Starting phenix.real_space_refine on Wed Feb 4 22:09:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uu3_64504/02_2026/9uu3_64504.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uu3_64504/02_2026/9uu3_64504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uu3_64504/02_2026/9uu3_64504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uu3_64504/02_2026/9uu3_64504.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uu3_64504/02_2026/9uu3_64504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uu3_64504/02_2026/9uu3_64504.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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 6 5.49 5 S 76 5.16 5 C 8272 2.51 5 N 2330 2.21 5 O 2400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13084 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3107 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "C" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3387 Classifications: {'peptide': 427} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 401} Chain: "D" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3107 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "B" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3387 Classifications: {'peptide': 427} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 401} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.27, per 1000 atoms: 0.25 Number of scatterers: 13084 At special positions: 0 Unit cell: (112.772, 134.208, 146.324, 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 76 16.00 P 6 15.00 O 2400 8.00 N 2330 7.00 C 8272 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: 1.07 Conformation dependent library (CDL) restraints added in 640.9 milliseconds 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 33.9% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 69 through 77 removed outlier: 3.602A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.509A pdb=" N CYS A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.803A pdb=" N SER A 146 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 189 removed outlier: 3.841A pdb=" N CYS A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 184 " --> pdb=" O CYS A 180 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 removed outlier: 4.018A pdb=" N LEU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 276 removed outlier: 3.605A pdb=" N VAL A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 3.580A pdb=" N LYS A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 411 through 424 removed outlier: 3.589A pdb=" N ALA A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 81 Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.669A pdb=" N ARG C 102 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.663A pdb=" N LEU C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE C 115 " --> pdb=" O HIS C 111 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 131 removed outlier: 3.627A pdb=" N ARG C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 164 removed outlier: 3.661A pdb=" N LEU C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 removed outlier: 4.043A pdb=" N ASP C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 197 through 207 removed outlier: 3.834A pdb=" N ILE C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 223 through 236 removed outlier: 3.663A pdb=" N ILE C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 288 removed outlier: 3.536A pdb=" N ALA C 287 " --> pdb=" O ARG C 284 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG C 288 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 343 removed outlier: 3.563A pdb=" N LYS C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER C 340 " --> pdb=" O ASP C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 351 through 363 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.969A pdb=" N LEU C 367 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 368 " --> pdb=" O GLY C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 368' Processing helix chain 'C' and resid 392 through 403 removed outlier: 3.627A pdb=" N GLU C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 420 Processing helix chain 'C' and resid 426 through 438 removed outlier: 3.606A pdb=" N TYR C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 484 removed outlier: 3.684A pdb=" N TYR C 484 " --> pdb=" O ILE C 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 removed outlier: 3.509A pdb=" N PHE D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.649A pdb=" N ASP D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 123 Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.526A pdb=" N CYS D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.574A pdb=" N SER D 146 " --> pdb=" O LEU D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 190 removed outlier: 3.938A pdb=" N CYS D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 264 through 276 Processing helix chain 'D' and