Starting phenix.real_space_refine on Sun Apr 5 22:38:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u7n_63940/04_2026/9u7n_63940.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u7n_63940/04_2026/9u7n_63940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u7n_63940/04_2026/9u7n_63940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u7n_63940/04_2026/9u7n_63940.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u7n_63940/04_2026/9u7n_63940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u7n_63940/04_2026/9u7n_63940.map" } resolution = 4.19 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= 0.000 sd= 0.024 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 4 5.49 5 S 60 5.16 5 C 8512 2.51 5 N 2340 2.21 5 O 2644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13560 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3381 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3381 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3381 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3381 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OBZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OBZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OBZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OBZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.40, per 1000 atoms: 0.25 Number of scatterers: 13560 At special positions: 0 Unit cell: (92.92, 148.12, 80.04, 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 60 16.00 P 4 15.00 O 2644 8.00 N 2340 7.00 C 8512 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: 1.14 Conformation dependent library (CDL) restraints added in 397.7 milliseconds 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 42.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 43 through 59 removed outlier: 4.216A pdb=" N ILE A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 4.282A pdb=" N ARG A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.613A pdb=" N ARG A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 139 Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.765A pdb=" N ALA A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.853A pdb=" N ILE A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 3.717A pdb=" N ARG A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 248 through 263 removed outlier: 4.254A pdb=" N ASP A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N MET A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 284 removed outlier: 4.118A pdb=" N ALA A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.677A pdb=" N TYR A 314 " --> pdb=" O TRP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 removed outlier: 3.685A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 388 through 396 removed outlier: 3.641A pdb=" N LEU A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.507A pdb=" N ALA A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'A' and resid 449 through 460 Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.687A pdb=" N VAL B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.692A pdb=" N TYR B 109 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.856A pdb=" N ALA B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 170 removed outlier: 3.867A pdb=" N ILE B 165 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 removed outlier: 3.553A pdb=" N ARG B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 248 through 263 removed outlier: 4.278A pdb=" N ASP B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 284 removed outlier: 4.061A pdb=" N ALA B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.642A pdb=" N TYR B 314 " --> pdb=" O TRP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.802A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 388 through 396 removed outlier: 3.630A pdb=" N LEU B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 449 through 460 Processing helix chain 'C' and resid 6 through 11 removed outlier: 3.539A pdb=" N ILE C 11 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.588A pdb=" N GLY C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 87 removed outlier: 4.143A pdb=" N ARG C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.992A pdb=" N ALA C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 170 removed outlier: 3.945A pdb=" N ILE C 165 " --> pdb=" O THR C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 211 through 215 Processing helix chain 'C' and resid 248 through 263 removed outlier: 3.978A pdb=" N ASP C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 284 removed outlier: 3.871A pdb=" N GLY C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 276 " --> pdb=" O MET C 272 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 283 " --> pdb=" O LYS C 279 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 284 " --> pdb=" O VAL C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.597A pdb=" N TYR C 314 " --> pdb=" O TRP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 removed outlier: 4.027A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 388 through 395 Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.846A pdb=" N HIS C 409 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 450 through 460 removed outlier: 3.543A pdb=" N GLY C 460 " --> pdb=" O PHE C 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 removed outlier: 3.526A pdb=" N ILE D 11 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.525A pdb=" N GLY D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 removed outlier: 4.454A pdb=" N ARG D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 127 through 139 Processing helix chain 'D' and resid 151 through 161 removed outlier: 4.058A pdb=" N ALA D 155 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 170 removed outlier: 3.922A pdb=" N ILE D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 196 Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 247 through 263 removed outlier: 3.912A pdb=" N ASP D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET D 254 " --> pdb=" O ASP D 250 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 284 removed outlier: 3.868A pdb=" N GLY D 271 " --> pdb=" O GLY D 267 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA D 276 " --> pdb=" O MET D 272 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.601A pdb=" N TYR D 314 " --> pdb=" O TRP