final: 0.7972 (t80) REVERT: E 311 ASP cc_start: 0.8167 (t0) cc_final: 0.7871 (t0) REVERT: E 328 ASN cc_start: 0.8384 (m-40) cc_final: 0.8162 (m-40) REVERT: E 339 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7584 (tm-30) outliers start: 49 outliers final: 38 residues processed: 387 average time/residue: 0.1291 time to fit residues: 68.4019 Evaluate side-chains 404 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 361 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 246 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN D 281 ASN E 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105772 restraints weight = 17926.636| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.10 r_work: 0.3243 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12664 Z= 0.136 Angle : 0.578 7.499 17182 Z= 0.301 Chirality : 0.044 0.165 1978 Planarity : 0.005 0.054 2183 Dihedral : 4.826 51.842 1694 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.05 % Allowed : 18.87 % Favored : 77.08 % 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 aren not related in a simple way. whole: -0.16 (0.22), residues: 1552 helix: 1.41 (0.20), residues: 714 sheet: -0.65 (0.34), residues: 262 loop : -1.81 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 261 TYR 0.014 0.001 TYR B 223 PHE 0.027 0.001 PHE C 35 TRP 0.019 0.001 TRP D 364 HIS 0.003 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00316 (12664) covalent geometry : angle 0.57798 (17182) hydrogen bonds : bond 0.04641 ( 547) hydrogen bonds : angle 4.45590 ( 1617) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 360 time to evaluate : 0.510 Fit side-chains REVERT: A 61 ARG cc_start: 0.7891 (mtt-85) cc_final: 0.7535 (mtt-85) REVERT: A 118 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8192 (mmtt) REVERT: A 210 GLU cc_start: 0.8136 (tt0) cc_final: 0.7867 (tt0) REVERT: A 238 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7400 (tm-30) REVERT: A 261 ARG cc_start: 0.8139 (mtp-110) cc_final: 0.7557 (ttt90) REVERT: A 263 ASP cc_start: 0.6110 (p0) cc_final: 0.5594 (p0) REVERT: A 320 ARG cc_start: 0.8409 (ptt90) cc_final: 0.8162 (ptt90) REVERT: A 338 MET cc_start: 0.8211 (mmt) cc_final: 0.7790 (mmt) REVERT: B 182 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8157 (mt-10) REVERT: C 49 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7680 (tp) REVERT: C 52 ASN cc_start: 0.7991 (m-40) cc_final: 0.7707 (t0) REVERT: C 170 PHE cc_start: 0.8053 (t80) cc_final: 0.7640 (t80) REVERT: C 174 ARG cc_start: 0.7823 (mtp-110) cc_final: 0.7553 (mtp-110) REVERT: D 17 LEU cc_start: 0.8233 (tp) cc_final: 0.7925 (tp) REVERT: D 20 LEU cc_start: 0.8124 (mt) cc_final: 0.7918 (mp) REVERT: D 76 LEU cc_start: 0.7664 (tt) cc_final: 0.6945 (tt) REVERT: D 77 ASP cc_start: 0.6993 (m-30) cc_final: 0.5589 (m-30) REVERT: D 79 GLU cc_start: 0.7374 (mp0) cc_final: 0.6601 (mp0) REVERT: D 98 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: D 173 GLN cc_start: 0.8423 (mp10) cc_final: 0.8176 (mt0) REVERT: D 242 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7641 (tt) REVERT: D 248 ILE cc_start: 0.7775 (pt) cc_final: 0.7569 (pt) REVERT: D 263 ASP cc_start: 0.7313 (p0) cc_final: 0.6867 (p0) REVERT: D 365 VAL cc_start: 0.8800 (p) cc_final: 0.8516 (t) REVERT: E 52 ILE cc_start: 0.8008 (mm) cc_final: 0.7805 (tt) REVERT: E 98 LYS cc_start: 0.7938 (mmpt) cc_final: 0.7668 (mmtt) REVERT: E 109 ASN cc_start: 0.8364 (m-40) cc_final: 0.8103 (m110) REVERT: E 146 LYS cc_start: 0.8651 (mptt) cc_final: 0.8327 (mmmt) REVERT: E 171 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7752 (mt-10) REVERT: E 193 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7766 (tm-30) REVERT: E 311 ASP cc_start: 0.8241 (t0) cc_final: 0.7953 (t0) REVERT: E 328 ASN cc_start: 0.8477 (m-40) cc_final: 0.8238 (m-40) REVERT: E 339 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7588 (tm-30) REVERT: E 343 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8441 (mtmt) outliers start: 55 outliers final: 42 residues processed: 380 average time/residue: 0.1342 time to fit residues: 70.1167 Evaluate side-chains 405 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 