Starting phenix.real_space_refine on Thu Mar 5 04:17:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gf5_29978/03_2026/8gf5_29978_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gf5_29978/03_2026/8gf5_29978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gf5_29978/03_2026/8gf5_29978_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gf5_29978/03_2026/8gf5_29978_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gf5_29978/03_2026/8gf5_29978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gf5_29978/03_2026/8gf5_29978.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.089 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: 6 Type Number sf(0) Gaussians Ni 1 6.56 5 P 1 5.49 5 S 120 5.16 5 C 11981 2.51 5 N 3320 2.21 5 O 3704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19127 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4282 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 22, 'TRANS': 537} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MHS:plan-2': 1, 'AGM:plan-2': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3682 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 20, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MHS:plan-2': 1, 'AGM:plan-2': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3133 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 417} Chain: "D" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3143 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 419} Chain: "E" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1926 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "F" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1926 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "X" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 9, 'TRANS': 108} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'COM': 1, 'F43': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Classifications: {'peptide': 1} Time building chain proxies: 4.21, per 1000 atoms: 0.22 Number of scatterers: 19127 At special positions: 0 Unit cell: (98.12, 102.58, 137.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 1 28.00 S 120 16.00 P 1 15.00 O 3704 8.00 N 3320 7.00 C 11981 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: 1.83 Conformation dependent library (CDL) restraints added in 881.9 milliseconds 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 16 sheets defined 55.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 47 through 64 Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.877A pdb=" N TRP A 112 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.558A pdb=" N GLY A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 154 removed outlier: 3.719A pdb=" N HIS A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.644A pdb=" N ASP A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.521A pdb=" N VAL A 195 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 235 through 253 removed outlier: 4.162A pdb=" N ARG A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.982A pdb=" N ASP A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 312 through 329 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.522A pdb=" N ALA A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 352 removed outlier: 3.945A pdb=" N THR A 352 " --> pdb=" O ALA A 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 352' Processing helix chain 'A' and resid 354 through 371 Processing helix chain 'A' and resid 386 through 408 Processing helix chain 'A' and resid 408 through 415 Processing helix chain 'A' and resid 417 through 438 removed outlier: 3.718A pdb=" N ARG A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 459 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'A' and resid 504 through 518 removed outlier: 3.568A pdb=" N HIS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.538A pdb=" N LYS A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 removed outlier: 3.622A pdb=" N GLU A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.544A pdb=" N ILE A 567 " --> pdb=" O SER A 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.671A pdb=" N LEU B 100 " --> pdb=" O PRO B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 139 through 154 Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'B' and resid 197 through 202 Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 235 through 253 removed outlier: 4.256A pdb=" N ARG B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 312 through 330 removed outlier: 3.694A pdb=" N ALA B 317 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.915A pdb=" N ALA B 349 " --> pdb=" O TYR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 371 Processing helix chain 'B' and resid 386 through 408 Processing helix chain 'B' and resid 418 through 438 removed outlier: 3.576A pdb=" N ALA B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 459 Processing helix chain 'B' and resid 466 through 474 removed outlier: 3.868A pdb=" N ASP B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 496 through 500 removed outlier: 4.554A pdb=" N MET B 500 " --> pdb=" O ASN B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 518 removed