Starting phenix.real_space_refine on Fri Aug 7 11:13:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uki_64240/08_2026/9uki_64240.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uki_64240/08_2026/9uki_64240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uki_64240/08_2026/9uki_64240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uki_64240/08_2026/9uki_64240.map" model { file = "/net/cci-nas-00/data/ceres_data/9uki_64240/08_2026/9uki_64240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uki_64240/08_2026/9uki_64240.cif" } resolution = 3.64 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= 0.003 sd= 0.042 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 88 5.16 5 C 13051 2.51 5 N 3711 2.21 5 O 3900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20759 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2350 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "B" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2357 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain breaks: 1 Chain: "C" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2361 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain breaks: 1 Chain: "D" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2458 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain: "E" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2519 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "F" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2499 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 12, 'TRANS': 304} Chain: "f" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1597 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "G" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2423 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain: "I" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2102 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 1 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.05, per 1000 atoms: 0.20 Number of scatterers: 20759 At special positions: 0 Unit cell: (146.58, 133.318, 131.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 9 15.00 O 3900 8.00 N 3711 7.00 C 13051 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: 1.64 Conformation dependent library (CDL) restraints added in 962.6 milliseconds 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4924 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 24 sheets defined 49.1% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 50 through 64 Processing helix chain 'A' and resid 76 through 89 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.589A pdb=" N TRP A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.994A pdb=" N ILE A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.634A pdb=" N GLU A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 226 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 238 through 262 removed outlier: 3.932A pdb=" N GLU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 258 " --> pdb=" O MET A 254 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.618A pdb=" N ALA A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.747A pdb=" N ARG A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 removed outlier: 4.093A pdb=" N ALA A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.698A pdb=" N ILE B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 147 through 160 removed outlier: 3.985A pdb=" N PHE B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 210 removed outlier: 3.880A pdb=" N ASP B 209 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 removed outlier: 3.774A pdb=" N ALA B 233 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 238 through 261 removed outlier: 3.657A pdb=" N VAL B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 removed outlier: 3.863A pdb=" N ILE B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.599A pdb=" N ARG B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.850A pdb=" N PHE B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B 310 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 76 through 88 removed outlier: 3.768A pdb=" N ILE C 81 " --> pdb=" O LYS C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 149 through 159 removed outlier: 4.272A pdb=" N VAL C 153 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 removed outlier: 4.156A pdb=" N VAL C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE C 228 " --> pdb=" O ASN C 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 238 through 262 removed outlier: 3.775A pdb=" N ARG C 250 " --> pdb=" O ASN C 246 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 258 " --> pdb=" O MET C 254 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 removed outlier: 3.512A pdb=" N ILE C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 294 removed outlier: 3.503A pdb=" N ARG C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.982A pdb=" N ALA C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 50 through 64 removed outlier: 3.520A pdb=" N ASN D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.579A pdb=" N ILE D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.683A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 153 through 156 removed outlier: 4.132A pdb=" N ARG D 156 " --> pdb=" O VAL D 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 153 through 156' Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 234 through 237 removed outlier: 3.660A pdb=" N GLN D 237 " --> pdb=" O LYS D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 237' Processing helix chain 'D' and resid 238 through 261 removed outlier: 3.527A pdb=" N ARG D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 302 through 313 removed outlier: 3.844A pdb=" N VAL D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 22 Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 76 through 87 Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.502A pdb=" N LEU E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.607A pdb=" N TRP E 130 " --> pdb=" O GLY E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 150 through 155 removed outlier: 3.964A pdb=" N VAL E 153 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 154 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 221 through 233 Processing helix chain 'E' and resid 238 through 262 Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'E' and resid 285 through 294 Processing helix chain 'E' and resid 295 through 298 Processing helix chain 'E' and resid 302 through 314 Processing helix chain 'F' and resid 18 through 23 removed outlier: 3.501A pdb=" N GLY F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 63 Processing helix chain 'F' and resid 76 through 89 Processing helix chain 'F' and resid 102 through 107 Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 143 through 146 removed outlier: 3.828A pdb=" N GLY F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 143 through 146' Processing helix chain 'F' and resid 147 through 159 removed outlier: 4.153A pdb=" N VAL F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 removed outlier: 3.676A pdb=" N MET F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 233 Processing helix chain 'F' and resid 238 through 262 removed outlier: 3.508A pdb=" N ARG F 242 " --> pdb=" O ASN F 238 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 286 through 294 removed outlier: 3.562A pdb=" N PHE F 294 " --> pdb=" O PHE F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 298 removed outlier: 3.629A pdb=" N CYS F 298 " --> pdb=" O LEU F 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 295 through 298' Processing helix chain 'F' and resid 302 through 314 removed outlier: 3.663A pdb=" N VAL F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) Processing helix chain 'f' and resid 23 through 38 Processing helix chain 'f' and resid 68 through 85 removed outlier: 3.623A pdb=" N ARG f 85 " --> pdb=" O SER f 81 " (cutoff:3.500A) Processing helix chain 'f' and resid 90 through 95 Processing helix chain 'f' and resid 96 through 98 No H-bonds generated for 'chain 'f' and resid 96 through 98' Processing helix chain 'f' and resid 101 through 124 removed outlier: 4.308A pdb=" N ALA f 106 " --> pdb=" O LYS f 102 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE f 107 " --> pdb=" O GLN f 103 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY f 120 " --> pdb=" O VAL f 116 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 143 removed outlier: 4.325A pdb=" N ASN f 130 " --> pdb=" O GLY f 126 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA f 142 " --> pdb=" O LYS f 138 " (cutoff:3.500A) Processing helix chain 'f' and resid 154 through 168 removed outlier: 3.583A pdb=" N ALA f 158 " --> pdb=" O PRO f 154 " (cutoff:3.500A) Processing helix chain 'f' and resid 173 through 177 Processing helix chain 'f' and resid 178 through 199 removed outlier: 3.768A pdb=" N TRP f 183 " --> pdb=" O VAL f 179 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASP f 185 " --> pdb=" O GLU f 181 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRP f 186 " --> pdb=" O LEU f 182 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER f 192 " --> pdb=" O GLU f 188 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA f 193 " --> pdb=" O GLN f 189 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP f 194 " --> pdb=" O LYS f 190 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY f 199 " --> pdb=" O ILE f 195 " (cutoff:3.500A) Processing helix chain 'f' and resid 204 through 221 