360 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 310 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 114 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 144 optimal weight: 0.0470 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN D 281 ASN E 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107553 restraints weight = 17850.478| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.14 r_work: 0.3256 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12664 Z= 0.123 Angle : 0.578 9.242 17182 Z= 0.298 Chirality : 0.043 0.159 1978 Planarity : 0.005 0.052 2183 Dihedral : 4.675 52.398 1694 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.83 % Allowed : 19.16 % Favored : 77.01 % 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 aren not related in a simple way. whole: 0.01 (0.22), residues: 1552 helix: 1.58 (0.20), residues: 716 sheet: -0.58 (0.34), residues: 255 loop : -1.75 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 115 TYR 0.012 0.001 TYR B 223 PHE 0.027 0.001 PHE C 35 TRP 0.018 0.001 TRP D 364 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00282 (12664) covalent geometry : angle 0.57770 (17182) hydrogen bonds : bond 0.04272 ( 547) hydrogen bonds : angle 4.34187 ( 1617) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 357 time to evaluate : 0.502 Fit side-chains REVERT: A 61 ARG cc_start: 0.7803 (mtt-85) cc_final: 0.7438 (mtt-85) REVERT: A 210 GLU cc_start: 0.8304 (tt0) cc_final: 0.8028 (tt0) REVERT: A 238 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7219 (tm-30) REVERT: A 261 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.7619 (ttt90) REVERT: A 320 ARG cc_start: 0.8382 (ptt90) cc_final: 0.8146 (ptt90) REVERT: A 338 MET cc_start: 0.8348 (mmt) cc_final: 0.7910 (mmt) REVERT: A 349 ASP cc_start: 0.6817 (m-30) cc_final: 0.6553 (m-30) REVERT: A 362 ILE cc_start: 0.8440 (mm) cc_final: 0.8229 (mt) REVERT: B 182 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8136 (mt-10) REVERT: C 49 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7669 (tp) REVERT: C 52 ASN cc_start: 0.7929 (m-40) cc_final: 0.7623 (t0) REVERT: C 170 PHE cc_start: 0.8031 (t80) cc_final: 0.7605 (t80) REVERT: C 174 ARG cc_start: 0.7846 (mtp-110) cc_final: 0.7559 (mtp-110) REVERT: C 197 MET cc_start: 0.7863 (tpp) cc_final: 0.7413 (mmt) REVERT: D 75 MET cc_start: 0.7966 (mtp) cc_final: 0.7721 (mmm) REVERT: D 76 LEU cc_start: 0.7611 (tt) cc_final: 0.6914 (tt) REVERT: D 79 GLU cc_start: 0.7424 (mp0) cc_final: 0.6538 (mp0) REVERT: D 98 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6669 (m-80) REVERT: D 173 GLN cc_start: 0.8415 (mp10) cc_final: 0.8149 (mt0) REVERT: D 242 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7628 (tt) REVERT: D 248 ILE cc_start: 0.7727 (pt) cc_final: 0.5011 (mt) REVERT: D 263 ASP cc_start: 0.7127 (p0) cc_final: 0.6612 (p0) REVERT: D 298 ASP cc_start: 0.8427 (m-30) cc_final: 0.8087 (m-30) REVERT: D 365 VAL cc_start: 0.8766 (p) cc_final: 0.8472 (t) REVERT: E 52 ILE cc_start: 0.7919 (mm) cc_final: 0.7714 (tt) REVERT: E 98 LYS cc_start: 0.7860 (mmpt) cc_final: 0.7440 (mmmm) REVERT: E 109 ASN cc_start: 0.8385 (m-40) cc_final: 0.8067 (m110) REVERT: E 171 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7844 (mt-10) REVERT: E 193 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7853 (tm-30) REVERT: E 311 ASP cc_start: 0.8178 (t0) cc_final: 0.7796 (t0) REVERT: E 339 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7565 (tm-30) REVERT: E 343 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8362 (mtmt) outliers start: 52 outliers final: 37 residues processed: 376 average time/residue: 0.1312 time to fit residues: 68.4385 Evaluate side-chains 384 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 344 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 310 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 88 optimal weight: 0.0060 chunk 139 optimal weight: 0.9990 chunk 134 optimal weight: 0.4980 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN D 281 ASN E 174 GLN E 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106478 restraints weight = 