Starting phenix.real_space_refine on Mon Jun 16 21:25:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gf5_29978/06_2025/8gf5_29978_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gf5_29978/06_2025/8gf5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gf5_29978/06_2025/8gf5_29978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gf5_29978/06_2025/8gf5_29978.map" model { file = "/net/cci-nas-00/data/ceres_data/8gf5_29978/06_2025/8gf5_29978_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gf5_29978/06_2025/8gf5_29978_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.21, per 1000 atoms: 0.59 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: 5.19 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.90 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: 6.62 Time building geometry restraints manager: 5.70 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: 0.620 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: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.760 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:65.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.510 ------------------------------------------------------------------------------- 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 : 28.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP B 240 HIS 0.008 0.002 HIS B 454 PHE 0.025 0.002 PHE A 463 TYR 0.030 0.002 TYR A 336 ARG 0.006 0.001 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.16410 ( 961) hydrogen bonds : angle 6.44584 ( 2763) covalent geometry : bond 0.00647 (19492) covalent geometry : angle 0.74765 (26408) *********************** 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 : 2.303 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: 1.6352 time to fit residues: 357.6238 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 : 2.253 ------------------------------------------------------------------------------- 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 209 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 54 HIS F 138 GLN X 13 GLN X 36 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.068467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.058426 restraints weight = 58697.538| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.01 r_work: 0.2860 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19492 Z= 0.172 Angle : 0.630 11.218 26408 Z= 0.327 Chirality : 0.045 0.292 2908 Planarity : 0.005 0.072 3486 Dihedral : 5.540 59.919 2821 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 1.73 % Allowed : 7.39 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2479 helix: 0.98 (0.15), residues: 1254 sheet: -0.37 (0.48), residues: 118 loop : -0.75 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 447 HIS 0.006 0.001 HIS A 454 PHE 0.017 0.002 PHE X 113 TYR 0.020 0.002 TYR A 336 ARG 0.005 0.001 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 961) hydrogen bonds : angle 4.94656 ( 2763) covalent geometry : bond 0.00392 (19492) covalent geometry : angle 0.63021 (26408) *********************** 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: 34 poor density : 146 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8316 (mmm) REVERT: A 243 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7891 (ptp) REVERT: A 346 TYR cc_start: 0.8448 (m-10) cc_final: 0.8177 (m-10) REVERT: B 277 MET cc_start: 0.9310 (mmp) cc_final: 0.8876 (mmp) REVERT: B 280 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8588 (ppp) REVERT: B 316 ILE cc_start: 0.9068 (mm) cc_final: 0.8827 (mp) REVERT: C 337 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8518 (mm-30) REVERT: D 223 MET cc_start: 0.8513 (mtp) cc_final: 0.8129 (mtm) REVERT: E 100 TYR cc_start: 0.8758 (m-80) cc_final: 0.8346 (m-80) REVERT: X 29 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8108 (pttt) REVERT: X 100 LYS cc_start: 0.9194 (mtpp) cc_final: 0.8878 (ptpp) REVERT: X 111 PHE cc_start: 0.6434 (p90) cc_final: 0.6229 (p90) outliers start: 34 outliers final: 6 residues processed: 163 average time/residue: 1.7455 time to fit residues: 319.2208 Evaluate side-chains 126 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 2.458 ------------------------------------------------------------------------------- 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 243 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain F residue 123 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 9 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 330 GLN ** 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 191 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN X 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.066228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.055946 restraints weight = 59557.787| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.02 r_work: 0.2811 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19492 Z= 0.207 Angle : 0.607 11.128 26408 Z= 0.314 Chirality : 0.044 0.251 2908 Planarity : 0.005 0.067 3486 Dihedral : 5.328 57.451 2819 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.19 % Allowed : 9.94 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2479 