D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 336 removed outlier: 3.919A pdb=" N VAL D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG D 335 " --> pdb=" O GLY D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 388 through 395 Processing helix chain 'D' and resid 405 through 409 removed outlier: 3.672A pdb=" N HIS D 409 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'D' and resid 450 through 460 removed outlier: 3.648A pdb=" N GLY D 460 " --> pdb=" O PHE D 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 removed outlier: 4.716A pdb=" N VAL A 30 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 294 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS A 175 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N LEU A 293 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 3.711A pdb=" N TRP A 143 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.567A pdb=" N ALA A 178 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLY A 205 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 246 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP A 207 " --> pdb=" O VAL A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.661A pdb=" N MET A 368 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 386 " --> pdb=" O MET A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 416 through 417 removed outlier: 3.503A pdb=" N VAL A 439 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 436 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL A 447 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL A 438 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.738A pdb=" N VAL B 30 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 294 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N HIS B 175 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N LEU B 293 " --> pdb=" O HIS B 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 113 removed outlier: 6.204A pdb=" N ILE B 67 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP B 143 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.488A pdb=" N ALA B 178 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY B 205 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 246 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP B 207 " --> pdb=" O VAL B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 367 through 370 removed outlier: 3.710A pdb=" N MET B 368 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 386 " --> pdb=" O MET B 368 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 416 through 417 removed outlier: 3.751A pdb=" N GLY B 446 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLU B 440 " --> pdb=" O PRO B 444 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 18 removed outlier: 3.737A pdb=" N LEU C 294 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N HIS C 175 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LEU C 293 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL C 177 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE C 203 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE C 244 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY C 205 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL C 246 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP C 207 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 113 removed outlier: 7.133A pdb=" N CYS C 90 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 69 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP C 143 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 367 through 370 removed outlier: 3.740A pdb=" N MET C 368 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 386 " --> pdb=" O MET C 368 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 416 through 417 removed outlier: 3.844A pdb=" N VAL C 439 " --> pdb=" O ILE C 417 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 436 " --> pdb=" O VAL C 447 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL C 447 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL C 438 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 17 through 18 removed outlier: 3.778A pdb=" N LEU D 294 " --> pdb=" O LYS D 33 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N HIS D 175 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU D 293 " --> pdb=" O HIS D 175 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL D 177 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 203 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE D 244 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY D 205 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL D 246 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP D 207 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 113 removed outlier: 7.156A pdb=" N CYS D 90 " --> pdb=" O GLU D 112 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 69 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP D 143 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 367 through 370 removed outlier: 3.832A pdb=" N MET D 368 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 386 " --> pdb=" O MET D 368 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 416 through 417 removed outlier: 3.950A pdb=" N VAL D 439 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU D 436 " --> pdb=" O VAL D 447 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL D 447 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL D 438 " --> pdb=" O VAL D 445 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1359 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: 2.00 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4596 1.34 - 1.46: 2625 1.46 - 1.58: 6507 1.58 - 1.69: 4 1.69 - 1.81: 104 Bond restraints: 13836 Sorted by residual: bond pdb=" OP4 LLP C 44 " pdb=" P LLP C 44 " ideal model delta sigma weight residual 1.726 1.599 0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" OP4 LLP A 44 " pdb=" P LLP A 44 " ideal model delta sigma weight residual 1.726 1.608 0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" OP4 LLP D 44 " pdb=" P LLP D 44 " ideal model delta sigma weight residual 1.726 1.611 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" OP4 LLP B 44 " pdb=" P LLP B 44 " ideal model delta sigma weight residual 1.726 1.614 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C5' LLP B 44 " pdb=" OP4 LLP B 44 " ideal model delta sigma weight residual 