outlier: 3.845A pdb=" N HIS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 533 Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'C' and resid 22 through 25 Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 47 through 57 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 114 through 120 removed outlier: 3.775A pdb=" N ILE C 118 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 143 removed outlier: 4.148A pdb=" N THR C 128 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 149 through 159 removed outlier: 3.907A pdb=" N VAL C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 186 through 191 removed outlier: 4.220A pdb=" N LEU C 189 " --> pdb=" O GLY C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.633A pdb=" N ILE C 197 " --> pdb=" O MET C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 223 removed outlier: 3.711A pdb=" N ALA C 210 " --> pdb=" O MET C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 241 removed outlier: 4.096A pdb=" N ARG C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 261 through 277 Processing helix chain 'C' and resid 296 through 319 Processing helix chain 'C' and resid 321 through 323 No H-bonds generated for 'chain 'C' and resid 321 through 323' Processing helix chain 'C' and resid 324 through 341 removed outlier: 3.938A pdb=" N ASN C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 361 Processing helix chain 'C' and resid 369 through 373 removed outlier: 3.623A pdb=" N PHE C 373 " --> pdb=" O PRO C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 405 through 418 removed outlier: 6.938A pdb=" N LEU C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE C 413 " --> pdb=" O THR C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 425 through 431 Processing helix chain 'D' and resid 22 through 25 removed outlier: 3.707A pdb=" N ALA D 25 " --> pdb=" O MET D 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 25' Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 46 through 57 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 114 through 120 removed outlier: 3.675A pdb=" N ILE D 118 " --> pdb=" O PRO D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 143 removed outlier: 4.295A pdb=" N THR D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 156 Processing helix chain 'D' and resid 178 through 182 removed outlier: 3.773A pdb=" N ASN D 182 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 190 removed outlier: 3.986A pdb=" N LEU D 189 " --> pdb=" O GLY D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 204 through 223 Processing helix chain 'D' and resid 228 through 242 Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.674A pdb=" N ILE D 252 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 276 Processing helix chain 'D' and resid 296 through 318 Processing helix chain 'D' and resid 324 through 341 removed outlier: 4.351A pdb=" N LEU D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 347 Processing helix chain 'D' and resid 348 through 362 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 387 through 397 Processing helix chain 'D' and resid 405 through 419 removed outlier: 7.132A pdb=" N LEU D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE D 413 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 419 " --> pdb=" O ASP D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 425 Processing helix chain 'D' and resid 425 through 432 Processing helix chain 'E' and resid 12 through 24 Processing helix chain 'E' and resid 33 through 42 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 65 through 71 Processing helix chain 'E' and resid 74 through 79 removed outlier: 3.849A pdb=" N ALA E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 128 through 141 Processing helix chain 'E' and resid 205 through 212 Processing helix chain 'E' and resid 226 through 246 removed outlier: 3.531A pdb=" N ILE E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 Processing helix chain 'F' and resid 33 through 42 Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.724A pdb=" N GLY F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 71 Processing helix chain 'F' and resid 74 through 79 Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 128 through 141 Processing helix chain 'F' and resid 205 through 212 Processing helix chain 'F' and resid 226 through 246 Processing helix chain 'X' and resid 23 through 35 Processing helix chain 'X' and resid 95 through 108 removed outlier: 3.713A pdb=" N LYS X 100 " --> pdb=" O GLU X 96 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS X 107 " --> pdb=" O SER X 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 181 removed outlier: 3.793A pdb=" N ILE A 120 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 78 through 81 removed outlier: 6.269A pdb=" N GLY B 79 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU X 15 " --> pdb=" O ARG X 116 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG X 116 " --> pdb=" O GLU X 15 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 181 Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 8 removed outlier: 7.406A pdb=" N VAL C 5 " --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER C 17 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 7 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 99 through 103 removed outlier: 3.524A pdb=" N SER C 108 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 279 through 284 removed outlier: 7.013A pdb=" N PHE C 291 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 8 removed outlier: 7.254A pdb=" N VAL D 5 " --> pdb=" O SER D 17 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER D 17 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE D 7 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 99 through 103 removed outlier: 3.510A pdb=" N SER D 99 " --> pdb=" O GLN D 112 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 108 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 279 through 281 Processing sheet with id=AB3, first strand: chain 'E' and resid 83 through 88 Processing sheet with id=AB4, first strand: chain 'E' and resid 176 through 179 removed outlier: 5.638A pdb=" N LYS E 187 " --> pdb=" O ARG E 196 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N ARG E 196 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 83 through 88 removed outlier: 3.513A pdb=" N PHE F 88 " --> pdb=" O GLN F 122 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU F 125 " --> pdb=" O ASP F 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 176 through 179 removed outlier: 6.022A pdb=" N LYS F 187 " --> pdb=" O ARG F 196 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N ARG F 196 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 71 through 74 961 hydrogen bonds defined for protein. 2763 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 7441 1.38 - 1.56: 11835 1.56 - 1.74: 2 1.74 - 1.92: 210 1.92 - 2.10: 4 Bond restraints: 19492 Sorted by residual: bond pdb=" C1 TP7 B 601 " pdb=" O1 TP7 B 601 " ideal model delta sigma weight residual 1.226 1.430 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" N TP7 B 601 " pdb=" C1 TP7 B 601 " ideal model delta sigma weight residual 1.340 1.447 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" O4P TP7 B 601 " pdb=" P TP7 B 601 " ideal model delta sigma weight residual 1.704 1.607 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" CA ASN A 151 " pdb=" C ASN A 151 " ideal model delta sigma weight residual 1.522 1.472 0.051 1.36e-02 5.41e+03 1.39e+01 bond pdb=" CA GLU B 484 " pdb=" C GLU B 484 " ideal model delta sigma weight residual 1.520 1.477 0.043 1.20e-02 6.94e+03 1.27e+01 ... (remaining 19487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 26107 2.84 - 5.68: 270 5.68 - 8.52: 19 8.52 - 11.36: 9 11.36 - 14.20: 3 Bond angle restraints: 26408 Sorted by residual: angle pdb=" N LEU A 486 " pdb=" CA LEU A 486 " pdb=" C LEU A 486 " ideal model delta sigma weight residual 108.22 97.25 10.97 9.00e-01 1.23e+00 1.49e+02 angle pdb=" N GLY A 482 " pdb=" CA GLY A 482 " pdb=" C GLY A 482 " ideal model delta sigma weight residual 112.50 121.07 -8.57 1.16e+00 7.43e-01 5.45e+01 angle pdb=" N PHE A 466 " pdb=" CA PHE A 466 " pdb=" C PHE A 466 " ideal model delta sigma weight residual 113.50 104.58 8.92 1.23e+00 6.61e-01 5.26e+01 angle pdb=" N ALA A 283 " pdb=" CA ALA A 283 " pdb=" C ALA A 283 " ideal model delta sigma weight residual 111.07 118.69 -7.62 1.07e+00 8.73e-01 5.08e+01 angle pdb=" N ASN A 151 " pdb=" CA ASN A 151 " pdb=" C ASN A 151 " ideal model delta sigma weight residual 111.71 119.51 -7.80 1.15e+00 7.56e-01 4.60e+01 ... (remaining 26403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 10650 17.57 - 35.15: 852 35.15 - 52.72: 123 52.72 - 70.30: 24 70.30 - 87.87: 25 Dihedral angle restraints: 11674 sinusoidal: 4548 harmonic: 7126 Sorted by residual: dihedral pdb=" C HIS A 152 " pdb=" N HIS A 152 " pdb=" CA HIS A 152 " pdb=" CB HIS A 152 " ideal model delta harmonic sigma weight residual -122.60 -137.67 15.07 0 2.50e+00 1.60e-01 3.63e+01 dihedral pdb=" N HIS A 152 " pdb=" C HIS A 152 " pdb=" CA HIS A 152 " pdb=" CB HIS A 152 " ideal model delta harmonic sigma weight residual 122.80 136.49 -13.69 0 2.50e+00 1.60e-01 3.00e+01 dihedral pdb=" CA ASP C 346 " pdb=" C ASP C 346 " pdb=" N TYR C 347 " pdb=" CA TYR C 347 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 11671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2869 0.130 - 0.259: 31 0.259 - 0.389: 6 0.389 - 0.518: 1 0.518 - 0.648: 1 Chirality restraints: 2908 Sorted by residual: chirality pdb=" CA HIS A 152 " pdb=" N HIS A 152 " pdb=" C HIS A 152 " pdb=" CB HIS A 152 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA ASN A 151 " pdb=" N ASN A 151 " pdb=" C ASN A 151 " pdb=" CB ASN A 151 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C2D F43 A 602 " pdb=" C1D F43 A 602 " pdb=" C3D F43 A 602 " pdb=" C5D F43 A 602 " both_signs ideal model delta sigma weight residual False 2.60 2.95 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 2905 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB F43 A 602 " -0.146 2.00e-02 2.50e+03 1.85e-01 5.12e+02 pdb=" C1B F43 A 602 " -0.155 2.00e-02 2.50e+03 pdb=" C3B F43 A 602 " 0.288 2.00e-02 2.50e+03 pdb=" C4B F43 A 602 " -0.029 2.00e-02 2.50e+03 pdb=" CHC F43 A 602 " -0.172 2.00e-02 