removed outlier: 4.089A pdb=" N MET f 215 " --> pdb=" O THR f 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 335 removed outlier: 3.840A pdb=" N CYS G 335 " --> pdb=" O ALA G 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 331 through 335' Processing helix chain 'G' and resid 345 through 350 removed outlier: 4.350A pdb=" N GLN G 350 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 369 removed outlier: 3.919A pdb=" N GLY G 359 " --> pdb=" O GLN G 355 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG G 360 " --> pdb=" O GLY G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.874A pdb=" N ILE G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 450 removed outlier: 4.293A pdb=" N GLU G 447 " --> pdb=" O ALA G 443 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG G 448 " --> pdb=" O ARG G 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 475 Processing helix chain 'G' and resid 498 through 502 Processing helix chain 'G' and resid 520 through 534 removed outlier: 3.575A pdb=" N ARG G 530 " --> pdb=" O TRP G 526 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG G 534 " --> pdb=" O ARG G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 552 through 557 removed outlier: 4.527A pdb=" N VAL G 557 " --> pdb=" O SER G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 578 removed outlier: 4.600A pdb=" N GLU G 564 " --> pdb=" O GLY G 560 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 606 No H-bonds generated for 'chain 'G' and resid 604 through 606' Processing helix chain 'G' and resid 607 through 619 removed outlier: 4.451A pdb=" N GLU G 613 " --> pdb=" O GLY G 609 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN G 614 " --> pdb=" O ALA G 610 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER G 617 " --> pdb=" O GLU G 613 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE G 619 " --> pdb=" O LEU G 615 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 335 removed outlier: 3.630A pdb=" N LEU I 334 " --> pdb=" O GLU I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 352 removed outlier: 3.583A pdb=" N ARG I 342 " --> pdb=" O ALA I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 372 removed outlier: 3.805A pdb=" N GLY I 359 " --> pdb=" O GLN I 355 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG I 360 " --> pdb=" O GLY I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 424 through 428 removed outlier: 3.728A pdb=" N MET I 427 " --> pdb=" O SER I 424 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG I 428 " --> pdb=" O GLY I 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 424 through 428' Processing helix chain 'I' and resid 429 through 450 removed outlier: 3.849A pdb=" N THR I 433 " --> pdb=" O GLY I 429 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 474 Processing helix chain 'I' and resid 502 through 511 removed outlier: 4.056A pdb=" N LEU I 508 " --> pdb=" O ASN I 505 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET I 509 " --> pdb=" O LEU I 506 " (cutoff:3.500A) Processing helix chain 'I' and resid 525 through 533 removed outlier: 3.753A pdb=" N ARG I 530 " --> pdb=" O TRP I 526 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY I 533 " --> pdb=" O GLN I 529 " (cutoff:3.500A) Processing helix chain 'I' and resid 553 through 558 removed outlier: 4.094A pdb=" N VAL I 557 " --> pdb=" O SER I 553 " (cutoff:3.500A) Processing helix chain 'I' and resid 561 through 577 removed outlier: 3.708A pdb=" N ILE I 571 " --> pdb=" O LEU I 567 " (cutoff:3.500A) Processing helix chain 'I' and resid 610 through 620 removed outlier: 3.642A pdb=" N ALA I 616 " --> pdb=" O THR I 612 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER I 617 " --> pdb=" O GLU I 613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.532A pdb=" N VAL A 93 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASP A 141 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 95 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 136 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE A 182 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 138 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR A 184 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 140 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 67 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 115 removed outlier: 3.765A pdb=" N VAL A 118 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 96 removed outlier: 6.163A pdb=" N VAL B 93 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASP B 141 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 95 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU B 138 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR B 184 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE B 140 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 67 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 109 through 114 Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 96 removed outlier: 6.310A pdb=" N VAL C 136 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE C 182 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU C 138 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR C 184 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE C 140 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 67 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 115 Processing sheet with id=AB1, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.920A pdb=" N ARG C 171 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 17 Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 96 removed outlier: 6.554A pdb=" N VAL D 93 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP D 141 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL D 95 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL D 67 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 108 through 115 Processing sheet with id=AB5, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AB6, first strand: chain 'E' and resid 92 through 94 removed outlier: 6.275A pdb=" N LEU E 138 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR E 184 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE E 140 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL E 67 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ALA E 185 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL E 69 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N MET E 68 " --> pdb=" O THR E 215 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 108 through 113 Processing sheet with id=AB8, first strand: chain 'E' and resid 164 through 166 Processing sheet with id=AB9, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AC1, first strand: chain 'F' and resid 92 through 96 removed outlier: 6.414A pdb=" N VAL F 93 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP F 141 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL F 95 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU F 138 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR F 184 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE F 140 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 108 through 113 Processing sheet with id=AC3, first strand: chain 'f' and resid 43 through 44 removed outlier: 6.661A pdb=" N GLU f 43 " --> pdb=" O ALA f 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 327 through 330 removed outlier: 4.248A pdb=" N GLU G 327 " --> pdb=" O LEU G 487 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS G 489 " --> pdb=" O GLU G 327 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE G 455 " --> pdb=" O TYR G 492 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE G 458 " --> pdb=" O LEU G 421 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL G 416 " --> pdb=" O ILE G 540 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET G 542 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR G 418 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE G 544 " --> pdb=" O THR G 418 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL G 420 " --> pdb=" O ILE G 544 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N VAL G 599 " --> pdb=" O LEU G 582 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ALA G 584 " --> pdb=" O VAL G 599 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE G 601 " --> pdb=" O ALA G 584 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLY G 586 " --> pdb=" O ILE G 601 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 377 through 381 removed outlier: 3.606A pdb=" N ASP G 380 " --> pdb=" O TYR G 404 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR G 404 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 487 through 491 removed outlier: 4.092A pdb=" N LYS I 452 " --> pdb=" O THR I 415 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL I 416 " --> pdb=" O ILE I 540 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N MET I 542 " --> pdb=" O VAL I 416 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR I 418 " --> pdb=" O MET I 542 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE I 544 " --> pdb=" O THR I 418 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL I 420 " --> pdb=" O ILE I 544 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA I 584 " --> pdb=" O VAL I 599 " (cutoff:3.500A) 854 hydrogen bonds defined for protein. 