1.396 1.462 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 13831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.74: 18812 5.74 - 11.47: 2 11.47 - 17.21: 1 17.21 - 22.95: 0 22.95 - 28.68: 1 Bond angle restraints: 18816 Sorted by residual: angle pdb=" CE LLP B 44 " pdb=" NZ LLP B 44 " pdb=" C4' LLP B 44 " ideal model delta sigma weight residual 119.26 90.58 28.68 3.00e+00 1.11e-01 9.14e+01 angle pdb=" NZ LLP B 44 " pdb=" C4' LLP B 44 " pdb=" C4 LLP B 44 " ideal model delta sigma weight residual 120.09 102.98 17.11 3.00e+00 1.11e-01 3.25e+01 angle pdb=" C5' LLP D 44 " pdb=" OP4 LLP D 44 " pdb=" P LLP D 44 " ideal model delta sigma weight residual 117.41 128.82 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" OP2 LLP D 44 " pdb=" P LLP D 44 " pdb=" OP4 LLP D 44 " ideal model delta sigma weight residual 104.33 114.60 -10.27 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N ASP D 287 " pdb=" CA ASP D 287 " pdb=" CB ASP D 287 " ideal model delta sigma weight residual 114.17 110.39 3.78 1.14e+00 7.69e-01 1.10e+01 ... (remaining 18811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.78: 8109 32.78 - 65.56: 110 65.56 - 98.34: 6 98.34 - 131.12: 1 131.12 - 163.91: 2 Dihedral angle restraints: 8228 sinusoidal: 3132 harmonic: 5096 Sorted by residual: dihedral pdb=" CD LLP C 44 " pdb=" CE LLP C 44 " pdb=" NZ LLP C 44 " pdb=" C4' LLP C 44 " ideal model delta sinusoidal sigma weight residual -110.28 53.63 -163.91 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C4 OBZ A 501 " pdb=" C3 OBZ A 501 " pdb=" O2 OBZ A 501 " pdb=" N1 OBZ A 501 " ideal model delta sinusoidal sigma weight residual -179.07 -34.27 -144.80 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C4 OBZ B 501 " pdb=" C3 OBZ B 501 " pdb=" O2 OBZ B 501 " pdb=" N1 OBZ B 501 " ideal model delta sinusoidal sigma weight residual -179.07 -79.35 -99.72 1 3.00e+01 1.11e-03 1.25e+01 ... (remaining 8225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1163 0.025 - 0.050: 518 0.050 - 0.075: 206 0.075 - 0.100: 153 0.100 - 0.125: 64 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CA VAL D 93 " pdb=" N VAL D 93 " pdb=" C VAL D 93 " pdb=" CB VAL D 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA VAL C 93 " pdb=" N VAL C 93 " pdb=" C VAL C 93 " pdb=" CB VAL C 93 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA LLP D 44 " pdb=" N LLP D 44 " pdb=" C LLP D 44 " pdb=" CB LLP D 44 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 2101 not shown) Planarity restraints: 2480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP C 44 " 0.082 2.00e-02 2.50e+03 2.46e-01 6.04e+02 pdb=" NZ LLP C 44 " -0.308 2.00e-02 2.50e+03 pdb=" C4 LLP C 44 " -0.126 2.00e-02 2.50e+03 pdb=" C4' LLP C 44 " 0.352 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 44 " -0.146 2.00e-02 2.50e+03 2.06e-01 4.25e+02 pdb=" NZ LLP B 44 " 0.241 2.00e-02 2.50e+03 pdb=" C4 LLP B 44 " 0.160 2.00e-02 2.50e+03 pdb=" C4' LLP B 44 " -0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP D 44 " -0.093 2.00e-02 2.50e+03 1.95e-01 3.81e+02 pdb=" NZ LLP D 44 " 0.254 2.00e-02 2.50e+03 pdb=" C4 LLP D 44 " 0.102 2.00e-02 2.50e+03 pdb=" C4' LLP D 44 " -0.263 2.00e-02 2.50e+03 ... (remaining 2477 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 134 2.51 - 3.11: 11618 3.11 - 3.71: 20342 3.71 - 4.30: 27963 4.30 - 4.90: 44301 Nonbonded interactions: 104358 Sorted by model distance: nonbonded pdb=" CE LLP B 44 " pdb=" C4 LLP B 44 " model vdw 1.913 2.928 nonbonded pdb=" O VAL C 98 " pdb=" NH1 ARG C 103 " model vdw 2.068 3.120 nonbonded pdb=" N ASN C 20 " pdb=" OE2 GLU C 262 " model vdw 2.080 3.120 nonbonded pdb=" N ASN D 20 " pdb=" OE2 GLU D 262 " model vdw 2.088 3.120 nonbonded pdb=" O GLN B 147 " pdb=" OG1 THR B 182 " model vdw 2.100 3.040 ... (remaining 104353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.820 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 13836 Z= 0.172 Angle : 0.583 28.684 18816 Z= 0.285 Chirality : 0.041 0.125 2104 Planarity : 0.009 0.246 2480 Dihedral : 11.763 163.905 5020 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 40.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.89 % Favored : 92.05 % Rotamer: Outliers : 3.50 % Allowed : 9.79 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.20), residues: 1812 helix: 0.15 (0.20), residues: 648 sheet: -2.30 (0.30), residues: 256 loop : -1.66 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 134 TYR 0.013 0.001 TYR A 129 PHE 0.012 0.001 PHE A 316 TRP 0.009 0.001 TRP C 231 HIS 0.002 0.000 HIS D 348 Details of bonding type rmsd covalent geometry : bond 0.00332 (13836) covalent geometry : angle 0.58314 (18816) hydrogen bonds : bond 0.17643 ( 490) hydrogen bonds : angle 7.36109 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 410 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 THR cc_start: 0.8974 (p) cc_final: 0.8682 (t) REVERT: A 69 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: A 180 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7780 (mm) REVERT: A 264 MET cc_start: 0.8411 (mtm) cc_final: 0.8027 (mtp) REVERT: A 332 ASP cc_start: 0.5831 (OUTLIER) cc_final: 0.5270 (p0) REVERT: A 348 HIS cc_start: 0.7572 (m-70) cc_final: 0.6274 (m-70) REVERT: A 367 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8453 (mm-40) REVERT: B 20 ASN cc_start: 0.7587 (m-40) cc_final: 0.6963 (p0) REVERT: B 62 LYS cc_start: 0.8265 (mttt) cc_final: 0.7895 (ttpp) REVERT: B 152 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8405 (mp0) REVERT: B 254 MET cc_start: 0.5569 (tpp) cc_final: 0.5366 (tpp) REVERT: B 264 MET cc_start: 0.7912 (mtm) cc_final: 0.7357 (mtp) REVERT: B 282 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7470 (mm-30) REVERT: B 302 MET cc_start: 0.6696 (mmm) cc_final: 0.6299 (tpp) REVERT: B 311 MET cc_start: 0.6913 (ttm) cc_final: 0.6693 (ttm) REVERT: B 368 MET cc_start: 0.8357 (ptm) cc_final: 0.7462 (ptm) REVERT: C 50 LYS cc_start: 0.9165 (tptt) cc_final: 0.8961 (tptp) REVERT: C 185 THR cc_start: 0.7972 (m) cc_final: 0.7760 (m) REVERT: C 202 ARG cc_start: 0.6956 (mtp180) cc_final: 0.6636 (mtp85) REVERT: C 230 PHE cc_start: 0.7819 (p90) cc_final: 0.7167 (t80) REVERT: C 242 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5869 (tt0) REVERT: C 307 ASN cc_start: 0.8774 (t0) cc_final: 0.8454 (t0) REVERT: C 381 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7341 (mp0) REVERT: C 445 VAL cc_start: 