2.50e+03 pdb="NI F43 A 602 " 0.214 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N TP7 B 601 " -0.096 2.00e-02 2.50e+03 1.80e-01 4.06e+02 pdb=" CA TP7 B 601 " -0.017 2.00e-02 2.50e+03 pdb=" C1 TP7 B 601 " 0.352 2.00e-02 2.50e+03 pdb=" C2 TP7 B 601 " -0.126 2.00e-02 2.50e+03 pdb=" O1 TP7 B 601 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND F43 A 602 " -0.064 2.00e-02 2.50e+03 1.26e-01 2.38e+02 pdb=" C1D F43 A 602 " -0.084 2.00e-02 2.50e+03 pdb=" C2D F43 A 602 " 0.211 2.00e-02 2.50e+03 pdb=" C4D F43 A 602 " -0.127 2.00e-02 2.50e+03 pdb=" CHD F43 A 602 " -0.072 2.00e-02 2.50e+03 pdb="NI F43 A 602 " 0.135 2.00e-02 2.50e+03 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 268 2.59 - 3.17: 17878 3.17 - 3.74: 31511 3.74 - 4.32: 46807 4.32 - 4.90: 78026 Nonbonded interactions: 174490 Sorted by model distance: nonbonded pdb=" OG SER E 52 " pdb=" O HIS E 54 " model vdw 2.010 3.040 nonbonded pdb=" O ASN D 374 " pdb=" OG1 THR D 380 " model vdw 2.071 3.040 nonbonded pdb=" O ARG F 19 " pdb=" OG SER F 23 " model vdw 2.076 3.040 nonbonded pdb=" OD2 ASP A 174 " pdb=" OG1 THR A 226 " model vdw 2.084 3.040 nonbonded pdb=" OE2 GLU A 131 " pdb=" N VAL A 138 " model vdw 2.100 3.120 ... (remaining 174485 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and resid 3 through 431) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.960 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.204 19492 Z= 0.324 Angle : 0.748 14.203 26408 Z= 0.445 Chirality : 0.051 0.648 2908 Planarity : 0.008 0.185 3486 Dihedral : 13.489 87.871 7146 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % Rotamer: Outliers : 0.10 % Allowed : 0.61 % Favored : 99.29 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2479 helix: 0.57 (0.15), residues: 1223 sheet: -0.54 (0.48), residues: 124 loop : -0.91 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 287 TYR 0.030 0.002 TYR A 336 PHE 0.025 0.002 PHE A 463 TRP 0.020 0.002 TRP B 240 HIS 0.008 0.002 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00647 (19492) covalent geometry : angle 0.74765 (26408) hydrogen bonds : bond 0.16410 ( 961) hydrogen bonds : angle 6.44584 ( 2763) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: E 100 TYR cc_start: 0.8064 (m-80) cc_final: 0.7783 (m-80) REVERT: F 60 MET cc_start: 0.8516 (ttt) cc_final: 0.8211 (ttm) outliers start: 2 outliers final: 1 residues processed: 196 average time/residue: 0.7450 time to fit residues: 162.4631 Evaluate side-chains 123 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 197 ASN A 330 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS B 497 ASN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN F 138 GLN X 13 GLN X 36 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.069282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.058949 restraints weight = 58418.462| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.03 r_work: 0.2886 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19492 Z= 0.150 Angle : 0.627 11.878 26408 Z= 0.326 Chirality : 0.044 0.285 2908 Planarity : 0.005 0.073 3486 Dihedral : 5.534 58.400 2821 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 1.63 % Allowed : 7.39 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2479 helix: 0.97 (0.15), residues: 1259 sheet: -0.32 (0.46), residues: 132 loop : -0.78 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.020 0.002 TYR A 336 PHE 0.017 0.002 PHE C 357 TRP 0.018 0.002 TRP A 447 HIS 0.006 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00343 (19492) covalent geometry : angle 0.62736 (26408) hydrogen bonds : bond 0.04233 ( 961) hydrogen bonds : angle 4.99555 ( 2763) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8285 (mmm) REVERT: A 346 TYR cc_start: 0.8435 (m-10) cc_final: 0.8153 (m-10) REVERT: C 165 MET cc_start: 0.9022 (mtp) cc_final: 0.8654 (mtp) REVERT: D 223 MET cc_start: 0.8498 (mtp) cc_final: 0.8141 (mtm) REVERT: E 100 TYR cc_start: 0.8732 (m-80) cc_final: 0.8346 (m-80) REVERT: F 28 LYS cc_start: 0.8877 (tttm) cc_final: 0.8646 (tptp) REVERT: F 100 TYR cc_start: 0.8785 (m-80) cc_final: 0.8424 (m-80) REVERT: F 131 MET cc_start: 0.8712 (tmm) cc_final: 0.8487 (ttp) REVERT: X 29 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8298 (mtmm) REVERT: X 100 LYS cc_start: 0.9195 (mtpp) cc_final: 0.8898 (ptpp) REVERT: X 108 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7391 (ptt) REVERT: X 111 PHE cc_start: 0.6379 (p90) cc_final: 0.6158 (p90) outliers start: 32 outliers final: 6 residues processed: 165 average time/residue: 0.6370 time to fit residues: 118.4204 Evaluate side-chains 128 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain X residue 108 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 178 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 2 optimal weight: 0.0370 chunk 192 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 330 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.070584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.060466 restraints weight = 58715.599| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.07 r_work: 0.2914 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19492 Z= 0.111 