2448 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: 3.17 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7092 1.34 - 1.46: 4350 1.46 - 1.58: 9553 1.58 - 1.70: 12 1.70 - 1.82: 157 Bond restraints: 21164 Sorted by residual: bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" O3A ANP E 401 " pdb=" PB ANP E 401 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.78e+01 ... (remaining 21159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 28622 3.70 - 7.39: 116 7.39 - 11.09: 17 11.09 - 14.79: 0 14.79 - 18.48: 3 Bond angle restraints: 28758 Sorted by residual: angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 108.47 18.48 3.00e+00 1.11e-01 3.80e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 108.87 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" PB ANP E 401 " pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 126.95 109.35 17.60 3.00e+00 1.11e-01 3.44e+01 angle pdb=" CA PRO B 270 " pdb=" N PRO B 270 " pdb=" CD PRO B 270 " ideal model delta sigma weight residual 112.00 106.63 5.37 1.40e+00 5.10e-01 1.47e+01 angle pdb=" O1B ANP E 401 " pdb=" PB ANP E 401 " pdb=" O2B ANP E 401 " ideal model delta sigma weight residual 120.08 109.00 11.08 3.00e+00 1.11e-01 1.36e+01 ... (remaining 28753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10544 17.94 - 35.88: 1547 35.88 - 53.83: 488 53.83 - 71.77: 121 71.77 - 89.71: 54 Dihedral angle restraints: 12754 sinusoidal: 5149 harmonic: 7605 Sorted by residual: dihedral pdb=" CG ARG E 312 " pdb=" CD ARG E 312 " pdb=" NE ARG E 312 " pdb=" CZ ARG E 312 " ideal model delta sinusoidal sigma weight residual -90.00 -39.64 -50.36 2 1.50e+01 4.44e-03 1.26e+01 dihedral pdb=" CA ARG E 163 " pdb=" C ARG E 163 " pdb=" N LEU E 164 " pdb=" CA LEU E 164 " ideal model delta harmonic sigma weight residual 180.00 162.23 17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP F 46 " pdb=" CB ASP F 46 " pdb=" CG ASP F 46 " pdb=" OD1 ASP F 46 " ideal model delta sinusoidal sigma weight residual -30.00 -88.87 58.87 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 12751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2827 0.062 - 0.123: 398 0.123 - 0.185: 22 0.185 - 0.246: 0 0.246 - 0.308: 4 Chirality restraints: 3251 Sorted by residual: chirality pdb=" CB VAL E 95 " pdb=" CA VAL E 95 " pdb=" CG1 VAL E 95 " pdb=" CG2 VAL E 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3248 not shown) Planarity restraints: 3756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 269 " -0.074 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO B 270 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 90 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO A 91 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 135 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C ASN A 135 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN A 135 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 136 " 0.013 2.00e-02 2.50e+03 ... (remaining 3753 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 589 2.69 - 3.25: 20739 3.25 - 3.80: 33377 3.80 - 4.35: 41865 4.35 - 4.90: 68352 Nonbonded interactions: 164922 Sorted by model distance: nonbonded pdb=" O1B ANP E 401 " pdb=" O3G ANP E 401 " model vdw 2.142 3.040 nonbonded pdb=" O1B ANP D 401 " pdb=" O2G ANP D 401 " model vdw 2.204 3.040 nonbonded pdb=" O LYS A 232 " pdb=" NZ LYS A 232 " model vdw 2.236 3.120 nonbonded pdb=" OD2 ASP I 551 " pdb=" OG1 THR I 554 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP F 50 " pdb=" N ARG F 51 " model vdw 2.245 3.120 ... (remaining 164917 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' selection = (chain 'B' and resid 9 through 318) selection = (chain 'C' and (resid 9 through 188 or resid 203 through 318)) selection = (chain 'D' and (resid 9 through 188 or resid 203 through 318)) selection = (chain 'E' and (resid 9 through 188 or resid 203 through 318)) selection = (chain 'F' and (resid 9 through 188 or resid 203 through 318)) } ncs_group { reference = (chain 'G' and (resid 317 through 372 or resid 411 through 620)) selection = chain 'I' } 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 group one per residue 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: 3.860 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.200 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:1.060 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.004 0.147 21164 Z= 0.196 Angle : 0.668 18.484 28758 Z= 0.330 Chirality : 0.043 0.308 3251 Planarity : 0.005 0.109 3756 Dihedral : 19.808 89.710 7830 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.10 % Favored : 93.87 % Rotamer: Outliers : 0.55 % Allowed : 40.77 % Favored : 58.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2592 helix: 0.28 (0.16), residues: 1043 sheet: -0.73 (0.28), residues: 346 loop : -0.77 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG f 184 TYR 0.023 0.001 TYR F 219 PHE 0.031 0.001 PHE F 294 TRP 0.021 0.001 TRP A 90 HIS 0.004 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 (21164) covalent geometry : angle 0.66755 / 0.33 (28758) hydrogen bonds : bond 0.18222 / 12.86 ( 854) hydrogen bonds : angle 6.87732 / 4.79 ( 2448) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 561 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 TRP cc_start: 0.8375 (m100) cc_final: 0.7662 (m100) REVERT: A 254 MET cc_start: 0.8187 (tmm) cc_final: 0.7951 (tmm) REVERT: B 141 ASP cc_start: 0.7647 (t0) cc_final: 0.7199 (t0) REVERT: E 151 MET cc_start: 0.8024 (tpp) cc_final: 0.7788 (tpp) REVERT: F 144 ASP cc_start: 0.7514 (p0) cc_final: 0.7191 (p0) REVERT: F 147 ARG cc_start: 0.7561 (ttp-170) cc_final: 0.6892 (ttp80) REVERT: F 151 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6273 (mpp) outliers start: 12 outliers final: 7 residues processed: 562 average time/residue: 0.1427 time to fit residues: 119.2764 Evaluate side-chains 558 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 550 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain f residue 198 LEU Chi-restraints excluded: chain f residue 208 PHE Chi-restraints excluded: chain I residue 510 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN E 96 ASN ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN I 614 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.159813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125408 restraints weight = 33855.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129866 restraints weight = 16749.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132774 restraints weight = 10118.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134729 restraints weight = 7061.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135955 restraints weight = 5456.348| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 21164 Z= 0.309 Angle : 0.638 7.250 28758 Z= 0.341 Chirality : 0.046 0.274 3251 Planarity : 0.006 0.080 3756 Dihedral : 8.879 84.825 3005 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.41 % Allowed : 35.18 % Favored : 59.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.16), residues: 2592 helix: 0.28 (0.16), residues: 1061 sheet: -1.01 (0.28), residues: 318 loop : -1.01 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 156 TYR 0.021 0.002 TYR F 219 PHE 0.017 0.002 PHE E 140 TRP 0.025 0.002 TRP A 90 HIS 0.006 0.001 HIS E 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.31 (21164) covalent geometry : angle 0.63799 / 0.34 (28758) hydrogen bonds : bond 0.05276 / 3.64 ( 854) hydrogen bonds : angle 5.63572 / 4.01 ( 2448) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 599 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8807 (tp) cc_final: 0.8550 (tp) REVERT: A 89 ASN cc_start: 0.7820 (t0) cc_final: 0.7556 (t0) REVERT: A 94 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7525 (ttm170) REVERT: A 254 MET cc_start: 0.8165 (tmm) cc_final: 0.7892 (tmm) REVERT: A 296 ASN cc_start: 0.8460 (m-40) cc_final: 0.8166 (m110) REVERT: A 308 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6559 (tm-30) REVERT: B 30 VAL cc_start: 0.8240 (t) cc_final: 0.7804 (m) REVERT: B 141 ASP cc_start: 0.7786 (t0) cc_final: 0.7293 (t0) REVERT: B 248 MET cc_start: 0.7661 (ptm) cc_final: 0.7266 (ptm) REVERT: C 47 TYR cc_start: 0.8549 (t80) cc_final: 0.8024 (t80) REVERT: C 135 ASN cc_start: 0.8509 (p0) cc_final: 0.8249 (p0) REVERT: C 156 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7847 (ttm170) REVERT: C 240 GLU cc_start: 0.7310 (tp30) cc_final: 0.6920 (tp30) REVERT: C 275 THR cc_start: 0.8475 (m) cc_final: 0.7977 (m) REVERT: C 278 GLU cc_start: 0.7473 (tm-30) cc_final: 0.6694 (tm-30) REVERT: C 279 ASN cc_start: 0.8598 (m110) cc_final: 0.7600 (m110) REVERT: D 232 LYS cc_start: 0.8456 (tppt) cc_final: 0.8016 (ttpt) REVERT: E 69 VAL cc_start: 0.8079 (t) cc_final: 0.7746 (m) REVERT: E 174 ARG cc_start: 0.7709 (mmm-85) cc_final: 0.7485 (mmm-85) REVERT: E 192 ASP cc_start: 0.7057 (p0) cc_final: 0.6628 (p0) REVERT: E 208 MET cc_start: 0.6294 (mmm) cc_final: 0.6062 (mmm) REVERT: E 301 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8235 (tt) REVERT: F 144 ASP cc_start: 0.7753 (p0) cc_final: 0.7211 (p0) REVERT: F 320 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7541 (mt-10) REVERT: f 86 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: f 204 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7297 (t70) REVERT: f 210 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7362 (ptp90) REVERT: G 347 LEU cc_start: 0.3159 (OUTLIER) cc_final: 0.2488 (mm) REVERT: G 396 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7605 (mp) REVERT: G 539 LYS cc_start: 0.4894 (OUTLIER) cc_final: 0.4662 (mtmt) REVERT: I 323 ARG cc_start: 0.6707 (mmp-170) cc_final: 0.6363 (mmp80) REVERT: I 572 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8215 (mm-30) outliers start: 119 outliers final: 70 residues processed: 653 average time/residue: 0.1500 time to fit residues: 145.5531 Evaluate side-chains 666 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 586 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 86 GLN Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 198 LEU Chi-restraints excluded: chain f residue 204 ASP Chi-restraints excluded: chain f residue 208 PHE Chi-restraints excluded: chain f residue 210 ARG Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 390 ARG Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 542 MET Chi-restraints excluded: chain G residue 611 MET Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 564 GLU Chi-restraints excluded: chain I residue 567 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 164 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 256 optimal weight: 50.0000 chunk 175 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 182 optimal weight: 6.9990 chunk 243 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS D 80 HIS D 133 GLN E 96 ASN E 279 ASN F 186 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.163041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128398 restraints weight = 33716.