0.8077 (p) cc_final: 0.7872 (m) REVERT: D 202 ARG cc_start: 0.5737 (mtp180) cc_final: 0.5362 (mtt-85) REVERT: D 242 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6013 (pt0) REVERT: D 265 LEU cc_start: 0.9285 (tp) cc_final: 0.8818 (tp) REVERT: D 266 VAL cc_start: 0.9039 (m) cc_final: 0.8742 (p) REVERT: D 302 MET cc_start: 0.8760 (mmm) cc_final: 0.8095 (mmm) REVERT: D 307 ASN cc_start: 0.8709 (t0) cc_final: 0.8347 (t0) REVERT: D 368 MET cc_start: 0.8755 (ptm) cc_final: 0.8414 (ptp) REVERT: D 378 MET cc_start: 0.5935 (tpt) cc_final: 0.5021 (tpt) REVERT: D 397 GLU cc_start: 0.8566 (mt-10) cc_final: 0.7794 (tm-30) outliers start: 49 outliers final: 16 residues processed: 446 average time/residue: 0.1280 time to fit residues: 80.1124 Evaluate side-chains 284 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.0270 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 104 ASN ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 348 HIS B 367 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 GLN D 6 HIS D 147 GLN D 348 HIS D 367 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.167211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.142110 restraints weight = 27360.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145902 restraints weight = 17534.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.148632 restraints weight = 12429.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.150545 restraints weight = 9565.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.151971 restraints weight = 7857.698| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13836 Z= 0.160 Angle : 0.713 11.008 18816 Z= 0.358 Chirality : 0.048 0.192 2104 Planarity : 0.005 0.048 2480 Dihedral : 8.665 125.254 2028 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.90 % Favored : 92.88 % Rotamer: Outliers : 0.21 % Allowed : 6.50 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.20), residues: 1812 helix: 0.13 (0.20), residues: 652 sheet: -1.48 (0.29), residues: 308 loop : -1.65 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 335 TYR 0.022 0.002 TYR B 451 PHE 0.027 0.003 PHE B 316 TRP 0.011 0.002 TRP D 433 HIS 0.008 0.002 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00353 (13836) covalent geometry : angle 0.71321 (18816) hydrogen bonds : bond 0.04940 ( 490) hydrogen bonds : angle 6.01193 ( 1359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 343 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8472 (mtp) cc_final: 0.8244 (mtp) REVERT: A 213 TYR cc_start: 0.7445 (m-80) cc_final: 0.6990 (m-80) REVERT: A 264 MET cc_start: 0.8313 (mtm) cc_final: 0.7806 (mtp) REVERT: A 355 ASP cc_start: 0.6962 (t70) cc_final: 0.6677 (t70) REVERT: B 20 ASN cc_start: 0.7577 (m-40) cc_final: 0.6932 (p0) REVERT: B 106 LEU cc_start: 0.8495 (mt) cc_final: 0.8032 (mt) REVERT: B 144 LYS cc_start: 0.8365 (pptt) cc_final: 0.7954 (pptt) REVERT: B 264 MET cc_start: 0.7295 (mtm) cc_final: 0.6735 (mtp) REVERT: B 302 MET cc_start: 0.6485 (mmm) cc_final: 0.6188 (tpp) REVERT: B 344 LEU cc_start: 0.7176 (tp) cc_final: 0.6921 (tp) REVERT: B 346 HIS cc_start: 0.6308 (p-80) cc_final: 0.6020 (p-80) REVERT: B 374 GLU cc_start: 0.6277 (tp30) cc_final: 0.5371 (mp0) REVERT: C 51 MET cc_start: 0.8701 (mtp) cc_final: 0.8463 (mtp) REVERT: C 67 ILE cc_start: 0.9143 (mt) cc_final: 0.8867 (pt) REVERT: C 71 THR cc_start: 0.8317 (t) cc_final: 0.7402 (t) REVERT: C 84 GLN cc_start: 0.6759 (tt0) cc_final: 0.6513 (tt0) REVERT: C 230 PHE cc_start: 0.7378 (p90) cc_final: 0.6796 (t80) REVERT: C 262 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7633 (mm-30) REVERT: C 296 ASP cc_start: 0.7792 (t0) cc_final: 0.7548 (t70) REVERT: C 307 ASN cc_start: 0.8835 (t0) cc_final: 0.8575 (t0) REVERT: C 370 VAL cc_start: 0.8672 (m) cc_final: 0.8396 (m) REVERT: C 392 LEU cc_start: 0.8702 (mm) cc_final: 0.8207 (mm) REVERT: C 416 MET cc_start: 0.7462 (ttp) cc_final: 0.7102 (ttp) REVERT: D 47 ILE cc_start: 0.7366 (mt) cc_final: 0.7067 (mt) REVERT: D 51 MET cc_start: 0.7882 (ttm) cc_final: 0.7665 (ttm) REVERT: D 94 CYS cc_start: 0.8326 (m) cc_final: 0.7587 (m) REVERT: D 212 VAL cc_start: 0.8819 (t) cc_final: 0.8555 (t) REVERT: D 254 MET cc_start: 0.6496 (tpt) cc_final: 0.6187 (tpt) REVERT: D 265 LEU cc_start: 0.9116 (tp) cc_final: 0.8682 (tp) REVERT: D 266 VAL cc_start: 0.8935 (m) cc_final: 0.8681 (p) REVERT: D 302 MET cc_start: 0.8696 (mmm) cc_final: 0.7995 (mmm) REVERT: D 307 ASN cc_start: 0.8927 (t0) cc_final: 0.8654 (t0) REVERT: D 368 MET cc_start: 0.8566 (ptm) cc_final: 0.7952 (ptp) REVERT: D 378 MET cc_start: 0.5513 (tpt) cc_final: 0.4890 (tpt) REVERT: D 397 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7572 (tm-30) outliers start: 3 outliers final: 1 residues processed: 345 average time/residue: 0.1072 time to fit residues: 54.6813 Evaluate side-chains 262 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 17 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 157 HIS ** C 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 GLN D 147 GLN D 367 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.158032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133505 restraints weight = 28964.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.136973 restraints weight = 19006.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.139490 restraints weight = 13774.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.141305 restraints weight = 10774.