resid 320 through 330 removed outlier: 4.229A pdb=" N LYS D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 424 removed outlier: 3.611A pdb=" N ALA D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.684A pdb=" N ARG B 102 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.815A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 115 " --> pdb=" O HIS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 131 removed outlier: 3.612A pdb=" N ARG B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 164 removed outlier: 3.613A pdb=" N GLU B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 176 removed outlier: 3.566A pdb=" N ASP B 169 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 197 through 207 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.797A pdb=" N ILE B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 265 through 271 removed outlier: 3.604A pdb=" N CYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.628A pdb=" N ILE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.763A pdb=" N THR B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 351 through 363 removed outlier: 3.902A pdb=" N LEU B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.739A pdb=" N LEU B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 368 " --> pdb=" O GLY B 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 368' Processing helix chain 'B' and resid 392 through 403 removed outlier: 3.891A pdb=" N ILE B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 420 Processing helix chain 'B' and resid 426 through 438 removed outlier: 3.761A pdb=" N TYR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 484 removed outlier: 3.875A pdb=" N ILE B 481 " --> pdb=" O ASP B 478 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N HIS B 482 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR B 484 " --> pdb=" O ILE B 481 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 4.707A pdb=" N HIS A 19 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU A 111 " --> pdb=" O HIS A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 20 removed outlier: 4.707A pdb=" N HIS A 19 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU A 111 " --> pdb=" O HIS A 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 155 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 154 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 378 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A 376 " --> pdb=" O TYR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 235 through 241 removed outlier: 6.985A pdb=" N THR A 355 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL A 392 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 357 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 213 through 218 removed outlier: 3.577A pdb=" N CYS C 189 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 184 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL C 247 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL C 186 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 276 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 277 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR C 92 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU C 279 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL C 87 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 292 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 462 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL C 297 " --> pdb=" O SER C 460 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER C 460 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 312 through 316 Processing sheet with id=AA7, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.353A pdb=" N ARG D 108 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE D 153 " --> pdb=" O ARG D 108 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL D 110 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASN D 155 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.353A pdb=" N ARG D 108 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE D 153 " --> pdb=" O ARG D 108 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL D 110 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASN D 155 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR D 376 " --> pdb=" O TYR D 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 34 through 36 Processing sheet with id=AB1, first strand: chain 'D' and resid 235 through 241 removed outlier: 3.658A pdb=" N VAL D 241 " --> pdb=" O ARG D 401 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR D 355 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL D 392 " --> pdb=" O THR D 355 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL D 357 " --> pdb=" O VAL D 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 284 through 289 Processing sheet with id=AB3, first strand: chain 'B' and resid 213 through 217 removed outlier: 6.461A pdb=" N ILE