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132949 restraints weight = 16715.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.135984 restraints weight = 10124.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137889 restraints weight = 7025.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139207 restraints weight = 5461.857| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21164 Z= 0.161 Angle : 0.555 8.137 28758 Z= 0.291 Chirality : 0.043 0.240 3251 Planarity : 0.005 0.068 3756 Dihedral : 7.458 81.308 2995 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.50 % Allowed : 35.86 % Favored : 58.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.17), residues: 2592 helix: 0.48 (0.16), residues: 1062 sheet: -0.99 (0.28), residues: 333 loop : -0.97 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 156 TYR 0.021 0.001 TYR F 219 PHE 0.011 0.001 PHE F 179 TRP 0.017 0.001 TRP A 90 HIS 0.004 0.001 HIS D 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (21164) covalent geometry : angle 0.55515 / 0.29 (28758) hydrogen bonds : bond 0.04112 / 2.81 ( 854) hydrogen bonds : angle 5.26794 / 3.75 ( 2448) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 579 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.6904 (mmm-85) cc_final: 0.6202 (mpt180) REVERT: A 69 VAL cc_start: 0.7636 (t) cc_final: 0.7137 (p) REVERT: A 254 MET cc_start: 0.8210 (tmm) cc_final: 0.7979 (tmm) REVERT: A 308 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6321 (tm-30) REVERT: B 30 VAL cc_start: 0.8199 (t) cc_final: 0.7767 (m) REVERT: B 80 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7567 (t70) REVERT: B 141 ASP cc_start: 0.7766 (t0) cc_final: 0.7325 (t0) REVERT: B 248 MET cc_start: 0.7564 (ptm) cc_final: 0.7132 (ptm) REVERT: C 47 TYR cc_start: 0.8561 (t80) cc_final: 0.8047 (t80) REVERT: C 156 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7756 (ttm170) REVERT: C 236 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7556 (m-10) REVERT: C 275 THR cc_start: 0.8430 (m) cc_final: 0.7874 (m) REVERT: C 276 TRP cc_start: 0.8399 (t60) cc_final: 0.8052 (t-100) REVERT: C 278 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6720 (tm-30) REVERT: C 279 ASN cc_start: 0.8612 (m110) cc_final: 0.7539 (m110) REVERT: D 19 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6295 (mmt180) REVERT: D 232 LYS cc_start: 0.8463 (tppt) cc_final: 0.8057 (ttpt) REVERT: E 69 VAL cc_start: 0.8054 (t) cc_final: 0.7663 (m) REVERT: E 171 ARG cc_start: 0.7619 (ttp-110) cc_final: 0.7419 (ttp-110) REVERT: E 192 ASP cc_start: 0.6941 (p0) cc_final: 0.6529 (p0) REVERT: E 208 MET cc_start: 0.6488 (mmm) cc_final: 0.6074 (mmm) REVERT: E 301 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8176 (tt) REVERT: F 50 ASP cc_start: 0.7097 (t0) cc_final: 0.6885 (t0) REVERT: F 103 ARG cc_start: 0.7670 (tmm-80) cc_final: 0.7342 (ttt-90) REVERT: F 107 VAL cc_start: 0.8456 (p) cc_final: 0.8068 (t) REVERT: F 144 ASP cc_start: 0.7647 (p0) cc_final: 0.7058 (p0) REVERT: F 181 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7597 (tt) REVERT: F 320 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7424 (mt-10) REVERT: f 86 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: f 204 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7269 (t70) REVERT: f 210 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7274 (ptp90) REVERT: G 347 LEU cc_start: 0.2976 (OUTLIER) cc_final: 0.2746 (mt) REVERT: G 390 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6940 (mmp-170) REVERT: G 452 LYS cc_start: 0.7290 (mtpm) cc_final: 0.6974 (mtpm) REVERT: I 504 ARG cc_start: 0.5623 (ttp-110) cc_final: 0.5395 (ptp-110) REVERT: I 568 ARG cc_start: 0.8277 (mmm160) cc_final: 0.7756 (mmm160) REVERT: I 572 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8201 (mm-30) outliers start: 121 outliers final: 69 residues processed: 647 average time/residue: 0.1535 time to fit residues: 148.0074 Evaluate side-chains 656 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 576 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 86 GLN Chi-restraints excluded: chain f residue 111 VAL Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 198 LEU Chi-restraints excluded: chain f residue 204 ASP Chi-restraints excluded: chain f residue 208 PHE Chi-restraints excluded: chain f residue 210 ARG Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 ARG Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 515 LEU Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 564 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 256 optimal weight: 50.0000 chunk 154 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN A 135 ASN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN E 96 ASN F 80 HIS F 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.157578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123331 restraints weight = 34163.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127848 restraints weight = 16691.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130851 restraints weight = 10007.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132817 restraints weight = 6890.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133956 restraints weight = 5298.377| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21164 Z= 0.266 Angle : 0.614 9.563 28758 Z= 0.325 Chirality : 0.045 0.260 3251 Planarity : 0.005 0.067 3756 Dihedral : 7.247 81.082 2995 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 7.00 % Allowed : 34.45 % Favored : 58.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.16), residues: 2592 helix: 0.34 (0.16), residues: 1062 sheet: -0.94 (0.29), residues: 314 loop : -1.10 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 156 TYR 0.029 0.002 TYR F 219 PHE 0.014 0.001 PHE F 179 TRP 0.021 0.002 TRP A 90 HIS 0.006 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.27 (21164) covalent geometry : angle 0.61449 / 0.32 (28758) hydrogen bonds : bond 0.04647 / 3.19 ( 854) hydrogen bonds : angle 5.38845 / 3.84 ( 2448) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 599 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8038 (mtm-85) REVERT: A 48 LEU cc_start: 0.8825 (tp) cc_final: 0.8581 (tp) REVERT: A 65 ARG cc_start: 0.6945 (mmm-85) cc_final: 0.6292 (mpt-90) REVERT: A 69 VAL cc_start: 0.7723 (t) cc_final: 0.7064 (p) REVERT: A 94 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7588 (ttm170) REVERT: A 210 ARG cc_start: 0.7050 (mmp-170) cc_final: 0.6799 (mmp-170) REVERT: A 308 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6353 (tm-30) REVERT: B 30 VAL cc_start: 0.8246 (t) cc_final: 0.7791 (m) REVERT: B 72 TYR cc_start: 0.7797 (m-80) cc_final: 0.7574 (m-80) REVERT: B 141 ASP cc_start: 0.7782 (t0) cc_final: 0.7307 (t0) REVERT: B 223 ASP cc_start: 0.6132 (t0) cc_final: 0.5869 (t0) REVERT: C 47 TYR cc_start: 0.8589 (t80) cc_final: 0.8049 (t80) REVERT: C 156 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7820 (ttm170) REVERT: C 236 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7742 (m-10) REVERT: C 246 ASN cc_start: 0.8297 (m-40) cc_final: 0.7705 (m110) REVERT: C 275 THR cc_start: 0.8459 (m) cc_final: 0.7929 (m) REVERT: C 278 GLU cc_start: 0.7578 (tm-30) cc_final: 0.6832 (tm-30) REVERT: C 279 ASN cc_start: 0.8650 (m110) cc_final: 0.7618 (m110) REVERT: D 19 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6286 (mmt180) REVERT: D 232 LYS cc_start: 0.8530 (tppt) cc_final: 0.8134 (ttpt) REVERT: D 256 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.6883 (mpp80) REVERT: E 69 VAL cc_start: 0.8148 (t) cc_final: 0.7797 (m) REVERT: E 192 ASP cc_start: 0.7022 (p0) cc_final: 0.6612 (p0) REVERT: E 208 MET cc_start: 0.6528 (mmm) cc_final: 0.5975 (mmm) REVERT: E 301 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8143 (tt) REVERT: F 50 ASP cc_start: 0.7231 (t0) cc_final: 0.7026 (t0) REVERT: F 80 HIS cc_start: 0.6316 (OUTLIER) cc_final: 0.5943 (m90) REVERT: F 103 ARG cc_start: 0.7719 (tmm-80) cc_final: 0.7371 (ttt-90) REVERT: F 144 ASP cc_start: 0.7684 (p0) cc_final: 0.7092 (p0) REVERT: f 59 ARG cc_start: 0.5797 (mtt90) cc_final: 0.5528 (mtt90) REVERT: f 86 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: f 204 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7297 (t70) REVERT: f 210 