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.142625 restraints weight = 8939.646| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13836 Z= 0.275 Angle : 0.815 9.589 18816 Z= 0.419 Chirality : 0.052 0.194 2104 Planarity : 0.006 0.073 2480 Dihedral : 9.027 129.138 2028 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.65 % Favored : 89.24 % Rotamer: Outliers : 0.43 % Allowed : 6.64 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.19), residues: 1812 helix: -0.32 (0.20), residues: 648 sheet: -1.26 (0.32), residues: 268 loop : -1.98 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 450 TYR 0.033 0.002 TYR B 221 PHE 0.026 0.003 PHE A 316 TRP 0.026 0.002 TRP B 310 HIS 0.009 0.002 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00625 (13836) covalent geometry : angle 0.81548 (18816) hydrogen bonds : bond 0.05181 ( 490) hydrogen bonds : angle 6.28819 ( 1359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 286 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8421 (pm20) cc_final: 0.8065 (pm20) REVERT: A 213 TYR cc_start: 0.7587 (m-80) cc_final: 0.7013 (m-80) REVERT: A 264 MET cc_start: 0.8234 (mtm) cc_final: 0.7674 (mtp) REVERT: A 355 ASP cc_start: 0.7231 (t70) cc_final: 0.6881 (t70) REVERT: B 20 ASN cc_start: 0.7796 (m-40) cc_final: 0.7141 (p0) REVERT: B 144 LYS cc_start: 0.8311 (pptt) cc_final: 0.7755 (pptt) REVERT: C 50 LYS cc_start: 0.9029 (tppt) cc_final: 0.8794 (mmmt) REVERT: C 185 THR cc_start: 0.8233 (m) cc_final: 0.7970 (m) REVERT: C 230 PHE cc_start: 0.7371 (p90) cc_final: 0.6644 (t80) REVERT: C 296 ASP cc_start: 0.8238 (t0) cc_final: 0.7948 (t0) REVERT: C 311 MET cc_start: 0.7034 (tpp) cc_final: 0.6819 (tpp) REVERT: C 410 MET cc_start: 0.7585 (ptt) cc_final: 0.7197 (ptt) REVERT: D 20 ASN cc_start: 0.7536 (m-40) cc_final: 0.7153 (m-40) REVERT: D 47 ILE cc_start: 0.7744 (mt) cc_final: 0.7388 (mt) REVERT: D 265 LEU cc_start: 0.9259 (tp) cc_final: 0.8772 (tp) REVERT: D 266 VAL cc_start: 0.9004 (m) cc_final: 0.8718 (p) REVERT: D 272 MET cc_start: 0.8561 (tpp) cc_final: 0.8156 (tpp) REVERT: D 302 MET cc_start: 0.8727 (mmm) cc_final: 0.8160 (mmm) REVERT: D 368 MET cc_start: 0.8651 (ptm) cc_final: 0.8269 (ptp) REVERT: D 378 MET cc_start: 0.5846 (tpt) cc_final: 0.5037 (tpt) REVERT: D 397 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7554 (tm-30) outliers start: 6 outliers final: 3 residues processed: 291 average time/residue: 0.1014 time to fit residues: 44.2807 Evaluate side-chains 221 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 218 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 133 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS C 104 ASN D 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.163498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.139626 restraints weight = 28300.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.143297 restraints weight = 18241.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.146033 restraints weight = 12988.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.147978 restraints weight = 9959.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.149406 restraints weight = 8124.215| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13836 Z= 0.146 Angle : 0.689 9.106 18816 Z= 0.349 Chirality : 0.047 0.196 2104 Planarity : 0.005 0.065 2480 Dihedral : 8.711 121.625 2028 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.34 % Favored : 92.60 % Rotamer: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.19), residues: 1812 helix: 0.08 (0.20), residues: 648 sheet: -1.28 (0.30), residues: 304 loop : -1.80 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.017 0.001 TYR D 451 PHE 0.028 0.002 PHE B 316 TRP 0.015 0.002 TRP D 231 HIS 0.009 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00329 (13836) covalent geometry : angle 0.68862 (18816) hydrogen bonds : bond 0.04314 ( 490) hydrogen bonds : angle 5.67859 ( 1359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 TYR cc_start: 0.7515 (m-80) cc_final: 0.7032 (m-80) REVERT: A 264 MET cc_start: 0.8376 (mtm) cc_final: 0.7965 (mtp) REVERT: A 355 ASP cc_start: 0.7105 (t70) cc_final: 0.6714 (t70) REVERT: B 20 ASN cc_start: 0.7775 (m-40) cc_final: 0.7224 (p0) REVERT: B 134 ARG cc_start: 0.7350 (mmp-170) cc_final: 0.5916 (ptt180) REVERT: B 144 LYS cc_start: 0.8270 (pptt) cc_final: 0.7624 (pptt) REVERT: B 368 MET cc_start: 0.8039 (ptm) cc_final: 0.7453 (ptm) REVERT: B 374 GLU cc_start: 0.6031 (tp30) cc_final: 0.5283 (tp30) REVERT: B 378 MET cc_start: 0.1762 (mmm) cc_final: 0.0991 (mmm) REVERT: C 50 LYS cc_start: 0.9017 (tppt) cc_final: 0.8742 (mmmt) REVERT: C 230 PHE cc_start: 0.7341 (p90) cc_final: 0.6688 (t80) REVERT: C 246 VAL cc_start: 0.7617 (t) cc_final: 0.7385 (t) REVERT: C 296 ASP cc_start: 0.8083 (t0) cc_final: 0.7820 (t0) REVERT: C 307 ASN cc_start: 0.8719 (t0) cc_final: 0.8452 (t0) REVERT: C 352 THR cc_start: 0.8535 (p) cc_final: 0.8118 (p) REVERT: C 368 MET cc_start: 0.8728 (ptm) cc_final: 0.8339 (ptm) REVERT: C 370 VAL cc_start: 0.8328 (m) cc_final: 0.8085 (m) REVERT: C 392 LEU cc_start: 0.8755 (mm) cc_final: 0.8236 (mm) REVERT: C 410 MET cc_start: 0.7491 (ptt) cc_final: 0.6999 (ptt) REVERT: D 17 VAL cc_start: 0.8825 (m) cc_final: 0.8573 (p) REVERT: D 266 VAL cc_start: 0.8928 (m) cc_final: 0.8615 (p) REVERT: D 272 MET cc_start: 0.8414 (tpp) cc_final: 0.8002 (tpp) REVERT: D 302 MET cc_start: 0.8725 (mmm) cc_final: 0.8120 (mmm) REVERT: D 368 MET cc_start: 0.8637 (ptm) cc_final: 0.8194 (ptp) REVERT: D 370 VAL cc_start: 0.8412 (m) cc_final: 0.8203 (m) REVERT: D 378 MET cc_start: 0.5583 (tpt) cc_final: 0.4994 (tpt) REVERT: D 397 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7536 (tm-30) outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.1082 time to fit residues: 48.2533 Evaluate side-chains 232 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 123 optimal weight: 0.1980 chunk 135 optimal weight: 0.0980 chunk 74 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 164 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN B 5 GLN B 6 HIS B 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.167539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.142511 restraints weight = 28000.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146374 restraints weight = 18060.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.149179 restraints weight = 12883.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.151208 restraints weight = 9912.