17848.583| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.03 r_work: 0.3242 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12664 Z= 0.160 Angle : 0.612 9.848 17182 Z= 0.315 Chirality : 0.045 0.222 1978 Planarity : 0.005 0.052 2183 Dihedral : 4.760 51.592 1694 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.24 % Allowed : 20.04 % Favored : 76.71 % 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 aren not related in a simple way. whole: -0.01 (0.22), residues: 1552 helix: 1.58 (0.20), residues: 714 sheet: -0.60 (0.34), residues: 256 loop : -1.78 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 115 TYR 0.016 0.001 TYR B 223 PHE 0.031 0.002 PHE C 35 TRP 0.021 0.002 TRP D 364 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00382 (12664) covalent geometry : angle 0.61226 (17182) hydrogen bonds : bond 0.04828 ( 547) hydrogen bonds : angle 4.40075 ( 1617) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 357 time to evaluate : 0.565 Fit side-chains REVERT: A 25 LYS cc_start: 0.7834 (tptt) cc_final: 0.7610 (tptt) REVERT: A 61 ARG cc_start: 0.7842 (mtt-85) cc_final: 0.7489 (mtt-85) REVERT: A 186 MET cc_start: 0.8545 (mtm) cc_final: 0.8315 (mtp) REVERT: A 210 GLU cc_start: 0.8199 (tt0) cc_final: 0.7945 (tt0) REVERT: A 238 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7279 (tm-30) REVERT: A 261 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7698 (ttt90) REVERT: A 338 MET cc_start: 0.8382 (mmt) cc_final: 0.7969 (mmt) REVERT: A 358 GLN cc_start: 0.8447 (tp-100) cc_final: 0.8012 (tp40) REVERT: B 182 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8168 (mt-10) REVERT: C 49 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7699 (tp) REVERT: C 170 PHE cc_start: 0.8092 (t80) cc_final: 0.7683 (t80) REVERT: C 174 ARG cc_start: 0.7885 (mtp-110) cc_final: 0.7623 (mtp-110) REVERT: C 197 MET cc_start: 0.7931 (tpp) cc_final: 0.7420 (mmt) REVERT: D 75 MET cc_start: 0.7910 (mtp) cc_final: 0.7677 (mmm) REVERT: D 76 LEU cc_start: 0.7697 (tt) cc_final: 0.6984 (tt) REVERT: D 79 GLU cc_start: 0.7436 (mp0) cc_final: 0.6637 (mp0) REVERT: D 98 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6780 (m-80) REVERT: D 173 GLN cc_start: 0.8382 (mp10) cc_final: 0.8088 (mt0) REVERT: D 242 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7726 (tt) REVERT: D 248 ILE cc_start: 0.7788 (pt) cc_final: 0.5187 (mt) REVERT: D 263 ASP cc_start: 0.7234 (p0) cc_final: 0.6628 (p0) REVERT: D 264 GLU cc_start: 0.7654 (tt0) cc_final: 0.7283 (tp30) REVERT: D 298 ASP cc_start: 0.8375 (m-30) cc_final: 0.8093 (m-30) REVERT: D 365 VAL cc_start: 0.8822 (p) cc_final: 0.8490 (t) REVERT: E 98 LYS cc_start: 0.7874 (mmpt) cc_final: 0.7569 (mmmm) REVERT: E 109 ASN cc_start: 0.8325 (m-40) cc_final: 0.8052 (m110) REVERT: E 171 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7823 (mt-10) REVERT: E 193 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7905 (tm-30) REVERT: E 196 TYR cc_start: 0.8347 (t80) cc_final: 0.8062 (t80) REVERT: E 311 ASP cc_start: 0.8186 (t0) cc_final: 0.7867 (t0) REVERT: E 339 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7607 (tm-30) REVERT: E 343 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8406 (mtmt) outliers start: 44 outliers final: 38 residues processed: 378 average time/residue: 0.1315 time to fit residues: 68.7180 Evaluate side-chains 399 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 358 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 246 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 41 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN D 281 ASN E 174 GLN ** E 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107835 restraints weight = 17845.294| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.03 r_work: 0.3252 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12664 Z= 0.135 Angle : 0.600 10.163 17182 Z= 0.308 Chirality : 0.044 0.215 1978 Planarity : 0.005 0.051 2183 Dihedral : 4.704 51.777 1694 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.24 % Allowed : 20.56 % Favored : 76.20 % 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 aren not related in a simple way. whole: 0.07 (0.22), residues: 