B 184 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL B 247 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B 186 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA B 277 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR B 92 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 279 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU B 294 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS B 464 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 312 through 316 removed outlier: 3.511A pdb=" N GLY B 323 " --> pdb=" O GLU B 315 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1212 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: 2.13 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2161 1.32 - 1.44: 3514 1.44 - 1.57: 7577 1.57 - 1.69: 10 1.69 - 1.81: 114 Bond restraints: 13376 Sorted by residual: bond pdb=" C LYS C 457 " pdb=" N CYS C 458 " ideal model delta sigma weight residual 1.331 1.403 -0.073 1.29e-02 6.01e+03 3.18e+01 bond pdb=" C ILE D 174 " pdb=" N PRO D 175 " ideal model delta sigma weight residual 1.334 1.252 0.082 1.51e-02 4.39e+03 2.98e+01 bond pdb=" O3B COA B 501 " pdb=" P3B COA B 501 " ideal model delta sigma weight residual 1.683 1.590 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" O3B COA C 501 " pdb=" P3B COA C 501 " ideal model delta sigma weight residual 1.683 1.613 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C ARG C 262 " pdb=" N ASP C 263 " ideal model delta sigma weight residual 1.332 1.379 -0.047 1.53e-02 4.27e+03 9.32e+00 ... (remaining 13371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 17730 2.45 - 4.91: 342 4.91 - 7.36: 69 7.36 - 9.82: 13 9.82 - 12.27: 4 Bond angle restraints: 18158 Sorted by residual: angle pdb=" C GLY B 455 " pdb=" N PHE B 456 " pdb=" CA PHE B 456 " ideal model delta sigma weight residual 122.46 129.26 -6.80 1.41e+00 5.03e-01 2.32e+01 angle pdb=" C GLY C 455 " pdb=" N PHE C 456 " pdb=" CA PHE C 456 " ideal model delta sigma weight residual 122.46 129.23 -6.77 1.41e+00 5.03e-01 2.31e+01 angle pdb=" N PHE D 78 " pdb=" CA PHE D 78 " pdb=" C PHE D 78 " ideal model delta sigma weight residual 109.81 119.13 -9.32 2.21e+00 2.05e-01 1.78e+01 angle pdb=" C3B COA C 501 " pdb=" O3B COA C 501 " pdb=" P3B COA C 501 " ideal model delta sigma weight residual 119.83 107.56 12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" C GLN A 208 " pdb=" N SER A 209 " pdb=" CA SER A 209 " ideal model delta sigma weight residual 121.80 131.67 -9.87 2.44e+00 1.68e-01 1.64e+01 ... (remaining 18153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 7299 17.76 - 35.52: 671 35.52 - 53.29: 121 53.29 - 71.05: 33 71.05 - 88.81: 6 Dihedral angle restraints: 8130 sinusoidal: 3306 harmonic: 4824 Sorted by residual: dihedral pdb=" CA PHE C 456 " pdb=" C PHE C 456 " pdb=" N LYS C 457 " pdb=" CA LYS C 457 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PHE B 456 " pdb=" C PHE B 456 " pdb=" N LYS B 457 " pdb=" CA LYS B 457 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA SER B 454 " pdb=" C SER B 454 " pdb=" N GLY B 455 " pdb=" CA GLY B 455 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 8127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1700 0.071 - 0.142: 275 0.142 - 0.213: 17 0.213 - 0.284: 12 0.284 - 0.355: 2 Chirality restraints: 2006 Sorted by residual: chirality pdb=" CAP COA C 501 " pdb=" C9P COA C 501 " pdb=" CBP COA C 501 " pdb=" OAP COA C 501 " both_signs ideal model delta sigma weight residual False -2.50 -2.15 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C2B COA C 501 " pdb=" C1B COA C 501 " pdb=" C3B COA C 501 " pdb=" O2B COA C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA PHE C 456 " pdb=" N PHE C 456 " pdb=" C PHE C 456 " pdb=" CB PHE C 456 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2003 not shown) Planarity restraints: 2354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P COA B 501 " -0.307 2.00e-02 2.50e+03 2.57e-01 8.26e+02 pdb=" C5P COA B 501 " 0.078 2.00e-02 2.50e+03 pdb=" C6P COA B 501 " -0.186 2.00e-02 2.50e+03 pdb=" N4P COA B 501 " 0.441 2.00e-02 2.50e+03 pdb=" O5P COA B 501 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P COA B 501 " -0.306 2.00e-02 2.50e+03 2.56e-01 8.22e+02 pdb=" C9P COA B 501 " 0.082 2.00e-02 2.50e+03 pdb=" CAP COA B 501 " -0.187 2.00e-02 2.50e+03 pdb=" N8P COA B 501 " 0.438 2.00e-02 2.50e+03 pdb=" O9P COA B 501 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P COA C 501 " 0.259 2.00e-02 2.50e+03 2.21e-01 6.11e+02 pdb=" C9P COA C 501 " -0.073 2.00e-02 2.50e+03 pdb=" CAP COA C 501 " -0.025 2.00e-02 2.50e+03 pdb=" N8P COA C 501 " -0.362 2.00e-02 2.50e+03 pdb=" O9P COA C 501 " 0.201 2.00e-02 2.50e+03 ... (remaining 2351 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3824 2.81 - 3.33: 11204 3.33 - 3.85: 21696 3.85 - 4.38: 25970 4.38 - 4.90: 44538 Nonbonded interactions: 107232 Sorted by model distance: nonbonded pdb=" O TYR B 95 " pdb=" OH