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.152669 restraints weight = 8103.344| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13836 Z= 0.126 Angle : 0.654 9.190 18816 Z= 0.328 Chirality : 0.046 0.183 2104 Planarity : 0.005 0.067 2480 Dihedral : 8.538 115.000 2028 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.34 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.20), residues: 1812 helix: 0.31 (0.20), residues: 648 sheet: -0.49 (0.34), residues: 248 loop : -1.80 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 299 TYR 0.021 0.001 TYR A 221 PHE 0.028 0.002 PHE C 316 TRP 0.028 0.002 TRP D 231 HIS 0.009 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00273 (13836) covalent geometry : angle 0.65399 (18816) hydrogen bonds : bond 0.03756 ( 490) hydrogen bonds : angle 5.35146 ( 1359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 TYR cc_start: 0.7295 (m-80) cc_final: 0.6904 (m-80) REVERT: A 264 MET cc_start: 0.8241 (mtm) cc_final: 0.7938 (mtp) REVERT: A 318 ARG cc_start: 0.8325 (mtt180) cc_final: 0.8092 (mtt180) REVERT: B 20 ASN cc_start: 0.7647 (m-40) cc_final: 0.7208 (p0) REVERT: B 104 ASN cc_start: 0.7508 (m-40) cc_final: 0.6815 (p0) REVERT: B 134 ARG cc_start: 0.7354 (mmp-170) cc_final: 0.5844 (ptt180) REVERT: B 144 LYS cc_start: 0.8205 (pptt) cc_final: 0.7659 (pptt) REVERT: B 360 LEU cc_start: 0.7964 (mt) cc_final: 0.7636 (mt) REVERT: B 368 MET cc_start: 0.7845 (ptm) cc_final: 0.7129 (ttt) REVERT: C 51 MET cc_start: 0.8891 (mtp) cc_final: 0.8447 (mtp) REVERT: C 230 PHE cc_start: 0.7381 (p90) cc_final: 0.6695 (t80) REVERT: C 265 LEU cc_start: 0.7561 (tp) cc_final: 0.7204 (tp) REVERT: C 272 MET cc_start: 0.7782 (tpp) cc_final: 0.7543 (tpp) REVERT: C 307 ASN cc_start: 0.8710 (t0) cc_final: 0.8357 (t0) REVERT: C 368 MET cc_start: 0.8564 (ptm) cc_final: 0.8306 (ptm) REVERT: C 370 VAL cc_start: 0.8404 (m) cc_final: 0.8157 (m) REVERT: C 392 LEU cc_start: 0.8755 (mm) cc_final: 0.8235 (mm) REVERT: C 410 MET cc_start: 0.7500 (ptt) cc_final: 0.6951 (ptt) REVERT: C 430 LEU cc_start: 0.9178 (tp) cc_final: 0.8876 (tp) REVERT: D 17 VAL cc_start: 0.8826 (m) cc_final: 0.8608 (p) REVERT: D 94 CYS cc_start: 0.8884 (m) cc_final: 0.8523 (m) REVERT: D 266 VAL cc_start: 0.8886 (m) cc_final: 0.8594 (p) REVERT: D 368 MET cc_start: 0.8625 (ptm) cc_final: 0.8323 (ptp) REVERT: D 378 MET cc_start: 0.6241 (tpp) cc_final: 0.5908 (tpp) REVERT: D 397 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7563 (tm-30) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1058 time to fit residues: 48.2078 Evaluate side-chains 226 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 164 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 169 optimal weight: 0.5980 chunk 89 optimal weight: 0.0670 chunk 144 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN D 348 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.167111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142161 restraints weight = 27577.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.145974 restraints weight = 17811.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.148731 restraints weight = 12712.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.150737 restraints weight = 9798.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.152170 restraints weight = 8022.851| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13836 Z= 0.125 Angle : 0.665 9.626 18816 Z= 0.333 Chirality : 0.046 0.169 2104 Planarity : 0.006 0.065 2480 Dihedral : 8.414 110.321 2028 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.84 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.20), residues: 1812 helix: 0.36 (0.21), residues: 648 sheet: -0.82 (0.31), residues: 296 loop : -1.75 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 450 TYR 0.015 0.001 TYR D 451 PHE 0.027 0.002 PHE C 316 TRP 0.012 0.001 TRP D 231 HIS 0.008 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00282 (13836) covalent geometry : angle 0.66453 (18816) hydrogen bonds : bond 0.03683 ( 490) hydrogen bonds : angle 5.29712 ( 1359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.9276 (p0) cc_final: 0.9021 (p0) REVERT: A 264 MET cc_start: 0.8229 (mtm) cc_final: 0.7932 (mtp) REVERT: A 355 ASP cc_start: 0.6966 (t70) cc_final: 0.6605 (t70) REVERT: B 20 ASN cc_start: 0.7614 (m-40) cc_final: 0.7260 (p0) REVERT: B 134 ARG cc_start: 0.7378 (mmp-170) cc_final: 0.5866 (ptt180) REVERT: B 144 LYS cc_start: 0.8265 (pptt) cc_final: 0.7685 (pptt) REVERT: B 360 LEU cc_start: 0.7980 (mt) cc_final: 0.7726 (mt) REVERT: B 368 MET cc_start: 0.7920 (ptm) cc_final: 0.7011 (ttt) REVERT: B 378 MET cc_start: 0.1594 (mmm) cc_final: 0.0992 (mmm) REVERT: B 451 TYR cc_start: 0.6580 (t80) cc_final: 0.6332 (t80) REVERT: C 20 ASN cc_start: 0.7887 (m-40) cc_final: 0.7318 (m110) REVERT: C 51 MET cc_start: 0.8889 (mtp) cc_final: 0.8673 (mtp) REVERT: C 230 PHE cc_start: 0.7431 (p90) cc_final: 0.6692 (t80) REVERT: C 265 LEU cc_start: 0.7581 (tp) cc_final: 0.7271 (tp) REVERT: C 272 MET cc_start: 0.7825 (tpp) cc_final: 0.7611 (tpp) REVERT: C 307 ASN cc_start: 0.8616 (t0) cc_final: 0.8310 (t0) REVERT: C 352 THR cc_start: 0.8112 (p) cc_final: 0.7896 (p) REVERT: C 368 MET cc_start: 0.8645 (ptm) cc_final: 0.8402 (ptm) REVERT: C 370 VAL cc_start: 0.8359 (m) cc_final: 0.8134 (m) REVERT: C 392 LEU cc_start: 0.8853 (mm) cc_final: 0.8301 (mm) REVERT: C 410 MET cc_start: 0.7365 (ptt) cc_final: 0.6777 (ptt) REVERT: C 450 ARG cc_start: 0.7978 (mtm180) cc_final: 0.6974 (mtt180) REVERT: D 94 CYS cc_start: 0.8727 (m) cc_final: 0.8236 (m) REVERT: D 147 GLN cc_start: 0.7304 (mp10) cc_final: 0.7006 (mp10) REVERT: D 202 ARG cc_start: 0.4951 (mtp180) cc_final: 0.4237 (mtp180) REVERT: D 266 VAL cc_start: 0.8894 (m) cc_final: 0.8606 (p) REVERT: D 302 MET cc_start: 0.8792 (mmm) cc_final: 0.7976 (mmm) REVERT: D 368 MET cc_start: 0.8586 (ptm) cc_final: 0.8237 (ptp) REVERT: D 378 MET cc_start: 0.6244 (tpp) cc_final: 0.5878 (tpp) REVERT: D 397 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7555 (tm-30) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1073 time to fit residues: 45.7199 Evaluate side-chains 230 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 145 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 2 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.160305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136004 restraints weight = 28267.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.139575 restraints weight = 18456.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142083 restraints weight = 13330.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.143962 restraints weight = 10419.