Angle : 0.553 10.065 26408 Z= 0.283 Chirality : 0.042 0.238 2908 Planarity : 0.004 0.064 3486 Dihedral : 5.072 59.835 2819 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.78 % Allowed : 9.99 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.17), residues: 2479 helix: 1.25 (0.15), residues: 1257 sheet: -0.65 (0.48), residues: 115 loop : -0.54 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.014 0.001 TYR D 365 PHE 0.014 0.001 PHE F 101 TRP 0.017 0.001 TRP B 447 HIS 0.007 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00246 (19492) covalent geometry : angle 0.55325 (26408) hydrogen bonds : bond 0.03437 ( 961) hydrogen bonds : angle 4.59402 ( 2763) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8137 (tmm) REVERT: A 168 HIS cc_start: 0.8720 (t-90) cc_final: 0.8363 (t-90) REVERT: A 291 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: A 346 TYR cc_start: 0.8417 (m-10) cc_final: 0.8136 (m-10) REVERT: B 102 TYR cc_start: 0.9193 (p90) cc_final: 0.8955 (p90) REVERT: B 277 MET cc_start: 0.9258 (mmp) cc_final: 0.8898 (mmp) REVERT: B 316 ILE cc_start: 0.9068 (mm) cc_final: 0.8863 (mp) REVERT: C 403 MET cc_start: 0.8894 (tpt) cc_final: 0.8475 (ttt) REVERT: D 191 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7595 (p0) REVERT: D 359 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7915 (t80) REVERT: E 100 TYR cc_start: 0.8660 (m-80) cc_final: 0.8259 (m-80) REVERT: F 100 TYR cc_start: 0.8701 (m-80) cc_final: 0.8341 (m-80) REVERT: F 184 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9023 (mp) REVERT: X 29 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8101 (mtmm) REVERT: X 70 LYS cc_start: 0.8451 (mmtm) cc_final: 0.7990 (mmtm) REVERT: X 111 PHE cc_start: 0.6537 (p90) cc_final: 0.6227 (p90) outliers start: 35 outliers final: 5 residues processed: 172 average time/residue: 0.6617 time to fit residues: 127.8781 Evaluate side-chains 135 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 184 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 27 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 214 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 238 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.069041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.059025 restraints weight = 59231.296| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.08 r_work: 0.2880 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19492 Z= 0.138 Angle : 0.562 10.271 26408 Z= 0.286 Chirality : 0.042 0.234 2908 Planarity : 0.004 0.060 3486 Dihedral : 4.990 59.064 2819 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.53 % Allowed : 11.78 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2479 helix: 1.45 (0.15), residues: 1244 sheet: -0.31 (0.47), residues: 127 loop : -0.47 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.014 0.001 TYR E 243 PHE 0.015 0.001 PHE F 101 TRP 0.014 0.001 TRP A 447 HIS 0.006 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00313 (19492) covalent geometry : angle 0.56209 (26408) hydrogen bonds : bond 0.03473 ( 961) hydrogen bonds : angle 4.47715 ( 2763) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8553 (tptt) REVERT: A 125 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: A 168 HIS cc_start: 0.8753 (t-90) cc_final: 0.8350 (t-90) REVERT: A 243 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7981 (ptt) REVERT: A 346 TYR cc_start: 0.8449 (m-10) cc_final: 0.8165 (m-10) REVERT: C 403 MET cc_start: 0.8931 (tpt) cc_final: 0.8489 (ttt) REVERT: E 100 TYR cc_start: 0.8752 (m-80) cc_final: 0.8351 (m-80) REVERT: F 100 TYR cc_start: 0.8743 (m-80) cc_final: 0.8371 (m-80) REVERT: F 184 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9079 (mp) REVERT: X 13 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: X 29 LYS cc_start: 0.8468 (mtmm) cc_final: 0.8176 (mtmm) REVERT: X 44 MET cc_start: 0.8406 (ttt) cc_final: 0.8182 (tpp) REVERT: X 70 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8037 (mmtm) REVERT: X 72 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7757 (mp) REVERT: X 111 PHE cc_start: 0.6461 (p90) cc_final: 0.6197 (p90) outliers start: 30 outliers final: 8 residues processed: 152 average time/residue: 0.6223 time to fit residues: 106.5494 Evaluate side-chains 135 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain X residue 13 GLN Chi-restraints excluded: chain X residue 72 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 234 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 148 optimal weight: 0.0670 chunk 44 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 198 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 130 optimal weight: 0.5980 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.068175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.058181 restraints weight = 59231.916| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.07 r_work: 0.2862 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19492 Z= 0.151 Angle : 0.572 10.311 26408 Z= 0.288 Chirality : 0.042 0.210 2908 Planarity : 0.004 0.059 3486 Dihedral : 4.954 55.780 2819 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.04 % Allowed : 11.88 