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7333 (ptp90) REVERT: G 390 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6953 (mmp-170) REVERT: G 396 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7608 (mp) REVERT: G 452 LYS cc_start: 0.7299 (mtpm) cc_final: 0.6980 (mtpm) REVERT: G 539 LYS cc_start: 0.4903 (OUTLIER) cc_final: 0.4682 (mtmt) REVERT: G 542 MET cc_start: 0.6886 (ttm) cc_final: 0.6517 (ttm) REVERT: I 572 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8120 (mm-30) REVERT: I 606 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6054 (mt-10) outliers start: 154 outliers final: 99 residues processed: 682 average time/residue: 0.1521 time to fit residues: 154.6934 Evaluate side-chains 705 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 590 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 90 TRP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 86 GLN Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 149 THR Chi-restraints excluded: chain f residue 198 LEU Chi-restraints excluded: chain f residue 204 ASP Chi-restraints excluded: chain f residue 208 PHE Chi-restraints excluded: chain f residue 210 ARG Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 ARG Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 515 LEU Chi-restraints excluded: chain I residue 554 THR Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 606 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 213 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN C 80 HIS ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 133 GLN ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.156155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121949 restraints weight = 33835.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126412 restraints weight = 16680.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129354 restraints weight = 10050.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131276 restraints weight = 6947.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132554 restraints weight = 5340.408| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 21164 Z= 0.346 Angle : 0.661 9.078 28758 Z= 0.351 Chirality : 0.047 0.292 3251 Planarity : 0.006 0.067 3756 Dihedral : 7.290 83.213 2993 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 7.64 % Allowed : 35.14 % Favored : 57.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.16), residues: 2592 helix: 0.22 (0.16), residues: 1052 sheet: -1.24 (0.28), residues: 320 loop : -1.20 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 94 TYR 0.029 0.002 TYR F 219 PHE 0.016 0.002 PHE F 179 TRP 0.039 0.002 TRP C 276 HIS 0.019 0.001 HIS F 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.35 (21164) covalent geometry : angle 0.66118 / 0.35 (28758) hydrogen bonds : bond 0.04983 / 3.42 ( 854) hydrogen bonds : angle 5.53000 / 3.94 ( 2448) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 607 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.8038 (mtm-85) REVERT: A 48 LEU cc_start: 0.8843 (tp) cc_final: 0.8610 (tp) REVERT: A 65 ARG cc_start: 0.6994 (mmm-85) cc_final: 0.6389 (mpt-90) REVERT: A 69 VAL cc_start: 0.7739 (t) cc_final: 0.7070 (p) REVERT: A 94 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7623 (ttm170) REVERT: A 182 PHE cc_start: 0.7751 (m-10) cc_final: 0.7532 (m-10) REVERT: A 210 ARG cc_start: 0.7122 (mmp-170) cc_final: 0.6871 (mmp-170) REVERT: A 254 MET cc_start: 0.8231 (tmm) cc_final: 0.8013 (tmm) REVERT: A 257 GLN cc_start: 0.8319 (tp40) cc_final: 0.7793 (mp10) REVERT: A 296 ASN cc_start: 0.8377 (m110) cc_final: 0.8064 (m110) REVERT: A 308 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6376 (tm-30) REVERT: B 72 TYR cc_start: 0.7821 (m-80) cc_final: 0.7598 (m-80) REVERT: B 141 ASP cc_start: 0.7808 (t0) cc_final: 0.7363 (t0) REVERT: B 223 ASP cc_start: 0.6265 (t0) cc_final: 0.6024 (t0) REVERT: B 308 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6936 (mm-30) REVERT: C 47 TYR cc_start: 0.8670 (t80) cc_final: 0.7901 (t80) REVERT: C 80 HIS cc_start: 0.8170 (m-70) cc_final: 0.7668 (m90) REVERT: C 156 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7902 (ttm170) REVERT: C 204 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7578 (p0) REVERT: C 246 ASN cc_start: 0.8352 (m-40) cc_final: 0.7827 (m110) REVERT: C 275 THR cc_start: 0.8501 (m) cc_final: 0.8020 (m) REVERT: C 276 TRP cc_start: 0.8395 (t60) cc_final: 0.8034 (t-100) REVERT: C 278 GLU cc_start: 0.7602 (tm-30) cc_final: 0.6866 (tm-30) REVERT: C 279 ASN cc_start: 0.8656 (m110) cc_final: 0.7658 (m110) REVERT: D 232 LYS cc_start: 0.8569 (tppt) cc_final: 0.8186 (ttpt) REVERT: D 256 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.6707 (mpp80) REVERT: D 300 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5839 (mp0) REVERT: D 312 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7676 (mtp-110) REVERT: E 69 VAL cc_start: 0.8176 (t) cc_final: 0.7824 (m) REVERT: E 192 ASP cc_start: 0.7065 (p0) cc_final: 0.6662 (p0) REVERT: E 208 MET cc_start: 0.6531 (mmm) cc_final: 0.5933 (mmm) REVERT: E 301 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8112 (tt) REVERT: F 50 ASP cc_start: 0.7278 (t0) cc_final: 0.7048 (t0) REVERT: F 103 ARG cc_start: 0.7740 (tmm-80) cc_final: 0.7389 (ttt-90) REVERT: F 144 ASP cc_start: 0.7694 (p0) cc_final: 0.7124 (p0) REVERT: F 202 GLN cc_start: 0.7254 (tp40) cc_final: 0.7035 (tp40) REVERT: F 320 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7603 (mt-10) REVERT: f 59 ARG cc_start: 0.5843 (mtt90) cc_final: 0.5528 (mtt180) REVERT: f 184 ARG cc_start: 0.8027 (ttm110) cc_final: 0.7712 (mtm110) REVERT: f 198 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8601 (mm) REVERT: f 204 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7322 (t70) REVERT: f 210 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7361 (ptp90) REVERT: G 390 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6957 (mmp-170) REVERT: G 396 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7622 (mp) REVERT: G 452 LYS cc_start: 0.7269 (mtpm) cc_final: 0.6961 (mtpm) REVERT: G 483 ARG cc_start: 0.7430 (ttp80) cc_final: 0.7165 (ttp80) REVERT: G 539 LYS cc_start: 0.5003 (OUTLIER) cc_final: 0.4758 (mtmt) REVERT: G 542 MET cc_start: 0.6963 (ttm) cc_final: 0.6595 (ttm) REVERT: G 605 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6157 (tp30) REVERT: I 572 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8095 (mm-30) REVERT: I 606 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6051 (mt-10) outliers start: 168 outliers final: 127 residues processed: 702 average time/residue: 0.1627 time to fit residues: 169.7949 Evaluate side-chains 741 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 598 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 235 HIS Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 90 TRP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 235 HIS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 43 GLU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 149 THR Chi-restraints excluded: chain f residue 198 LEU Chi-restraints excluded: chain f residue 204 ASP Chi-restraints excluded: chain f residue 210 ARG Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 ARG Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 605 GLU Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 515 LEU Chi-restraints excluded: chain I residue 554 THR Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 564 GLU Chi-restraints excluded: chain I residue 606 GLU Chi-restraints excluded: chain I residue 611 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 132 optimal weight: 0.5980 chunk 240 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 231 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN C 80 HIS C 279 ASN E 96 ASN F 80 HIS F 186 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 561 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.159035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126530 restraints weight = 33586.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130886 restraints weight = 16476.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133740 restraints weight = 9815.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135625 restraints weight = 6727.