TYR B 430 " model vdw 2.285 3.040 nonbonded pdb=" NE1 TRP D 167 " pdb=" O GLY D 172 " model vdw 2.302 3.120 nonbonded pdb=" O TYR C 95 " pdb=" OH TYR C 430 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR D 53 " pdb=" OH TYR D 379 " model vdw 2.310 3.040 nonbonded pdb=" O SER B 193 " pdb=" OG SER B 193 " model vdw 2.320 3.040 ... (remaining 107227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.590 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.006 0.093 13376 Z= 0.263 Angle : 0.877 12.272 18158 Z= 0.468 Chirality : 0.055 0.355 2006 Planarity : 0.011 0.257 2354 Dihedral : 14.418 88.810 5034 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.81 (0.16), residues: 1668 helix: -4.19 (0.11), residues: 514 sheet: -2.62 (0.23), residues: 366 loop : -2.64 (0.18), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 157 TYR 0.026 0.002 TYR A 379 PHE 0.039 0.002 PHE B 359 TRP 0.015 0.001 TRP D 167 HIS 0.005 0.001 HIS D 169 Details of bonding type rmsd covalent geometry : bond 0.00589 (13376) covalent geometry : angle 0.87723 (18158) hydrogen bonds : bond 0.24254 ( 437) hydrogen bonds : angle 9.49307 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 ASN cc_start: 0.8201 (m-40) cc_final: 0.7928 (m110) REVERT: A 233 ASP cc_start: 0.7956 (t0) cc_final: 0.7368 (t0) REVERT: A 234 MET cc_start: 0.6779 (mmt) cc_final: 0.5775 (mmt) REVERT: A 381 MET cc_start: 0.7402 (mmm) cc_final: 0.7063 (mmm) REVERT: A 407 LEU cc_start: 0.9118 (mt) cc_final: 0.8698 (mt) REVERT: C 213 ARG cc_start: 0.8177 (mpt90) cc_final: 0.7814 (mmt-90) REVERT: C 220 MET cc_start: 0.8958 (mtp) cc_final: 0.8684 (mtp) REVERT: C 293 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7579 (ttm110) REVERT: D 68 ASP cc_start: 0.8333 (m-30) cc_final: 0.8008 (m-30) REVERT: D 118 MET cc_start: 0.8407 (ttp) cc_final: 0.8009 (ttt) REVERT: D 330 LYS cc_start: 0.8667 (ptpt) cc_final: 0.8375 (ptpt) REVERT: B 83 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.7576 (ttp-170) REVERT: B 180 LYS cc_start: 0.8547 (pttp) cc_final: 0.8317 (mmtt) REVERT: B 319 GLN cc_start: 0.8336 (mp10) cc_final: 0.7891 (mp10) REVERT: B 469 ILE cc_start: 0.8394 (mm) cc_final: 0.8156 (mm) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.1702 time to fit residues: 46.4313 Evaluate side-chains 145 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN C 369 ASN D 19 HIS ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN B 144 ASN B 258 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.135971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096763 restraints weight = 19651.450| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.84 r_work: 0.3145 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13376 Z= 0.129 Angle : 0.608 9.277 18158 Z= 0.313 Chirality : 0.044 0.205 2006 Planarity : 0.006 0.058 2354 Dihedral : 9.089 82.504 1972 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.08 % Allowed : 9.54 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.17), residues: 1668 helix: -2.66 (0.18), residues: 522 sheet: -2.07 (0.25), residues: 344 loop : -2.22 (0.19), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 123 TYR 0.017 0.001 TYR D 53 PHE 0.027 0.001 PHE B 359 TRP 0.017 0.001 TRP D 167 HIS 0.003 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00290 (13376) covalent geometry : angle 0.60791 (18158) hydrogen bonds : bond 0.03982 ( 437) hydrogen bonds : angle 6.10893 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 ASN cc_start: 0.8046 (m-40) cc_final: 0.7790 (m110) REVERT: A 233 ASP cc_start: 0.8100 (t0) cc_final: 0.7378 (t0) REVERT: A 234 MET cc_start: 0.6065 (mmt) cc_final: 0.5166 (mmt) REVERT: A 407 LEU cc_start: 0.8452 (mt) cc_final: 0.8082 (mt) REVERT: C 220 MET cc_start: 0.8849 (mtp) cc_final: 0.8543 (mtp) REVERT: C 262 ARG cc_start: 0.8421 (mtm180) cc_final: 0.8184 (mtm180) REVERT: C 293 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7522 (ttm110) REVERT: D 68 ASP cc_start: 0.8528 (m-30) cc_final: 0.8211 (m-30) REVERT: D 330 LYS cc_start: 0.8758 (ptpt) cc_final: 0.8494 (ptpt) REVERT: B 83 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7289 (ttp-110) REVERT: B 180 LYS cc_start: 0.8549 (pttp) cc_final: 0.8106 (mmtt) REVERT: B 262 ARG cc_start: 0.7589 (mtm110) cc_final: 0.7125 (mtp-110) REVERT: B 361 ARG cc_start: 0.7000 (mmt-90) cc_final: 0.6613 (mmm160) REVERT: B 469 ILE cc_start: 0.8376 (mm) cc_final: 0.8147 (mm) outliers start: 15 outliers final: 6 residues processed: 173 average time/residue: 0.1517 time to fit residues: 36.1936 Evaluate side-chains 146 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain B residue 144 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 2 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN D 273 GLN D 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.091035 restraints weight = 20164.969| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.92 r_work: 0.3053 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 