1552 helix: 1.63 (0.20), residues: 716 sheet: -0.50 (0.34), residues: 264 loop : -1.78 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 115 TYR 0.014 0.001 TYR B 223 PHE 0.022 0.001 PHE C 42 TRP 0.020 0.001 TRP D 364 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00314 (12664) covalent geometry : angle 0.60014 (17182) hydrogen bonds : bond 0.04476 ( 547) hydrogen bonds : angle 4.33027 ( 1617) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 366 time to evaluate : 0.496 Fit side-chains REVERT: A 25 LYS cc_start: 0.7821 (tptt) cc_final: 0.7591 (tptt) REVERT: A 61 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7488 (mtt-85) REVERT: A 210 GLU cc_start: 0.8181 (tt0) cc_final: 0.7906 (tt0) REVERT: A 234 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7962 (mt-10) REVERT: A 261 ARG cc_start: 0.8136 (mtp-110) cc_final: 0.7728 (ttt90) REVERT: A 338 MET cc_start: 0.8374 (mmt) cc_final: 0.7974 (mmt) REVERT: A 358 GLN cc_start: 0.8424 (tp-100) cc_final: 0.8003 (tp40) REVERT: B 182 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8167 (mt-10) REVERT: C 34 ARG cc_start: 0.8343 (ptm-80) cc_final: 0.8129 (ptm-80) REVERT: C 49 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7687 (tp) REVERT: C 170 PHE cc_start: 0.8095 (t80) cc_final: 0.7688 (t80) REVERT: C 174 ARG cc_start: 0.7882 (mtp-110) cc_final: 0.7632 (mtp-110) REVERT: C 197 MET cc_start: 0.7894 (tpp) cc_final: 0.7388 (mmt) REVERT: D 17 LEU cc_start: 0.8328 (tp) cc_final: 0.8092 (tp) REVERT: D 75 MET cc_start: 0.7914 (mtp) cc_final: 0.7680 (mmm) REVERT: D 76 LEU cc_start: 0.7628 (tt) cc_final: 0.6893 (tt) REVERT: D 79 GLU cc_start: 0.7351 (mp0) cc_final: 0.6552 (mp0) REVERT: D 98 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: D 173 GLN cc_start: 0.8361 (mp10) cc_final: 0.8073 (mt0) REVERT: D 235 ILE cc_start: 0.8524 (mt) cc_final: 0.8254 (tt) REVERT: D 242 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7723 (tt) REVERT: D 248 ILE cc_start: 0.7747 (pt) cc_final: 0.5055 (mt) REVERT: D 263 ASP cc_start: 0.7185 (p0) cc_final: 0.6548 (p0) REVERT: D 298 ASP cc_start: 0.8389 (m-30) cc_final: 0.8070 (m-30) REVERT: D 365 VAL cc_start: 0.8808 (p) cc_final: 0.8474 (t) REVERT: E 98 LYS cc_start: 0.7897 (mmpt) cc_final: 0.7574 (mmmm) REVERT: E 109 ASN cc_start: 0.8309 (m-40) cc_final: 0.8041 (m-40) REVERT: E 171 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7812 (mt-10) REVERT: E 193 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7877 (tm-30) REVERT: E 311 ASP cc_start: 0.8150 (t0) cc_final: 0.7827 (t0) REVERT: E 339 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7585 (tm-30) REVERT: E 343 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8260 (mtmm) outliers start: 44 outliers final: 38 residues processed: 384 average time/residue: 0.1311 time to fit residues: 69.5756 Evaluate side-chains 401 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 360 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 269 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN D 281 ASN E 174 GLN ** E 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107633 restraints weight = 17861.109| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.01 r_work: 0.3258 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12664 Z= 0.135 Angle : 0.600 10.034 17182 Z= 0.308 Chirality : 0.044 0.210 1978 Planarity : 0.005 0.051 2183 Dihedral : 4.684 51.673 1694 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.02 % Allowed : 20.93 % Favored : 76.05 % 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 aren not related in a simple way. whole: 0.10 (0.22), residues: 1552 helix: 1.66 (0.20), residues: 717 sheet: -0.50 (0.33), residues: 264 loop : -1.77 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 115 TYR 0.013 0.001 TYR B 223 PHE 0.025 0.001 PHE C 35 TRP 0.020 0.001 TRP D 364 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00316 (12664) covalent geometry : angle 0.59968 (17182) hydrogen bonds : bond 0.04436 ( 547) hydrogen bonds : angle 4.31711 ( 1617) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3257.17 seconds wall clock time: 56 minutes 23.45 seconds (3383.45 seconds total)