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136671 restraints weight = 5132.080| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21164 Z= 0.136 Angle : 0.559 9.175 28758 Z= 0.291 Chirality : 0.042 0.279 3251 Planarity : 0.005 0.067 3756 Dihedral : 6.322 81.351 2988 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 6.41 % Allowed : 36.45 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2592 helix: 0.47 (0.16), residues: 1071 sheet: -1.01 (0.28), residues: 346 loop : -1.05 (0.19), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 504 TYR 0.021 0.001 TYR F 219 PHE 0.011 0.001 PHE F 179 TRP 0.024 0.001 TRP C 276 HIS 0.005 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (21164) covalent geometry : angle 0.55909 / 0.29 (28758) hydrogen bonds : bond 0.03718 / 2.55 ( 854) hydrogen bonds : angle 5.15458 / 3.68 ( 2448) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 587 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7933 (mtm-85) REVERT: A 48 LEU cc_start: 0.8823 (tp) cc_final: 0.8573 (tp) REVERT: A 65 ARG cc_start: 0.6891 (mmm-85) cc_final: 0.6377 (mpt180) REVERT: A 69 VAL cc_start: 0.7673 (t) cc_final: 0.7087 (p) REVERT: A 110 ASP cc_start: 0.5799 (OUTLIER) cc_final: 0.5434 (p0) REVERT: A 229 VAL cc_start: 0.8245 (t) cc_final: 0.8011 (t) REVERT: A 254 MET cc_start: 0.8243 (tmm) cc_final: 0.8022 (tmm) REVERT: A 256 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7725 (mtt180) REVERT: A 257 GLN cc_start: 0.8155 (tp40) cc_final: 0.7677 (mp10) REVERT: A 296 ASN cc_start: 0.8327 (m110) cc_final: 0.8061 (m110) REVERT: A 308 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6194 (tm-30) REVERT: B 69 VAL cc_start: 0.8199 (t) cc_final: 0.7773 (m) REVERT: B 72 TYR cc_start: 0.7797 (m-80) cc_final: 0.7530 (m-80) REVERT: B 141 ASP cc_start: 0.7790 (t0) cc_final: 0.7381 (t0) REVERT: B 223 ASP cc_start: 0.5930 (t0) cc_final: 0.5713 (t0) REVERT: B 248 MET cc_start: 0.7482 (ptm) cc_final: 0.7131 (ptm) REVERT: C 47 TYR cc_start: 0.8562 (t80) cc_final: 0.7879 (t80) REVERT: C 156 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7817 (ttm170) REVERT: C 246 ASN cc_start: 0.8227 (m-40) cc_final: 0.7665 (m110) REVERT: C 275 THR cc_start: 0.8456 (m) cc_final: 0.7910 (m) REVERT: C 276 TRP cc_start: 0.8353 (t60) cc_final: 0.8007 (t-100) REVERT: C 278 GLU cc_start: 0.7500 (tm-30) cc_final: 0.6812 (tm-30) REVERT: C 279 ASN cc_start: 0.8669 (m-40) cc_final: 0.7676 (m110) REVERT: C 308 GLU cc_start: 0.7740 (tt0) cc_final: 0.7459 (tm-30) REVERT: D 19 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.6236 (mmt180) REVERT: D 232 LYS cc_start: 0.8504 (tppt) cc_final: 0.8254 (ttpt) REVERT: D 256 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6464 (mpp80) REVERT: E 69 VAL cc_start: 0.8105 (t) cc_final: 0.7679 (m) REVERT: E 138 LEU cc_start: 0.8091 (tp) cc_final: 0.7873 (tt) REVERT: E 163 ARG cc_start: 0.7622 (mmm160) cc_final: 0.7410 (mmm160) REVERT: E 174 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.7518 (mmm-85) REVERT: E 192 ASP cc_start: 0.6970 (p0) cc_final: 0.6601 (p0) REVERT: E 208 MET cc_start: 0.6619 (mmm) cc_final: 0.6173 (tpp) REVERT: E 296 ASN cc_start: 0.8474 (m-40) cc_final: 0.8246 (m110) REVERT: E 300 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: E 301 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8019 (tt) REVERT: F 50 ASP cc_start: 0.7204 (t0) cc_final: 0.6930 (t0) REVERT: F 103 ARG cc_start: 0.7697 (tmm-80) cc_final: 0.7405 (ttt-90) REVERT: F 107 VAL cc_start: 0.8441 (p) cc_final: 0.8059 (t) REVERT: F 144 ASP cc_start: 0.7517 (p0) cc_final: 0.6902 (p0) REVERT: F 181 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7583 (tt) REVERT: F 291 ARG cc_start: 0.4540 (mtt-85) cc_final: 0.4047 (mtt-85) REVERT: F 320 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7386 (mt-10) REVERT: f 59 ARG cc_start: 0.5750 (mtt90) cc_final: 0.5497 (mtt180) REVERT: f 184 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7784 (ttm110) REVERT: f 204 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7222 (t70) REVERT: f 210 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7233 (ptp90) REVERT: G 396 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7609 (mp) REVERT: G 452 LYS cc_start: 0.7284 (mtpm) cc_final: 0.6950 (mtpm) REVERT: G 542 MET cc_start: 0.6802 (ttm) cc_final: 0.6403 (ttm) REVERT: I 501 ARG cc_start: 0.7627 (mtm180) cc_final: 0.7338 (ttm110) REVERT: I 568 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7821 (mmt180) REVERT: I 572 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8043 (mm-30) REVERT: I 606 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.6012 (mt-10) outliers start: 141 outliers final: 93 residues processed: 673 average time/residue: 0.1517 time to fit residues: 151.6141 Evaluate side-chains 680 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 574 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 235 HIS Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 90 TRP Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 149 THR Chi-restraints excluded: chain f residue 204 ASP Chi-restraints excluded: chain f residue 210 ARG Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 554 THR Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 565 ARG Chi-restraints excluded: chain I residue 606 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 118 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 135 ASN B 284 ASN ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN F 186 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.161439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126902 restraints weight = 33948.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131393 restraints weight = 16819.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134384 restraints weight = 10221.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136324 restraints weight = 7099.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.137638 restraints weight = 5497.848| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21164 Z= 0.206 Angle : 0.597 9.875 28758 Z= 0.312 Chirality : 0.044 0.314 3251 Planarity : 0.005 0.066 3756 Dihedral : 6.167 79.917 2986 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 6.73 % Allowed : 36.09 % Favored : 57.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2592 helix: 0.47 (0.16), residues: 1064 sheet: -1.10 (0.27), residues: 357 loop : -1.05 (0.19), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 312 TYR 0.026 0.001 TYR F 219 PHE 0.013 0.001 PHE F 179 TRP 0.017 0.001 TRP C 276 HIS 0.005 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (21164) covalent geometry : angle 0.59684 / 0.31 (28758) hydrogen bonds : bond 0.04043 / 2.77 ( 854) hydrogen bonds : angle 5.18182 / 3.70 ( 2448) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 592 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.8013 (mtm-85) REVERT: A 48 LEU cc_start: 0.8840 (tp) cc_final: 0.8594 (tp) REVERT: A 65 ARG cc_start: 0.6915 (mmm-85) cc_final: 0.6393 (mpt180) REVERT: A 69 VAL cc_start: 0.7665 (t) cc_final: 0.6949 (p) REVERT: A 94 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7573 (ttm170) REVERT: A 110 ASP cc_start: 0.5834 (OUTLIER) cc_final: 0.5482 (p0) REVERT: A 215 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.7756 (p) REVERT: A 254 MET cc_start: 0.8251 (tmm) cc_final: 0.8001 (tmm) REVERT: A 256 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7865 (mtt180) REVERT: A 257 GLN cc_start: 0.8215 (tp40) cc_final: 0.7742 (mp10) REVERT: A 296 ASN cc_start: 0.8328 (m110) cc_final: 0.8059 (m110) REVERT: A 308 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6269 (tm-30) REVERT: B 69 VAL cc_start: 0.8215 (t) cc_final: 0.7789 (m) REVERT: B 72 TYR cc_start: 0.7812 (m-80) cc_final: 0.7552 (m-80) REVERT: B 141 ASP cc_start: 0.7805 (t0) cc_final: 0.7385 (t0) REVERT: B 223 ASP cc_start: 0.6069 (t0) cc_final: 0.5848 (t0) REVERT: B 308 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6905 (mm-30) REVERT: C 47 TYR cc_start: 0.8586 (t80) cc_final: 0.7897 (t80) REVERT: C 156 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7761 (ttm170) REVERT: C 246 ASN cc_start: 0.8257 (m-40) cc_final: 0.7701 (m110) REVERT: C 257 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8180 (tp40) REVERT: C 275 THR cc_start: 0.8498 (m) cc_final: 0.8004 (m) REVERT: C 276 TRP cc_start: 0.8324 (t60) cc_final: 0.8076 (t-100) REVERT: C 278 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6786 (tm-30) REVERT: C 279 ASN cc_start: 0.8680 (m-40) cc_final: 0.7691 (m110) REVERT: D 19 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.6243 (mmt180) REVERT: D 232 LYS cc_start: 0.8529 (tppt) cc_final: 0.8290 (ttpt) REVERT: D 256 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6431 (mpp80) REVERT: E 69 VAL cc_start: 0.8088 (t) cc_final: 0.7735 (m) REVERT: E 192 ASP cc_start: 0.7019 (p0) cc_final: 0.6632 (p0) REVERT: E 208 MET cc_start: 0.6611 (mmm) cc_final: 0.6020 (mmm) REVERT: E 300 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: E 301 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8005 (tt) REVERT: F 50 ASP cc_start: 0.7259 (t0) cc_final: 0.6991 (t0) REVERT: F 94 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7848 (mtm180) REVERT: F 103 ARG cc_start: 0.7763 (tmm-80) cc_final: 0.7421 (ttt-90) REVERT: F 144 ASP cc_start: 0.7561 (p0) cc_final: 0.6948 (p0) REVERT: f 59 ARG cc_start: 0.5804 (mtt90) cc_final: 0.5556 (mtt180) REVERT: f 184 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7799 (ttm110) REVERT: f 204 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7233 (t70) REVERT: f 210 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7258 (ptp90) REVERT: G 396 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7636 (mp) REVERT: G 452 LYS cc_start: 0.7292 (mtpm) cc_final: 0.6952 (mtpm) REVERT: G 542 MET cc_start: 0.6863 (ttm) cc_final: 0.6487 (ttm) REVERT: G 605 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6179 (tp30) REVERT: I 328 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7319 (mm-30) REVERT: I 501 ARG cc_start: 0.7634 (mtm180) cc_final: 0.7371 (ttm110) REVERT: I 542 MET cc_start: 0.7035 (ttm) cc_final: 0.6696 (ttm) REVERT: I 572 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8072 (mm-30) REVERT: I 606 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.6013 (mt-10) outliers start: 148 outliers final: 110 residues processed: 684 average time/residue: 0.1525 time to fit residues: 155.4934 Evaluate side-chains 716 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 590 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 235 HIS Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 90 TRP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 149 THR Chi-restraints excluded: chain f residue 204 ASP Chi-restraints excluded: chain f residue 210 ARG Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 605 GLU Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 515 LEU Chi-restraints excluded: chain I residue 554 THR Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 565 ARG Chi-restraints excluded: chain I residue 606 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 74 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 221 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 89 ASN A 135 ASN D 80 HIS D 133 GLN E 279 ASN F 186 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.160367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126514 restraints weight = 33738.