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.17), residues: 2479 helix: 1.50 (0.15), residues: 1244 sheet: -0.63 (0.53), residues: 98 loop : -0.39 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.018 0.001 TYR E 243 PHE 0.016 0.001 PHE E 101 TRP 0.013 0.001 TRP A 447 HIS 0.007 0.001 HIS D 382 Details of bonding type rmsd covalent geometry : bond 0.00343 (19492) covalent geometry : angle 0.57151 (26408) hydrogen bonds : bond 0.03471 ( 961) hydrogen bonds : angle 4.43380 ( 2763) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8543 (tptt) REVERT: A 125 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8221 (mmm) REVERT: A 168 HIS cc_start: 0.8748 (t-90) cc_final: 0.8327 (t-90) REVERT: A 243 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7869 (ptt) REVERT: A 247 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8828 (mtm) REVERT: A 291 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: A 346 TYR cc_start: 0.8450 (m-10) cc_final: 0.8193 (m-10) REVERT: B 484 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7122 (pm20) REVERT: C 403 MET cc_start: 0.8954 (tpt) cc_final: 0.8647 (ttt) REVERT: D 59 MET cc_start: 0.9248 (ptp) cc_final: 0.8507 (ptm) REVERT: D 223 MET cc_start: 0.8497 (mtp) cc_final: 0.8267 (mtt) REVERT: E 100 TYR cc_start: 0.8815 (m-80) cc_final: 0.8371 (m-80) REVERT: F 100 TYR cc_start: 0.8769 (m-80) cc_final: 0.8420 (m-80) REVERT: F 184 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9031 (mp) REVERT: X 44 MET cc_start: 0.8438 (ttt) cc_final: 0.8087 (tpp) REVERT: X 70 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8056 (mmtm) REVERT: X 111 PHE cc_start: 0.6671 (p90) cc_final: 0.6355 (p90) outliers start: 40 outliers final: 13 residues processed: 159 average time/residue: 0.6850 time to fit residues: 122.6224 Evaluate side-chains 141 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 184 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 88 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 185 optimal weight: 0.0000 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 HIS ** D 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.066454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.056588 restraints weight = 59597.915| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.04 r_work: 0.2820 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 19492 Z= 0.230 Angle : 0.621 12.053 26408 Z= 0.314 Chirality : 0.044 0.224 2908 Planarity : 0.004 0.055 3486 Dihedral : 5.072 52.949 2819 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.78 % Allowed : 12.49 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.17), residues: 2479 helix: 1.49 (0.15), residues: 1238 sheet: -0.42 (0.52), residues: 107 loop : -0.42 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.023 0.002 TYR E 243 PHE 0.018 0.002 PHE E 101 TRP 0.015 0.002 TRP B 240 HIS 0.008 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00522 (19492) covalent geometry : angle 0.62141 (26408) hydrogen bonds : bond 0.03765 ( 961) hydrogen bonds : angle 4.48770 ( 2763) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8590 (tptt) REVERT: A 125 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8188 (mmm) REVERT: A 168 HIS cc_start: 0.8688 (t-90) cc_final: 0.8294 (t-90) REVERT: A 243 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7984 (ptt) REVERT: A 291 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: A 346 TYR cc_start: 0.8448 (m-10) cc_final: 0.8156 (m-10) REVERT: A 451 MET cc_start: 0.9106 (tpp) cc_final: 0.8873 (mmp) REVERT: B 484 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7394 (pm20) REVERT: C 403 MET cc_start: 0.8994 (tpt) cc_final: 0.8695 (ttt) REVERT: D 59 MET cc_start: 0.9291 (ptp) cc_final: 0.8689 (ptm) REVERT: D 223 MET cc_start: 0.8584 (mtp) cc_final: 0.8223 (mtt) REVERT: E 100 TYR cc_start: 0.8971 (m-80) cc_final: 0.8493 (m-80) REVERT: F 184 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9078 (mp) REVERT: X 44 MET cc_start: 0.8426 (ttt) cc_final: 0.8042 (tpp) REVERT: X 70 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8071 (mmtm) outliers start: 35 outliers final: 17 residues processed: 144 average time/residue: 0.6223 time to fit residues: 101.2431 Evaluate side-chains 136 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 184 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 14 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 34 optimal weight: 0.0000 chunk 80 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** 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 = 0.3236 r_free = 0.3236 target = 0.067795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.057851 restraints weight = 59194.688| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.06 r_work: 0.2856 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19492 Z= 0.133 Angle : 0.580 10.421 26408 Z= 0.288 Chirality : 0.042 0.228 2908 Planarity : 0.004 0.051 3486 Dihedral : 4.962 49.058 2819 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.58 % Allowed : 12.90 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.17), residues: 2479 helix: 1.59 (0.15), residues: 1239 sheet: -0.76 (0.55), residues: 93 loop : -0.37 