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.145118 restraints weight = 8617.220| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13836 Z= 0.207 Angle : 0.743 9.883 18816 Z= 0.378 Chirality : 0.049 0.214 2104 Planarity : 0.006 0.066 2480 Dihedral : 8.562 102.015 2028 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.83 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.19), residues: 1812 helix: 0.18 (0.20), residues: 640 sheet: -0.92 (0.31), residues: 296 loop : -1.86 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 260 TYR 0.018 0.002 TYR A 451 PHE 0.029 0.003 PHE A 316 TRP 0.021 0.002 TRP C 310 HIS 0.009 0.002 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00468 (13836) covalent geometry : angle 0.74261 (18816) hydrogen bonds : bond 0.04216 ( 490) hydrogen bonds : angle 5.61672 ( 1359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8830 (m-40) cc_final: 0.8581 (m110) REVERT: A 264 MET cc_start: 0.8276 (mtm) cc_final: 0.7991 (mtp) REVERT: B 20 ASN cc_start: 0.7757 (m-40) cc_final: 0.7290 (p0) REVERT: B 134 ARG cc_start: 0.7512 (mmp-170) cc_final: 0.6005 (ptt180) REVERT: B 144 LYS cc_start: 0.8231 (pptt) cc_final: 0.7725 (pptt) REVERT: B 348 HIS cc_start: 0.5783 (m-70) cc_final: 0.5525 (m-70) REVERT: B 368 MET cc_start: 0.8091 (ptm) cc_final: 0.7604 (ptm) REVERT: B 378 MET cc_start: 0.1986 (mmm) cc_final: 0.1326 (mmm) REVERT: C 185 THR cc_start: 0.7743 (m) cc_final: 0.7511 (m) REVERT: C 230 PHE cc_start: 0.7293 (p90) cc_final: 0.6327 (t80) REVERT: C 307 ASN cc_start: 0.8674 (t0) cc_final: 0.8436 (t0) REVERT: C 368 MET cc_start: 0.8761 (ptm) cc_final: 0.8445 (ptm) REVERT: C 392 LEU cc_start: 0.8891 (mm) cc_final: 0.8359 (mm) REVERT: C 410 MET cc_start: 0.7528 (ptt) cc_final: 0.7066 (ptt) REVERT: D 147 GLN cc_start: 0.7460 (mp10) cc_final: 0.6984 (mp10) REVERT: D 202 ARG cc_start: 0.5008 (mtp180) cc_final: 0.4522 (mtp180) REVERT: D 266 VAL cc_start: 0.8856 (m) cc_final: 0.8563 (p) REVERT: D 302 MET cc_start: 0.8717 (mmm) cc_final: 0.7963 (mmm) REVERT: D 307 ASN cc_start: 0.8686 (t0) cc_final: 0.8480 (t0) REVERT: D 354 ARG cc_start: 0.7648 (tmm160) cc_final: 0.7059 (tmm-80) REVERT: D 368 MET cc_start: 0.8742 (ptm) cc_final: 0.8337 (ptp) REVERT: D 378 MET cc_start: 0.6442 (tpp) cc_final: 0.5938 (tpp) REVERT: D 397 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7217 (tm-30) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1105 time to fit residues: 45.6599 Evaluate side-chains 219 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 75 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.161058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.136904 restraints weight = 28047.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.140429 restraints weight = 18406.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142944 restraints weight = 13349.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.144801 restraints weight = 10448.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146140 restraints weight = 8651.055| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13836 Z= 0.176 Angle : 0.729 14.056 18816 Z= 0.367 Chirality : 0.048 0.225 2104 Planarity : 0.006 0.068 2480 Dihedral : 8.508 105.017 2028 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.50 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.19), residues: 1812 helix: 0.17 (0.20), residues: 640 sheet: -0.96 (0.31), residues: 296 loop : -1.87 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 450 TYR 0.015 0.002 TYR D 451 PHE 0.028 0.003 PHE A 316 TRP 0.024 0.002 TRP C 310 HIS 0.011 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00400 (13836) covalent geometry : angle 0.72942 (18816) hydrogen bonds : bond 0.04012 ( 490) hydrogen bonds : angle 5.52017 ( 1359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.8206 (mtm) cc_final: 0.7759 (mtp) REVERT: B 20 ASN cc_start: 0.7685 (m-40) cc_final: 0.7222 (p0) REVERT: B 134 ARG cc_start: 0.7501 (mmp-170) cc_final: 0.6011 (ptt180) REVERT: B 144 LYS cc_start: 0.8207 (pptt) cc_final: 0.7692 (pptt) REVERT: B 348 HIS cc_start: 0.5556 (m-70) cc_final: 0.5348 (m-70) REVERT: B 368 MET cc_start: 0.8086 (ptm) cc_final: 0.7723 (ptm) REVERT: B 378 MET cc_start: 0.1969 (mmm) cc_final: 0.1366 (mmm) REVERT: C 20 ASN cc_start: 0.8236 (m-40) cc_final: 0.7616 (m110) REVERT: C 230 PHE cc_start: 0.7323 (p90) cc_final: 0.6350 (t80) REVERT: C 307 ASN cc_start: 0.8689 (t0) cc_final: 0.8462 (t0) REVERT: C 368 MET cc_start: 0.8798 (ptm) cc_final: 0.8520 (ptm) REVERT: C 392 LEU cc_start: 0.8856 (mm) cc_final: 0.8409 (mm) REVERT: C 410 MET cc_start: 0.7505 (ptt) cc_final: 0.7081 (ptt) REVERT: D 94 CYS cc_start: 0.8628 (m) cc_final: 0.7990 (m) REVERT: D 147 GLN cc_start: 0.7429 (mp10) cc_final: 0.6920 (mp10) REVERT: D 202 ARG cc_start: 0.4931 (mtp180) cc_final: 0.4279 (mtp180) REVERT: D 254 MET cc_start: 0.7162 (tpt) cc_final: 0.6915 (tpt) REVERT: D 266 VAL cc_start: 0.8902 (m) cc_final: 0.8645 (p) REVERT: D 302 MET cc_start: 0.8689 (mmm) cc_final: 0.7858 (mmm) REVERT: D 307 ASN cc_start: 0.8715 (t0) cc_final: 0.8503 (t0) REVERT: D 354 ARG cc_start: 0.7719 (tmm160) cc_final: 0.7125 (tmm-80) REVERT: D 368 MET cc_start: 0.8664 (ptm) cc_final: 0.8318 (ptp) REVERT: D 397 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7230 (tm-30) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1082 time to fit residues: 44.1333 Evaluate side-chains 218 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 86 optimal weight: 0.0770 chunk 142 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN ** B 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 GLN ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.166215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141604 restraints weight = 27924.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145341 restraints weight = 18175.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.148123 restraints weight = 13045.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.150147 restraints weight = 10061.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.151642 restraints weight = 8219.133| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13836 Z= 0.126 Angle : 0.702 14.669 18816 Z= 0.348 Chirality : 0.046 0.202 2104 Planarity : 0.006 0.067 2480 Dihedral : 8.308 108.701 2028 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.17 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.20), residues: 1812 helix: 0.30 (0.21), residues: 644 sheet: -1.08 (0.35), residues: 228 loop : -1.62 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 450 TYR 0.016 0.001 TYR D 451 PHE 0.030 0.002 PHE C 316 TRP 0.016 0.002 TRP C 310 HIS 0.010 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00283 (13836) covalent geometry : angle 0.70195 (18816) hydrogen bonds : bond 0.03616 ( 490) hydrogen bonds : angle 5.30624 ( 1359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8495 (mtp) cc_final: 0.7887 (mtt) REVERT: A 264 MET cc_start: 0.8284 (mtm) cc_final: 0.7952 (mtp) REVERT: A 410 