13376 Z= 0.296 Angle : 0.688 8.285 18158 Z= 0.353 Chirality : 0.048 0.285 2006 Planarity : 0.005 0.052 2354 Dihedral : 8.835 83.479 1972 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.24 % Allowed : 12.14 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.19), residues: 1668 helix: -1.98 (0.21), residues: 520 sheet: -1.82 (0.26), residues: 344 loop : -2.01 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 50 TYR 0.018 0.002 TYR D 150 PHE 0.036 0.002 PHE B 456 TRP 0.020 0.002 TRP D 167 HIS 0.004 0.001 HIS D 47 Details of bonding type rmsd covalent geometry : bond 0.00710 (13376) covalent geometry : angle 0.68766 (18158) hydrogen bonds : bond 0.04272 ( 437) hydrogen bonds : angle 5.82750 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8046 (t0) cc_final: 0.7373 (t0) REVERT: A 234 MET cc_start: 0.5675 (mmt) cc_final: 0.4731 (mmt) REVERT: A 407 LEU cc_start: 0.8411 (mt) cc_final: 0.8072 (mt) REVERT: C 178 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7946 (ttmm) REVERT: C 262 ARG cc_start: 0.8418 (mtm180) cc_final: 0.8197 (mtm180) REVERT: C 293 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7619 (ttm110) REVERT: D 250 HIS cc_start: 0.8549 (m90) cc_final: 0.8247 (m90) REVERT: D 330 LYS cc_start: 0.8762 (ptpt) cc_final: 0.8504 (ptpt) REVERT: D 359 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7212 (ptt) REVERT: B 83 ARG cc_start: 0.7601 (ttp-170) cc_final: 0.7318 (ttp-110) REVERT: B 180 LYS cc_start: 0.8493 (pttp) cc_final: 0.8027 (mmmt) REVERT: B 262 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7341 (mtp-110) REVERT: B 361 ARG cc_start: 0.7028 (mmt-90) cc_final: 0.6737 (mmm160) REVERT: B 404 GLN cc_start: 0.8090 (mp10) cc_final: 0.7511 (mp10) outliers start: 31 outliers final: 20 residues processed: 156 average time/residue: 0.1354 time to fit residues: 30.1736 Evaluate side-chains 148 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 473 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.094385 restraints weight = 19876.927| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.92 r_work: 0.3108 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13376 Z= 0.134 Angle : 0.576 7.201 18158 Z= 0.294 Chirality : 0.044 0.253 2006 Planarity : 0.004 0.046 2354 Dihedral : 8.256 80.826 1972 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.73 % Allowed : 14.16 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.19), residues: 1668 helix: -1.59 (0.21), residues: 528 sheet: -1.50 (0.27), residues: 320 loop : -1.84 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 50 TYR 0.014 0.001 TYR D 53 PHE 0.030 0.001 PHE C 456 TRP 0.013 0.001 TRP A 167 HIS 0.003 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00314 (13376) covalent geometry : angle 0.57557 (18158) hydrogen bonds : bond 0.03306 ( 437) hydrogen bonds : angle 5.37200 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.547 Fit side-chains REVERT: A 233 ASP cc_start: 0.7986 (t0) cc_final: 0.7343 (t0) REVERT: A 234 MET cc_start: 0.5534 (mmt) cc_final: 0.4584 (mmt) REVERT: A 289 ARG cc_start: 0.7085 (mmt180) cc_final: 0.6762 (tpt170) REVERT: C 178 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7913 (ttmm) REVERT: C 230 ASP cc_start: 0.7593 (t0) cc_final: 0.7215 (m-30) REVERT: C 293 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7545 (ttm110) REVERT: D 116 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7839 (ptm160) REVERT: D 250 HIS cc_start: 0.8579 (m90) cc_final: 0.8241 (m90) REVERT: D 330 LYS cc_start: 0.8760 (ptpt) cc_final: 0.8529 (ptpt) REVERT: D 359 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.6871 (ptt) REVERT: B 180 LYS cc_start: 0.8439 (pttp) cc_final: 0.7975 (mmtt) REVERT: B 262 ARG cc_start: 0.7685 (mtm110) cc_final: 0.7279 (mtp-110) REVERT: B 361 ARG cc_start: 0.6984 (mmt-90) cc_final: 0.6696 (tpt170) REVERT: B 404 GLN cc_start: 0.8100 (mp10) cc_final: 0.7496 (mp10) outliers start: 24 outliers final: 13 residues processed: 162 average time/residue: 0.1368 time to fit residues: 31.3612 Evaluate side-chains 152 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 473 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 67 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 135 optimal weight: 0.0770 chunk 113 optimal weight: 0.3980 chunk 70 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.095456 restraints weight = 19922.727| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.93 r_work: 0.3125 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13376 Z= 0.118 Angle : 0.563 8.450 18158 Z= 0.286 Chirality : 0.043 0.217 2006 Planarity : 0.004 0.048 2354 Dihedral : 7.921 81.813 1972 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.52 % Allowed : 14.67 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.19), residues: 1668 helix: -1.33 (0.22), residues: 530 sheet: -1.30 (0.27), residues: 320 loop : -1.71 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 