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.019 0.001 TYR E 243 PHE 0.014 0.001 PHE F 101 TRP 0.014 0.001 TRP A 447 HIS 0.007 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00300 (19492) covalent geometry : angle 0.57985 (26408) hydrogen bonds : bond 0.03401 ( 961) hydrogen bonds : angle 4.38509 ( 2763) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8664 (tppt) REVERT: A 125 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8097 (tmm) REVERT: A 168 HIS cc_start: 0.8745 (t-90) cc_final: 0.8368 (t-90) REVERT: A 243 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7823 (ptt) REVERT: A 291 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: A 346 TYR cc_start: 0.8416 (m-10) cc_final: 0.8141 (m-10) REVERT: C 403 MET cc_start: 0.9007 (tpt) cc_final: 0.8749 (ttt) REVERT: D 59 MET cc_start: 0.9231 (ptp) cc_final: 0.8892 (ptm) REVERT: D 223 MET cc_start: 0.8666 (mtp) cc_final: 0.8346 (mtt) REVERT: E 100 TYR cc_start: 0.8851 (m-80) cc_final: 0.8344 (m-80) REVERT: E 125 GLU cc_start: 0.8215 (tt0) cc_final: 0.7797 (tt0) REVERT: F 100 TYR cc_start: 0.8756 (m-80) cc_final: 0.8413 (m-80) REVERT: F 169 MET cc_start: 0.8170 (ttm) cc_final: 0.7933 (ttm) REVERT: F 184 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9052 (mp) REVERT: X 44 MET cc_start: 0.8407 (ttt) cc_final: 0.8051 (tpp) REVERT: X 70 LYS cc_start: 0.8491 (mmtm) cc_final: 0.8161 (mmtm) outliers start: 31 outliers final: 14 residues processed: 150 average time/residue: 0.6651 time to fit residues: 113.0862 Evaluate side-chains 142 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 184 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.0670 chunk 145 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN ** E 189 GLN ** 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 = 0.3245 r_free = 0.3245 target = 0.067548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.057434 restraints weight = 59497.460| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.06 r_work: 0.2862 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19492 Z= 0.136 Angle : 0.579 11.181 26408 Z= 0.288 Chirality : 0.042 0.224 2908 Planarity : 0.004 0.052 3486 Dihedral : 4.880 47.100 2819 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.38 % Allowed : 13.67 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2479 helix: 1.65 (0.15), residues: 1249 sheet: -0.61 (0.52), residues: 107 loop : -0.36 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.017 0.001 TYR E 243 PHE 0.015 0.001 PHE F 101 TRP 0.016 0.001 TRP A 447 HIS 0.008 0.001 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00308 (19492) covalent geometry : angle 0.57902 (26408) hydrogen bonds : bond 0.03364 ( 961) hydrogen bonds : angle 4.34832 ( 2763) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8547 (tptt) REVERT: A 125 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8172 (tmm) REVERT: A 168 HIS cc_start: 0.8646 (t-90) cc_final: 0.8277 (t-90) REVERT: A 243 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7889 (ptt) REVERT: A 245 ILE cc_start: 0.9058 (mp) cc_final: 0.8781 (pp) REVERT: A 291 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: A 346 TYR cc_start: 0.8353 (m-10) cc_final: 0.8061 (m-10) REVERT: B 102 TYR cc_start: 0.8971 (p90) cc_final: 0.8742 (p90) REVERT: C 403 MET cc_start: 0.9011 (tpt) cc_final: 0.8771 (ttt) REVERT: D 59 MET cc_start: 0.9211 (ptp) cc_final: 0.8955 (ptm) REVERT: D 223 MET cc_start: 0.8576 (mtp) cc_final: 0.8255 (mtt) REVERT: E 100 TYR cc_start: 0.8803 (m-80) cc_final: 0.8344 (m-80) REVERT: E 125 GLU cc_start: 0.8210 (tt0) cc_final: 0.7798 (tt0) REVERT: F 100 TYR cc_start: 0.8782 (m-80) cc_final: 0.8506 (m-80) REVERT: F 169 MET cc_start: 0.8176 (ttm) cc_final: 0.7916 (ttm) REVERT: F 184 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9078 (mp) REVERT: X 44 MET cc_start: 0.8387 (ttt) cc_final: 0.7991 (tpp) REVERT: X 70 LYS cc_start: 0.8496 (mmtm) cc_final: 0.8165 (mmtm) outliers start: 27 outliers final: 13 residues processed: 141 average time/residue: 0.6548 time to fit residues: 104.3577 Evaluate side-chains 137 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 184 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 161 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 224 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 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 = 0.3226 r_free = 0.3226 target = 0.067354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.057439 restraints weight = 58908.979| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.03 r_work: 0.2847 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19492 Z= 0.163 Angle : 0.607 12.774 26408 Z= 0.299 Chirality : 0.043 0.225 2908 Planarity : 0.004 0.051 3486 Dihedral : 4.930 46.816 2819 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.17 % Allowed : 14.07 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2479 helix: 1.67 (0.15), residues: 1248 sheet: -0.74 (0.54), residues: 95 loop : -0.37 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.025 0.001 TYR E 243 PHE 0.016 0.001 PHE F 101 TRP 0.013 0.001 TRP A 447 HIS 0.007 0.001 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00373 (19492) covalent geometry : angle 0.60739 (26408) hydrogen bonds : bond 0.03475 ( 961) hydrogen bonds : angle 4.37856 ( 2763) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8173 (tmm) REVERT: A 168 HIS cc_start: 0.8621 (t-90) cc_final: 0.8263 (t-90) REVERT: A 243 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7880 (ptt) REVERT: A 291 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 346 TYR cc_start: 0.8425 (m-10) cc_final: 0.8125 (m-10) REVERT: B 102 TYR cc_start: 0.8949 (p90) cc_final: 0.8739 (p90) REVERT: D 59 MET cc_start: 0.9258 (ptp) cc_final: 0.8959 (ptm) REVERT: D 223 MET cc_start: 0.8526 (mtp) cc_final: 0.8193 (mtt) REVERT: E 100 TYR cc_start: 0.8843 (m-80) cc_final: 0.8367 (m-80) REVERT: E 125 GLU cc_start: 0.8205 (tt0) cc_final: 0.7789 (tt0) REVERT: F 100 TYR cc_start: 0.8821 (m-80) cc_final: 0.8531 (m-80) REVERT: F 169 MET cc_start: 0.8181 (ttm) cc_final: 0.7938 (ttm) REVERT: F 184 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9086 (mp) REVERT: X 44 MET cc_start: 0.8402 (ttt) cc_final: 0.7989 (tpp) REVERT: X 70 LYS cc_start: 0.8504 (mmtm) cc_final: 0.8175 (mmtm) REVERT: X 77 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7442 (mt0) outliers start: 23 outliers final: 15 residues processed: 139 average time/residue: 0.6872 time to fit residues: 107.6816 Evaluate side-chains 140 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 184 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 238 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 245 optimal weight: 20.0000 chunk 228 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** 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 = 0.3218 r_free = 0.3218 target = 0.067119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057216 restraints weight = 59418.657| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.03 r_work: 0.2834 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19492 Z= 0.182 Angle : 0.623 12.964 26408 Z= 0.308 Chirality : 0.043 0.226 2908 Planarity : 0.004 0.050 3486 Dihedral : 5.001 47.707 2819 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.12 % Allowed : 14.28 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2479 helix: 1.67 (0.15), residues: 1245 sheet: -0.75 (0.54), residues: 95 loop : -0.37 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.029 0.001 TYR E 243 PHE 0.016 0.001 PHE E 101 TRP 0.013 0.001 TRP D 158 HIS 0.008 0.001 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00414 (19492) covalent geometry : angle 0.62306 (26408) hydrogen bonds : bond 0.03584 ( 961) hydrogen bonds : angle 4.41747 ( 2763) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8142 (tmm) REVERT: A 168 HIS cc_start: 0.8555 (t-90) cc_final: 0.8187 (t-90) REVERT: A 243 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7922 (ptt) REVERT: A 245 ILE cc_start: 0.9060 (mp) cc_final: 0.8806 (pp) REVERT: A 291 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: A 346 TYR cc_start: 0.8410 (m-10) cc_final: 0.8102 (m-10) REVERT: B 451 MET cc_start: 0.9370 (tpp) cc_final: 0.9058 (mtp) REVERT: D 59 MET cc_start: 0.9306 (ptp) cc_final: 0.8927 (ptm) REVERT: E 100 TYR cc_start: 0.8886 (m-80) cc_final: 0.8406 (m-80) REVERT: E 125 GLU cc_start: 0.8213 (tt0) cc_final: 0.7801 (tt0) REVERT: F 100 TYR cc_start: 0.8851 (m-80) cc_final: 0.8554 (m-80) REVERT: F 184 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9080 (mp) REVERT: X 44 MET cc_start: 0.8395 (ttt) cc_final: 0.7968 (tpp) REVERT: X 70 LYS cc_start: 0.8520 (mmtm) cc_final: 0.8173 (mmtm) REVERT: X 77 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7436 (mt0) outliers start: 22 outliers final: 15 residues processed: 136 average time/residue: 0.6489 time to fit residues: 99.8699 Evaluate side-chains 141 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 184 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 82 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 157 optimal weight: 0.0870 chunk 158 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** 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 = 0.3260 r_free = 0.3260 target = 0.068172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.058012 restraints weight = 58971.864| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.06 r_work: 0.2877 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19492 Z= 0.124 Angle : 0.596 12.763 26408 Z= 0.292 Chirality : 0.042 0.216 2908 Planarity : 0.004 0.052 3486 Dihedral : 4.871 45.900 2819 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.22 % Allowed : 14.33 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: 1.05 (0.17), residues: 2479 helix: 1.77 (0.15), residues: 1243 sheet: -0.22 (0.50), residues: 119 loop : -0.39 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.033 0.001 TYR B 102 PHE 0.013 0.001 PHE F 101 TRP 0.014 0.001 TRP A 447 HIS 0.006 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00284 (19492) covalent geometry : angle 0.59554 (26408) hydrogen bonds : bond 0.03278 ( 961) hydrogen bonds : angle 4.36251 ( 2763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4075.62 seconds wall clock time: 71 minutes 13.97 seconds (4273.97 seconds total)