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131022 restraints weight = 16685.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134030 restraints weight = 10043.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136005 restraints weight = 6918.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137195 restraints weight = 5305.747| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21164 Z= 0.153 Angle : 0.584 10.825 28758 Z= 0.302 Chirality : 0.043 0.291 3251 Planarity : 0.005 0.066 3756 Dihedral : 5.958 77.944 2986 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 6.27 % Allowed : 36.55 % Favored : 57.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2592 helix: 0.50 (0.16), residues: 1066 sheet: -1.01 (0.27), residues: 346 loop : -1.00 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 312 TYR 0.026 0.001 TYR F 219 PHE 0.011 0.001 PHE F 179 TRP 0.017 0.001 TRP A 90 HIS 0.006 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (21164) covalent geometry : angle 0.58431 / 0.30 (28758) hydrogen bonds : bond 0.03723 / 2.55 ( 854) hydrogen bonds : angle 5.08916 / 3.64 ( 2448) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 599 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7952 (mtm-85) REVERT: A 48 LEU cc_start: 0.8821 (tp) cc_final: 0.8575 (tp) REVERT: A 65 ARG cc_start: 0.6867 (mmm-85) cc_final: 0.6517 (mpt90) REVERT: A 69 VAL cc_start: 0.7670 (t) cc_final: 0.6923 (p) REVERT: A 94 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7432 (ttm170) REVERT: A 215 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.7733 (p) REVERT: A 229 VAL cc_start: 0.8270 (t) cc_final: 0.8036 (t) REVERT: A 254 MET cc_start: 0.8236 (tmm) cc_final: 0.7983 (tmm) REVERT: A 256 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7852 (mtt180) REVERT: A 257 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7722 (mp10) REVERT: A 296 ASN cc_start: 0.8311 (m110) cc_final: 0.8027 (m110) REVERT: A 308 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6218 (tm-30) REVERT: B 69 VAL cc_start: 0.8192 (t) cc_final: 0.7757 (m) REVERT: B 72 TYR cc_start: 0.7752 (m-80) cc_final: 0.7442 (m-80) REVERT: B 141 ASP cc_start: 0.7813 (t0) cc_final: 0.7436 (t0) REVERT: B 223 ASP cc_start: 0.5918 (t0) cc_final: 0.5710 (t0) REVERT: B 308 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6814 (mm-30) REVERT: C 47 TYR cc_start: 0.8585 (t80) cc_final: 0.7867 (t80) REVERT: C 156 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7742 (ttm170) REVERT: C 246 ASN cc_start: 0.8228 (m-40) cc_final: 0.7706 (m110) REVERT: C 257 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8179 (tp40) REVERT: C 275 THR cc_start: 0.8489 (m) cc_final: 0.7997 (m) REVERT: C 276 TRP cc_start: 0.8280 (t60) cc_final: 0.8056 (t-100) REVERT: C 278 GLU cc_start: 0.7519 (tm-30) cc_final: 0.6862 (tm-30) REVERT: C 279 ASN cc_start: 0.8667 (m-40) cc_final: 0.7715 (m110) REVERT: C 308 GLU cc_start: 0.7765 (tt0) cc_final: 0.7493 (tm-30) REVERT: D 19 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.6244 (mmt180) REVERT: D 256 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6207 (mpp80) REVERT: E 69 VAL cc_start: 0.8070 (t) cc_final: 0.7698 (m) REVERT: E 158 LEU cc_start: 0.8343 (mp) cc_final: 0.8018 (mp) REVERT: E 192 ASP cc_start: 0.6990 (p0) cc_final: 0.6632 (p0) REVERT: E 208 MET cc_start: 0.6643 (mmm) cc_final: 0.6205 (tpp) REVERT: E 300 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: E 301 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7992 (tt) REVERT: F 50 ASP cc_start: 0.7258 (t0) cc_final: 0.6977 (t0) REVERT: F 144 ASP cc_start: 0.7522 (p0) cc_final: 0.6904 (p0) REVERT: f 85 ARG cc_start: 0.7408 (tpp80) cc_final: 0.7038 (tpp80) REVERT: f 178 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6838 (tp40) REVERT: f 204 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7213 (t70) REVERT: f 210 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7216 (ptp90) REVERT: G 396 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7656 (mp) REVERT: G 452 LYS cc_start: 0.7276 (mtpm) cc_final: 0.6941 (mtpm) REVERT: G 542 MET cc_start: 0.6807 (ttm) cc_final: 0.6426 (ttm) REVERT: G 605 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6171 (tp30) REVERT: I 501 ARG cc_start: 0.7614 (mtm180) cc_final: 0.7366 (ttm110) REVERT: I 510 MET cc_start: 0.7136 (mmm) cc_final: 0.6864 (tmm) REVERT: I 542 MET cc_start: 0.7028 (ttm) cc_final: 0.6685 (ttm) REVERT: I 572 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8051 (mm-30) REVERT: I 606 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6039 (mt-10) outliers start: 138 outliers final: 105 residues processed: 681 average time/residue: 0.1566 time to fit residues: 158.3691 Evaluate side-chains 708 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 586 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 257 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 235 HIS Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 149 THR Chi-restraints excluded: chain f residue 178 GLN Chi-restraints excluded: chain f residue 204 ASP Chi-restraints excluded: chain f residue 210 ARG Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 605 GLU Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 515 LEU Chi-restraints excluded: chain I residue 554 THR Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 565 ARG Chi-restraints excluded: chain I residue 606 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 54 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 251 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN F 186 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.161131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127118 restraints weight = 33863.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131638 restraints weight = 16822.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134519 restraints weight = 10165.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136440 restraints weight = 7090.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.137796 restraints weight = 5492.832| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21164 Z= 0.196 Angle : 0.615 11.390 28758 Z= 0.317 Chirality : 0.044 0.309 3251 Planarity : 0.005 0.065 3756 Dihedral : 5.934 75.839 2986 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.91 % Allowed : 37.50 % Favored : 56.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.17), residues: 2592 helix: 0.48 (0.16), residues: 1057 sheet: -0.95 (0.28), residues: 325 loop : -1.05 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG f 184 TYR 0.026 0.001 TYR F 219 PHE 0.014 0.001 PHE F 259 TRP 0.028 0.002 TRP G 377 HIS 0.007 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (21164) covalent geometry : angle 0.61516 / 0.32 (28758) hydrogen bonds : bond 0.03975 / 2.73 ( 854) hydrogen bonds : angle 5.15534 / 3.68 ( 2448) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 586 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7979 (mtm-85) REVERT: A 48 LEU cc_start: 0.8834 (tp) cc_final: 0.8589 (tp) REVERT: A 65 ARG cc_start: 0.6891 (mmm-85) cc_final: 0.6530 (mpt90) REVERT: A 69 VAL cc_start: 0.7670 (t) cc_final: 0.6906 (p) REVERT: A 94 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7445 (ttm170) REVERT: A 215 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.7710 (p) REVERT: A 254 MET cc_start: 0.8233 (tmm) cc_final: 0.7947 (tmm) REVERT: A 256 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7880 (mtt180) REVERT: A 257 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7774 (mp10) REVERT: A 296 ASN cc_start: 0.8284 (m110) cc_final: 0.8006 (m110) REVERT: A 308 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6277 (tm-30) REVERT: B 69 VAL cc_start: 0.8216 (t) cc_final: 0.7785 (m) REVERT: B 72 TYR cc_start: 0.7779 (m-80) cc_final: 0.7471 (m-80) REVERT: B 141 ASP cc_start: 0.7811 (t0) cc_final: 0.7416 (t0) REVERT: B 223 ASP cc_start: 0.6028 (t0) cc_final: 0.5808 (t0) REVERT: B 308 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6837 (mm-30) REVERT: C 47 TYR cc_start: 0.8593 (t80) cc_final: 0.7870 (t80) REVERT: C 156 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7739 (ttm170) REVERT: C 246 ASN cc_start: 0.8255 (m-40) cc_final: 0.7700 (m110) REVERT: C 257 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8204 (tp40) REVERT: C 275 THR cc_start: 0.8496 (m) cc_final: 0.7994 (m) REVERT: C 276 TRP cc_start: 0.8280 (t60) cc_final: 0.8055 (t-100) REVERT: C 278 GLU cc_start: 0.7537 (tm-30) cc_final: 0.6866 (tm-30) REVERT: C 279 ASN cc_start: 0.8686 (m-40) cc_final: 0.7740 (m110) REVERT: D 19 ARG cc_start: 0.6533 (OUTLIER) cc_final: 0.6252 (mmt180) REVERT: D 232 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8351 (ttpt) REVERT: D 256 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6205 (mpp80) REVERT: E 69 VAL cc_start: 0.8088 (t) cc_final: 0.7738 (m) REVERT: E 94 ARG