373 TYR 0.014 0.001 TYR D 53 PHE 0.026 0.001 PHE C 456 TRP 0.011 0.001 TRP A 167 HIS 0.002 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00277 (13376) covalent geometry : angle 0.56338 (18158) hydrogen bonds : bond 0.03075 ( 437) hydrogen bonds : angle 5.16360 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.517 Fit side-chains REVERT: A 233 ASP cc_start: 0.7975 (t0) cc_final: 0.7326 (t0) REVERT: A 234 MET cc_start: 0.5499 (mmt) cc_final: 0.4510 (mmt) REVERT: C 153 MET cc_start: 0.7826 (ttm) cc_final: 0.7447 (ttp) REVERT: C 178 LYS cc_start: 0.8191 (ttmt) cc_final: 0.7910 (ttmm) REVERT: C 293 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7522 (ttm110) REVERT: C 319 GLN cc_start: 0.8151 (mp10) cc_final: 0.7605 (mp10) REVERT: D 116 ARG cc_start: 0.8257 (ttm-80) cc_final: 0.7729 (ttt180) REVERT: D 250 HIS cc_start: 0.8604 (m90) cc_final: 0.8317 (m90) REVERT: D 359 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6950 (ptt) REVERT: B 180 LYS cc_start: 0.8422 (pttp) cc_final: 0.7971 (mmtt) REVERT: B 262 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7277 (mtp-110) REVERT: B 361 ARG cc_start: 0.7174 (mmt-90) cc_final: 0.6873 (tpt170) REVERT: B 404 GLN cc_start: 0.8028 (mp10) cc_final: 0.7462 (mp10) outliers start: 21 outliers final: 14 residues processed: 164 average time/residue: 0.1288 time to fit residues: 30.5384 Evaluate side-chains 154 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 473 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 23 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 353 ASN D 372 GLN B 145 HIS B 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.133905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.093023 restraints weight = 19857.999| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.91 r_work: 0.3087 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13376 Z= 0.204 Angle : 0.603 8.957 18158 Z= 0.306 Chirality : 0.045 0.265 2006 Planarity : 0.004 0.045 2354 Dihedral : 7.928 81.359 1972 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.95 % Allowed : 15.61 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.20), residues: 1668 helix: -1.22 (0.22), residues: 528 sheet: -1.17 (0.27), residues: 320 loop : -1.64 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.014 0.001 TYR D 53 PHE 0.039 0.002 PHE C 456 TRP 0.014 0.001 TRP D 167 HIS 0.003 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00490 (13376) covalent geometry : angle 0.60253 (18158) hydrogen bonds : bond 0.03380 ( 437) hydrogen bonds : angle 5.16139 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.542 Fit side-chains REVERT: A 233 ASP cc_start: 0.7991 (t0) cc_final: 0.7349 (t0) REVERT: A 234 MET cc_start: 0.5561 (mmt) cc_final: 0.4613 (mmt) REVERT: A 289 ARG cc_start: 0.7105 (mmt180) cc_final: 0.6464 (mmm160) REVERT: C 178 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7945 (ttmm) REVERT: C 230 ASP cc_start: 0.7708 (t0) cc_final: 0.7324 (m-30) REVERT: C 293 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7544 (ttm110) REVERT: C 319 GLN cc_start: 0.8234 (mp10) cc_final: 0.7603 (mp10) REVERT: D 116 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7697 (ttt180) REVERT: D 222 MET cc_start: 0.7084 (mtm) cc_final: 0.6851 (mpp) REVERT: D 359 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.6885 (ptt) REVERT: B 180 LYS cc_start: 0.8430 (pttp) cc_final: 0.7970 (mmtt) REVERT: B 262 ARG cc_start: 0.7736 (mtm110) cc_final: 0.7327 (mtp-110) REVERT: B 329 GLU cc_start: 0.8586 (mm-30) cc_final: 0.7746 (pm20) REVERT: B 404 GLN cc_start: 0.8020 (mp10) cc_final: 0.7488 (mp10) outliers start: 27 outliers final: 19 residues processed: 155 average time/residue: 0.1282 time to fit residues: 28.6801 Evaluate side-chains 150 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 473 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 60 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN D 372 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.134160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.092935 restraints weight = 19827.308| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.93 r_work: 0.3086 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13376 Z= 0.190 Angle : 0.599 9.907 18158 Z= 0.303 Chirality : 0.045 0.257 2006 Planarity : 0.004 0.044 2354 Dihedral : 7.789 80.248 1972 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.88 % Allowed : 15.90 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.20), residues: 1668 helix: -1.10 (0.22), residues: 528 sheet: -1.10 (0.27), residues: 322 loop : -1.55 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.014 0.001 TYR D 53 PHE 0.036 0.002 PHE C 456 TRP 0.014 0.001 TRP D 167 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00458 (13376) covalent geometry : angle 0.59850 (18158) hydrogen bonds : bond 0.03298 ( 437) hydrogen bonds : angle 5.09650 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.637 