MET cc_start: 0.3547 (ttp) cc_final: 0.3241 (ttp) REVERT: B 20 ASN cc_start: 0.7592 (m-40) cc_final: 0.7183 (p0) REVERT: B 134 ARG cc_start: 0.7393 (mmp-170) cc_final: 0.5935 (ptt180) REVERT: B 144 LYS cc_start: 0.8136 (pptt) cc_final: 0.7605 (pptt) REVERT: B 209 GLU cc_start: 0.7623 (pm20) cc_final: 0.7379 (pm20) REVERT: B 368 MET cc_start: 0.8202 (ptm) cc_final: 0.7875 (ptm) REVERT: B 378 MET cc_start: 0.2087 (mmm) cc_final: 0.1577 (mmm) REVERT: C 20 ASN cc_start: 0.8289 (m-40) cc_final: 0.7876 (m110) REVERT: C 50 LYS cc_start: 0.9173 (tppt) cc_final: 0.8737 (mmmt) REVERT: C 51 MET cc_start: 0.8903 (mtp) cc_final: 0.8538 (mtp) REVERT: C 230 PHE cc_start: 0.7520 (p90) cc_final: 0.6758 (t80) REVERT: C 307 ASN cc_start: 0.8631 (t0) cc_final: 0.8309 (t0) REVERT: C 368 MET cc_start: 0.8815 (ptm) cc_final: 0.8608 (ptm) REVERT: C 392 LEU cc_start: 0.8855 (mm) cc_final: 0.8444 (mm) REVERT: C 410 MET cc_start: 0.7254 (ptt) cc_final: 0.6712 (ptt) REVERT: D 94 CYS cc_start: 0.8713 (m) cc_final: 0.8156 (m) REVERT: D 147 GLN cc_start: 0.7263 (mp10) cc_final: 0.6933 (mt0) REVERT: D 266 VAL cc_start: 0.8883 (m) cc_final: 0.8565 (p) REVERT: D 302 MET cc_start: 0.8742 (mmm) cc_final: 0.7955 (mmm) REVERT: D 354 ARG cc_start: 0.7602 (tmm160) cc_final: 0.7060 (tmm-80) REVERT: D 368 MET cc_start: 0.8636 (ptm) cc_final: 0.8337 (ptp) REVERT: D 397 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7474 (tm-30) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1011 time to fit residues: 42.0894 Evaluate side-chains 220 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 176 optimal weight: 0.0870 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 154 optimal weight: 0.3980 chunk 77 optimal weight: 0.0070 chunk 35 optimal weight: 0.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.167991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.143319 restraints weight = 27496.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.147180 restraints weight = 17870.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.150026 restraints weight = 12781.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152063 restraints weight = 9821.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.153573 restraints weight = 8007.826| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13836 Z= 0.123 Angle : 0.693 13.661 18816 Z= 0.342 Chirality : 0.045 0.156 2104 Planarity : 0.006 0.081 2480 Dihedral : 8.177 110.006 2028 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.84 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.20), residues: 1812 helix: 0.46 (0.21), residues: 620 sheet: -0.90 (0.35), residues: 228 loop : -1.55 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 415 TYR 0.016 0.001 TYR D 128 PHE 0.029 0.002 PHE C 316 TRP 0.017 0.001 TRP C 310 HIS 0.011 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00274 (13836) covalent geometry : angle 0.69267 (18816) hydrogen bonds : bond 0.03404 ( 490) hydrogen bonds : angle 5.28069 ( 1359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8423 (mp) cc_final: 0.8083 (mp) REVERT: A 38 ASN cc_start: 0.8255 (m-40) cc_final: 0.8037 (t0) REVERT: A 51 MET cc_start: 0.8526 (mtp) cc_final: 0.8116 (mtt) REVERT: A 264 MET cc_start: 0.8234 (mtm) cc_final: 0.7728 (mtp) REVERT: A 337 LYS cc_start: 0.6998 (tttt) cc_final: 0.6785 (mmtm) REVERT: A 410 MET cc_start: 0.3576 (ttp) cc_final: 0.3254 (ttp) REVERT: B 20 ASN cc_start: 0.7612 (m-40) cc_final: 0.7248 (p0) REVERT: B 104 ASN cc_start: 0.7432 (m110) cc_final: 0.6859 (p0) REVERT: B 134 ARG cc_start: 0.7428 (mmp-170) cc_final: 0.6012 (ptt180) REVERT: B 209 GLU cc_start: 0.7585 (pm20) cc_final: 0.7278 (pm20) REVERT: B 368 MET cc_start: 0.8142 (ptm) cc_final: 0.7797 (ptm) REVERT: B 378 MET cc_start: 0.2122 (mmm) cc_final: 0.1716 (mmm) REVERT: C 20 ASN cc_start: 0.8217 (m-40) cc_final: 0.7790 (m110) REVERT: C 50 LYS cc_start: 0.9149 (tppt) cc_final: 0.8712 (mmmt) REVERT: C 51 MET cc_start: 0.8916 (mtp) cc_final: 0.8551 (mtp) REVERT: C 230 PHE cc_start: 0.7529 (p90) cc_final: 0.6813 (t80) REVERT: C 307 ASN cc_start: 0.8635 (t0) cc_final: 0.8313 (t0) REVERT: C 378 MET cc_start: 0.2168 (tpt) cc_final: 0.1958 (tpt) REVERT: C 392 LEU cc_start: 0.8888 (mm) cc_final: 0.8481 (mm) REVERT: C 410 MET cc_start: 0.7295 (ptt) cc_final: 0.6724 (ptt) REVERT: D 100 GLU cc_start: 0.8032 (pm20) cc_final: 0.7269 (pm20) REVERT: D 254 MET cc_start: 0.6771 (tpt) cc_final: 0.6013 (tpt) REVERT: D 266 VAL cc_start: 0.8873 (m) cc_final: 0.8547 (p) REVERT: D 302 MET cc_start: 0.8796 (mmm) cc_final: 0.8426 (mmt) REVERT: D 354 ARG cc_start: 0.7589 (tmm160) cc_final: 0.7082 (tmm-80) REVERT: D 368 MET cc_start: 0.8561 (ptm) cc_final: 0.8301 (ptp) REVERT: D 397 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7436 (tm-30) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1063 time to fit residues: 44.5709 Evaluate side-chains 219 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 17 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 111 optimal weight: 0.1980 chunk 166 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.161262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137186 restraints weight = 28443.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.140677 restraints weight = 18467.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143287 restraints weight = 13293.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145142 restraints weight = 10318.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146508 restraints weight = 8516.425| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13836 Z= 0.195 Angle : 0.752 16.024 18816 Z= 0.378 Chirality : 0.048 0.279 2104 Planarity : 0.006 0.074 2480 Dihedral : 8.315 106.696 2028 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.16 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.20), residues: 1812 helix: 0.35 (0.20), residues: 636 sheet: -0.88 (0.34), residues: 256 loop : -1.71 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 103 TYR 0.015 0.002 TYR D 451 PHE 0.028 0.003 PHE A 316 TRP 0.026 0.002 TRP C 310 HIS 0.010 0.002 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00436 (13836) covalent geometry : angle 0.75216 (18816) hydrogen bonds : bond 0.03855 ( 490) hydrogen bonds : angle 5.47099 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.27 seconds wall clock time: 38 minutes 23.43 seconds (2303.43 seconds total)