cc_start: 0.7258 (mtp180) cc_final: 0.6678 (mtp180) REVERT: E 192 ASP cc_start: 0.7026 (p0) cc_final: 0.6659 (p0) REVERT: E 208 MET cc_start: 0.6674 (mmm) cc_final: 0.6109 (mmm) REVERT: E 300 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: E 301 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7992 (tt) REVERT: F 50 ASP cc_start: 0.7256 (t0) cc_final: 0.6992 (t0) REVERT: F 103 ARG cc_start: 0.7749 (tmm-80) cc_final: 0.7483 (ttt-90) REVERT: F 107 VAL cc_start: 0.8475 (p) cc_final: 0.8126 (t) REVERT: F 144 ASP cc_start: 0.7599 (p0) cc_final: 0.6966 (p0) REVERT: f 178 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6866 (tp40) REVERT: f 204 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7209 (t70) REVERT: f 210 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7182 (ptp90) REVERT: G 396 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7681 (mp) REVERT: G 452 LYS cc_start: 0.7289 (mtpm) cc_final: 0.6960 (mtpm) REVERT: G 542 MET cc_start: 0.6861 (ttm) cc_final: 0.6501 (ttm) REVERT: G 605 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6210 (tp30) REVERT: I 501 ARG cc_start: 0.7649 (mtm180) cc_final: 0.7391 (ttm110) REVERT: I 510 MET cc_start: 0.7142 (mmm) cc_final: 0.6884 (tmm) REVERT: I 542 MET cc_start: 0.7005 (ttm) cc_final: 0.6666 (ttm) REVERT: I 572 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8052 (mm-30) REVERT: I 606 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6060 (mt-10) outliers start: 130 outliers final: 107 residues processed: 664 average time/residue: 0.1628 time to fit residues: 161.0695 Evaluate side-chains 705 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 581 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 257 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 235 HIS Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 149 THR Chi-restraints excluded: chain f residue 178 GLN Chi-restraints excluded: chain f residue 204 ASP Chi-restraints excluded: chain f residue 210 ARG Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 605 GLU Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 515 LEU Chi-restraints excluded: chain I residue 554 THR Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 565 ARG Chi-restraints excluded: chain I residue 606 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 163 optimal weight: 0.0570 chunk 179 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 210 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 232 optimal weight: 20.0000 chunk 201 optimal weight: 0.0870 chunk 236 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN D 133 GLN D 186 ASN E 279 ASN F 186 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.164805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132009 restraints weight = 33763.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.136419 restraints weight = 16666.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.139282 restraints weight = 9967.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.141201 restraints weight = 6865.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.142415 restraints weight = 5268.918| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21164 Z= 0.115 Angle : 0.600 15.885 28758 Z= 0.302 Chirality : 0.042 0.322 3251 Planarity : 0.005 0.068 3756 Dihedral : 5.699 75.557 2986 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.14 % Allowed : 38.50 % Favored : 56.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2592 helix: 0.52 (0.16), residues: 1071 sheet: -0.81 (0.28), residues: 339 loop : -0.95 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG f 184 TYR 0.025 0.001 TYR F 219 PHE 0.016 0.001 PHE F 259 TRP 0.023 0.002 TRP B 276 HIS 0.006 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (21164) covalent geometry : angle 0.59953 / 0.30 (28758) hydrogen bonds : bond 0.03388 / 2.31 ( 854) hydrogen bonds : angle 4.99386 / 3.57 ( 2448) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 592 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7955 (mtm-85) REVERT: A 65 ARG cc_start: 0.6802 (mmm-85) cc_final: 0.6493 (mpt90) REVERT: A 69 VAL cc_start: 0.7628 (t) cc_final: 0.6998 (p) REVERT: A 94 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7416 (ttm170) REVERT: A 110 ASP cc_start: 0.5749 (OUTLIER) cc_final: 0.5394 (p0) REVERT: A 229 VAL cc_start: 0.8244 (t) cc_final: 0.8007 (t) REVERT: A 254 MET cc_start: 0.8227 (tmm) cc_final: 0.8011 (tmm) REVERT: A 257 GLN cc_start: 0.8139 (tp40) cc_final: 0.7652 (mp10) REVERT: A 294 PHE cc_start: 0.7747 (t80) cc_final: 0.7537 (t80) REVERT: A 296 ASN cc_start: 0.8275 (m110) cc_final: 0.7980 (m110) REVERT: A 308 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6221 (tm-30) REVERT: B 69 VAL cc_start: 0.8151 (t) cc_final: 0.7721 (m) REVERT: B 72 TYR cc_start: 0.7734 (m-80) cc_final: 0.7378 (m-80) REVERT: B 141 ASP cc_start: 0.7784 (t0) cc_final: 0.7475 (t0) REVERT: B 223 ASP cc_start: 0.5649 (t0) cc_final: 0.5431 (t0) REVERT: B 308 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6711 (mm-30) REVERT: C 47 TYR cc_start: 0.8565 (t80) cc_final: 0.7909 (t80) REVERT: C 246 ASN cc_start: 0.8188 (m-40) cc_final: 0.7677 (m110) REVERT: C 275 THR cc_start: 0.8457 (m) cc_final: 0.7976 (m) REVERT: C 276 TRP cc_start: 0.8239 (t60) cc_final: 0.8021 (t-100) REVERT: C 279 ASN cc_start: 0.8648 (m-40) cc_final: 0.8226 (m110) REVERT: C 308 GLU cc_start: 0.7745 (tt0) cc_final: 0.7469 (tm-30) REVERT: D 192 ASP cc_start: 0.6826 (p0) cc_final: 0.6301 (p0) REVERT: D 256 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6130 (mpp80) REVERT: E 69 VAL cc_start: 0.8030 (t) cc_final: 0.7650 (m) REVERT: E 94 ARG cc_start: 0.7090 (mtp180) cc_final: 0.6722 (mtp180) REVERT: E 138 LEU cc_start: 0.8116 (tp) cc_final: 0.7916 (tt) REVERT: E 156 ARG cc_start: 0.7229 (mmm-85) cc_final: 0.6637 (mmm-85) REVERT: E 192 ASP cc_start: 0.6922 (p0) cc_final: 0.6579 (p0) REVERT: E 300 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: E 301 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7966 (tt) REVERT: F 50 ASP cc_start: 0.7252 (t0) cc_final: 0.6953 (t0) REVERT: F 103 ARG cc_start: 0.7695 (tmm-80) cc_final: 0.7432 (ttt-90) REVERT: F 107 VAL cc_start: 0.8440 (p) cc_final: 0.8098 (t) REVERT: F 144 ASP cc_start: 0.7525 (p0) cc_final: 0.6814 (p0) REVERT: f 85 ARG cc_start: 0.7348 (tpp80) cc_final: 0.6994 (tpp80) REVERT: f 178 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6818 (tp40) REVERT: f 204 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7177 (t70) REVERT: f 210 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7037 (ptp90) REVERT: G 396 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7694 (mp) REVERT: G 452 LYS cc_start: 0.7250 (mtpm) cc_final: 0.6907 (mtpm) REVERT: G 483 ARG cc_start: 0.6871 (ttp80) cc_final: 0.6503 (ttp80) REVERT: G 542 MET cc_start: 0.6742 (ttm) cc_final: 0.6391 (ttm) REVERT: G 605 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6154 (tp30) REVERT: I 501 ARG cc_start: 0.7565 (mtm180) cc_final: 0.7323 (ttm110) REVERT: I 510 MET cc_start: 0.7003 (mmm) cc_final: 0.6737 (tmm) REVERT: I 542 MET cc_start: 0.6903 (ttm) cc_final: 0.6573 (ttm) REVERT: I 568 ARG cc_start: 0.8289 (mmm160) cc_final: 0.8077 (mmm160) REVERT: I 606 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6019 (mt-10) outliers start: 113 outliers final: 83 residues processed: 656 average time/residue: 0.1676 time to fit residues: 164.7471 Evaluate side-chains 677 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 581 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 235 HIS Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 149 THR Chi-restraints excluded: chain f residue 178 GLN Chi-restraints excluded: chain f residue 204 ASP Chi-restraints excluded: chain f residue 210 ARG Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 605 GLU Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 554 THR Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 606 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 209 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 222 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN E 279 ASN F 186 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.163763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129501 restraints weight = 33862.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134010 restraints weight = 16877.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136990 restraints weight = 10220.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.138928 restraints weight = 7141.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.140258 restraints weight = 5532.247| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21164 Z= 0.148 Angle : 0.607 14.319 28758 Z= 0.308 Chirality : 0.043 0.299 3251 Planarity : 0.005 0.067 3756 Dihedral : 5.648 73.859 2986 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.55 % Allowed : 38.95 % Favored : 56.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.17), residues: 2592 helix: 0.56 (0.16), residues: 1058 sheet: -0.89 (0.29), residues: 329 loop : -0.89 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG f 184 TYR 0.029 0.001 TYR F 219 PHE 0.016 0.001 PHE F 259 TRP 0.024 0.002 TRP B 276 HIS 0.007 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (21164) covalent geometry : angle 0.60657 / 0.31 (28758) hydrogen bonds : bond 0.03612 / 2.47 ( 854) hydrogen bonds : angle 5.00582 / 3.58 ( 2448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4243.36 seconds wall clock time: 73 minutes 35.07 seconds (4415.07 seconds total)