Fit side-chains REVERT: A 233 ASP cc_start: 0.8012 (t0) cc_final: 0.7367 (t0) REVERT: A 234 MET cc_start: 0.5538 (mmt) cc_final: 0.4631 (mmt) REVERT: A 288 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8366 (m) REVERT: A 289 ARG cc_start: 0.7105 (mmt180) cc_final: 0.6475 (mmm160) REVERT: C 159 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: C 178 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7951 (ttmm) REVERT: C 204 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8091 (t0) REVERT: C 293 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7600 (ttm110) REVERT: C 319 GLN cc_start: 0.8270 (mp10) cc_final: 0.7576 (mp10) REVERT: D 116 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7702 (ttt180) REVERT: D 250 HIS cc_start: 0.8590 (m90) cc_final: 0.8348 (m90) REVERT: D 359 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6899 (ptt) REVERT: B 180 LYS cc_start: 0.8418 (pttp) cc_final: 0.7970 (mmtt) REVERT: B 262 ARG cc_start: 0.7771 (mtm110) cc_final: 0.7390 (mtp-110) REVERT: B 404 GLN cc_start: 0.8032 (mp10) cc_final: 0.7493 (mp10) REVERT: B 474 ASN cc_start: 0.7264 (p0) cc_final: 0.7022 (p0) outliers start: 26 outliers final: 19 residues processed: 157 average time/residue: 0.1280 time to fit residues: 29.0637 Evaluate side-chains 153 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 473 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 25 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 372 GLN B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.095694 restraints weight = 19881.852| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.65 r_work: 0.3110 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13376 Z= 0.163 Angle : 0.583 8.115 18158 Z= 0.295 Chirality : 0.044 0.238 2006 Planarity : 0.004 0.044 2354 Dihedral : 7.623 79.927 1972 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.02 % Allowed : 16.62 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.20), residues: 1668 helix: -0.99 (0.22), residues: 528 sheet: -1.01 (0.28), residues: 320 loop : -1.51 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 373 TYR 0.013 0.001 TYR D 53 PHE 0.033 0.001 PHE C 456 TRP 0.013 0.001 TRP D 167 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00392 (13376) covalent geometry : angle 0.58266 (18158) hydrogen bonds : bond 0.03154 ( 437) hydrogen bonds : angle 5.01067 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.568 Fit side-chains REVERT: A 118 MET cc_start: 0.7905 (ttp) cc_final: 0.7538 (ttp) REVERT: A 233 ASP cc_start: 0.8052 (t0) cc_final: 0.7414 (t0) REVERT: A 234 MET cc_start: 0.5823 (mmt) cc_final: 0.4840 (mmt) REVERT: A 289 ARG cc_start: 0.7330 (mmt180) cc_final: 0.6987 (tpt170) REVERT: C 159 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: C 178 LYS cc_start: 0.8391 (ttmt) cc_final: 0.8128 (ttmm) REVERT: C 230 ASP cc_start: 0.8073 (t0) cc_final: 0.7739 (m-30) REVERT: C 293 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7901 (ttm110) REVERT: C 319 GLN cc_start: 0.8394 (mp10) cc_final: 0.7702 (mp10) REVERT: D 116 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.7817 (ttt180) REVERT: D 359 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7123 (ptt) REVERT: B 180 LYS cc_start: 0.8513 (pttp) cc_final: 0.8108 (mmtt) REVERT: B 262 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7733 (mtp-110) REVERT: B 404 GLN cc_start: 0.8204 (mp10) cc_final: 0.7632 (mp10) outliers start: 28 outliers final: 20 residues processed: 158 average time/residue: 0.1336 time to fit residues: 30.3198 Evaluate side-chains 152 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 473 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 10 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 41 optimal weight: 0.0000 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 250 HIS D 372 GLN B 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.096995 restraints weight = 20039.999| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.68 r_work: 0.3133 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13376 Z= 0.129 Angle : 0.568 8.568 18158 Z= 0.287 Chirality : 0.043 0.206 2006 Planarity : 0.004 0.045 2354 Dihedral : 7.416 79.769 1972 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.81 % Allowed : 16.91 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.20), residues: 1668 helix: -0.89 (0.22), residues: 534 sheet: -0.97 (0.28), residues: 322 loop : -1.47 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.018 0.001 TYR B 257 PHE 0.027 0.001 PHE C 456 TRP 0.011 0.001 TRP D 167 HIS 0.005 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00308 (13376) covalent geometry : angle 0.56761 (18158) hydrogen bonds : bond 0.02943 ( 437) hydrogen bonds : angle 4.91060 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.523 Fit side-chains REVERT: A 233 ASP cc_start: 0.8043 (t0) cc_final: 0.7404 (t0) REVERT: A 234 MET cc_start: 0.5813 (mmt) cc_final: 0.4793 (mmt) REVERT: A 289 ARG cc_start: 0.7244 (mmt180) cc_final: 0.6952 (tpt170) REVERT: A 407 LEU cc_start: 0.8393 (mt) cc_final: 0.8028 (mt) REVERT: C 159 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: C 178 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8106 (ttmm) REVERT: C 204 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8255 (t0) REVERT: C 230 ASP cc_start: 0.8021 (t0) cc_final: 0.7677 (m-30) REVERT: C 293 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7845 (ttm110) REVERT: C 319 GLN cc_start: 0.8362 (mp10) cc_final: 0.7693 (mp10) REVERT: C 327 SER cc_start: 0.8446 (t) cc_final: 0.8228 (m) REVERT: D 116 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.7888 (ttt180) REVERT: D 359 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7228 (ptt) REVERT: B 180 LYS cc_start: 0.8519 (pttp) cc_final: 0.8145 (mmtt) REVERT: B 262 ARG cc_start: 0.8064 (mtm110) cc_final: 0.7730 (mtp-110) REVERT: B 329 GLU cc_start: 0.8711 (mm-30) cc_final: 0.7926 (pm20) REVERT: B 336 ASP cc_start: 0.8187 (m-30) cc_final: 0.7814 (m-30) REVERT: B 402 ASN cc_start: 0.7251 (m-40) cc_final: 0.7016 (m-40) REVERT: B 404 GLN cc_start: 0.8225 (mp10) cc_final: 0.7627 (mp10) outliers start: 25 outliers final: 20 residues processed: 163 average time/residue: 0.1342 time to fit residues: 31.1988 Evaluate side-chains 165 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 473 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 110 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 372 GLN B 145 HIS B 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.093322 restraints weight = 20373.248| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.69 r_work: 0.3075 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13376 Z= 0.254 Angle : 0.649 9.698 18158 Z= 0.329 Chirality : 0.047 0.270 2006 Planarity : 0.004 0.041 2354 Dihedral : 7.663 78.516 1972 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.10 % Allowed : 16.47 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.20), residues: 1668 helix: -1.04 (0.22), residues: 532 sheet: -0.97 (0.28), residues: 322 loop : -1.49 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.015 0.002 TYR D 53 PHE 0.043 0.002 PHE C 456 TRP 0.016 0.001 TRP D 167 HIS 0.004 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00613 (13376) covalent geometry : angle 0.64943 (18158) hydrogen bonds : bond 0.03568 ( 437) hydrogen bonds : angle 5.14493 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.483 Fit side-chains REVERT: A 233 ASP cc_start: 0.8109 (t0) cc_final: 0.7446 (t0) REVERT: A 234 MET cc_start: 0.5842 (mmt) cc_final: 0.4881 (mmt) REVERT: A 381 MET cc_start: 0.7168 (mmm) cc_final: 0.6762 (mmm) REVERT: C 159 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: C 178 LYS cc_start: 0.8389 (ttmt) cc_final: 0.8140 (ttmm) REVERT: C 204 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8244 (t0) REVERT: C 230 ASP cc_start: 0.8196 (t0) cc_final: 0.7876 (m-30) REVERT: C 293 ARG cc_start: 0.8355 (ttp80) cc_final: 0.7921 (ttm110) REVERT: C 319 GLN cc_start: 0.8465 (mp10) cc_final: 0.7731 (mp10) REVERT: D 116 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.7729 (ttt180) REVERT: D 222 MET cc_start: 0.7169 (mtm) cc_final: 0.6851 (mpp) REVERT: D 359 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7007 (ptt) REVERT: B 180 LYS cc_start: 0.8552 (pttp) cc_final: 0.8187 (mmtt) REVERT: B 262 ARG cc_start: 0.8111 (mtm110) cc_final: 0.7760 (mtp-110) REVERT: B 404 GLN cc_start: 0.8256 (mp10) cc_final: 0.7695 (mp10) outliers start: 29 outliers final: 24 residues processed: 153 average time/residue: 0.1269 time to fit residues: 28.0029 Evaluate side-chains 152 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.1980 chunk 82 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 chunk 149 optimal weight: 0.0370 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 372 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098701 restraints weight = 20001.410| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.68 r_work: 0.3155 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13376 Z= 0.107 Angle : 0.570 8.611 18158 Z= 0.286 Chirality : 0.043 0.169 2006 Planarity : 0.004 0.046 2354 Dihedral : 7.204 77.931 1972 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.30 % Allowed : 17.41 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.20), residues: 1668 helix: -0.70 (0.23), residues: 528 sheet: -0.81 (0.28), residues: 318 loop : -1.39 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 123 TYR 0.014 0.001 TYR B 257 PHE 0.019 0.001 PHE C 456 TRP 0.016 0.001 TRP B 463 HIS 0.005 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00250 (13376) covalent geometry : angle 0.56980 (18158) hydrogen bonds : bond 0.02818 ( 437) hydrogen bonds : angle 4.87181 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3742.32 seconds wall clock time: 64 minutes 55.27 seconds (3895.27 seconds total)