helix: 1.14 (0.15), residues: 1253 sheet: -0.60 (0.49), residues: 113 loop : -0.59 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 447 HIS 0.006 0.001 HIS B 454 PHE 0.018 0.002 PHE F 101 TYR 0.016 0.002 TYR A 336 ARG 0.004 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 961) hydrogen bonds : angle 4.70425 ( 2763) covalent geometry : bond 0.00469 (19492) covalent geometry : angle 0.60689 (26408) *********************** 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 175 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8490 (tptt) REVERT: A 125 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: A 243 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7928 (ppp) REVERT: A 291 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: A 346 TYR cc_start: 0.8401 (m-10) cc_final: 0.8126 (m-10) REVERT: C 403 MET cc_start: 0.8990 (tpt) cc_final: 0.8585 (ttt) REVERT: D 142 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8552 (ptm) REVERT: D 191 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8057 (t0) REVERT: E 100 TYR cc_start: 0.8914 (m-80) cc_final: 0.8425 (m-80) REVERT: F 184 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9083 (mp) REVERT: F 185 MET cc_start: 0.9274 (ttt) cc_final: 0.8817 (tpp) REVERT: X 29 LYS cc_start: 0.8471 (mtmm) cc_final: 0.8085 (mtmm) REVERT: X 70 LYS cc_start: 0.8419 (mmtm) cc_final: 0.7970 (mmtm) REVERT: X 111 PHE cc_start: 0.6533 (p90) cc_final: 0.6328 (p90) outliers start: 43 outliers final: 10 residues processed: 158 average time/residue: 1.6468 time to fit residues: 294.5446 Evaluate side-chains 140 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 143 ILE 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 D residue 142 MET 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 Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain X residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 93 optimal weight: 9.9990 chunk 231 optimal weight: 0.7980 chunk 247 optimal weight: 9.9990 chunk 194 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 193 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.068512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058477 restraints weight = 58703.474| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.08 r_work: 0.2869 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19492 Z= 0.116 Angle : 0.555 10.414 26408 Z= 0.283 Chirality : 0.042 0.239 2908 Planarity : 0.004 0.061 3486 Dihedral : 5.064 53.366 2819 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.84 % Allowed : 11.42 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2479 helix: 1.38 (0.15), residues: 1246 sheet: -0.74 (0.50), residues: 110 loop : -0.48 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 447 HIS 0.007 0.001 HIS B 454 PHE 0.014 0.001 PHE F 101 TYR 0.012 0.001 TYR C 331 ARG 0.004 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 961) hydrogen bonds : angle 4.49674 ( 2763) covalent geometry : bond 0.00258 (19492) covalent geometry : angle 0.55487 (26408) *********************** 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 178 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8262 (mmm) REVERT: A 168 HIS cc_start: 0.8711 (t-90) cc_final: 0.8335 (t-90) REVERT: A 243 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7960 (ptt) REVERT: A 280 MET cc_start: 0.7446 (pmm) cc_final: 0.6636 (pmm) REVERT: A 346 TYR cc_start: 0.8427 (m-10) cc_final: 0.8190 (m-10) REVERT: B 102 TYR cc_start: 0.9225 (p90) cc_final: 0.9020 (p90) REVERT: B 451 MET cc_start: 0.9340 (tpp) cc_final: 0.9105 (mtp) REVERT: C 403 MET cc_start: 0.8955 (tpt) cc_final: 0.8652 (ttt) REVERT: D 223 MET cc_start: 0.8300 (mtp) cc_final: 0.7846 (mtm) REVERT: E 100 TYR cc_start: 0.8751 (m-80) cc_final: 0.8259 (m-80) REVERT: F 100 TYR cc_start: 0.8702 (m-80) cc_final: 0.8370 (m-80) REVERT: F 184 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9022 (mp) REVERT: X 44 MET cc_start: 0.8276 (ttt) cc_final: 0.7987 (tpp) REVERT: X 70 LYS cc_start: 0.8514 (mmtm) cc_final: 0.8090 (mmtm) REVERT: X 100 LYS cc_start: 0.9174 (ptpp) cc_final: 0.8886 (pttm) REVERT: X 111 PHE cc_start: 0.6564 (p90) cc_final: 0.6300 (p90) outliers start: 36 outliers final: 8 residues processed: 164 average time/residue: 1.4239 time to fit residues: 263.7324 Evaluate side-chains 131 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 2.205 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 107 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 182 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 103 optimal weight: 0.0050 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 246 optimal weight: 0.0000 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.070163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.060229 restraints weight = 58544.958| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.09 r_work: 0.2909 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19492 Z= 0.102 Angle : 0.547 9.754 26408 Z= 0.276 Chirality : 0.041 0.193 2908 Planarity : 0.004 0.057 3486 Dihedral : 4.815 51.018 2819 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.78 % Allowed : 12.34 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2479 helix: 1.59 (0.15), residues: 1237 sheet: -0.22 (0.49), residues: 123 loop : -0.40 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 447 HIS 0.007 0.001 HIS B 454 PHE 0.013 0.001 PHE F 101 TYR 0.012 0.001 TYR C 331 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 961) hydrogen bonds : angle 4.36060 ( 2763) covalent geometry : bond 0.00223 (19492) covalent geometry : angle 0.54747 (26408) *********************** 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 171 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8172 (tmm) REVERT: A 168 HIS cc_start: 0.8717 (t-90) cc_final: 0.8359 (t-90) REVERT: A 243 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7815 (ptt) REVERT: A 291 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: A 346 TYR cc_start: 0.8367 (m-10) cc_final: 0.8154 (m-10) REVERT: B 205 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: B 451 MET cc_start: 0.9335 (tpp) cc_final: 0.9053 (mtp) REVERT: C 403 MET cc_start: 0.8947 (tpt) cc_final: 0.8667 (ttt) REVERT: D 223 MET cc_start: 0.8111 (mtp) cc_final: 0.7896 (mtm) REVERT: E 100 TYR cc_start: 0.8673 (m-80) cc_final: 0.8257 (m-80) REVERT: E 125 GLU cc_start: 0.8118 (tt0) cc_final: 0.7663 (tt0) REVERT: F 100 TYR cc_start: 0.8650 (m-80) cc_final: 0.8354 (m-80) REVERT: F 169 MET cc_start: 0.8075 (ttm) cc_final: 0.7822 (ttm) REVERT: F 172 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7261 (ttp) REVERT: F 184 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9051 (mp) REVERT: X 44 MET cc_start: 0.8441 (ttt) cc_final: 0.8087 (tpp) REVERT: X 70 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8130 (mmtm) REVERT: X 111 PHE cc_start: 0.6651 (p90) cc_final: 0.6330 (p90) outliers start: 35 outliers final: 9 residues processed: 163 average time/residue: 1.3699 time to fit residues: 251.9725 Evaluate side-chains 136 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 2.249 ------------------------------------------------------------------------------- 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 243 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain B residue 205 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 172 MET 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 25 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** ** B 469 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 377 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.065908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.055945 restraints weight = 60294.782| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.06 r_work: 0.2797 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 19492 Z= 0.249 Angle : 0.639 11.463 26408 Z= 0.323 Chirality : 0.044 0.222 2908 Planarity : 0.004 0.056 3486 Dihedral : 5.095 52.427 2819 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.19 % Allowed : 12.34 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.17), residues: 2479 helix: 1.48 (0.15), residues: 1240 sheet: -0.28 (0.52), residues: 107 loop : -0.42 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 158 HIS 0.007 0.001 HIS B 454 PHE 0.019 0.002 PHE E 101 TYR 0.030 0.002 TYR B 102 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 961) hydrogen bonds : angle 4.49920 ( 2763) covalent geometry : bond 0.00557 (19492) covalent geometry : angle 0.63926 (26408) *********************** 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 163 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8518 (tptt) REVERT: A 125 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8229 (mmm) REVERT: A 168 HIS cc_start: 0.8668 (t-90) cc_final: 0.8295 (t-90) REVERT: A 291 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: A 346 TYR cc_start: 0.8398 (m-10) cc_final: 0.8156 (m-10) REVERT: A 451 MET cc_start: 0.9106 (tpp) cc_final: 0.8893 (mmp) REVERT: B 205 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: B 247 MET cc_start: 0.8506 (tpp) cc_final: 0.8278 (tpp) REVERT: C 403 MET cc_start: 0.9062 (tpt) cc_final: 0.8762 (ttt) REVERT: D 223 MET cc_start: 0.8505 (mtp) cc_final: 0.8247 (mtm) REVERT: E 100 TYR cc_start: 0.8997 (m-80) cc_final: 0.8529 (m-80) REVERT: F 184 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9103 (mp) REVERT: F 185 MET cc_start: 0.9135 (ttt) cc_final: 0.8620 (tpp) REVERT: X 44 MET cc_start: 0.8419 (ttt) cc_final: 0.8007 (tpp) REVERT: X 70 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8221 (mmtm) REVERT: X 100 LYS cc_start: 0.9222 (ptmm) cc_final: 0.8972 (ptpp) outliers start: 43 outliers final: 16 residues processed: 148 average time/residue: 1.4011 time to fit residues: 234.1896 Evaluate side-chains 134 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 2.115 ------------------------------------------------------------------------------- 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 143 ILE Chi-restraints excluded: chain A residue 255 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 205 GLU 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 Chi-restraints excluded: chain X residue 72 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 145 optimal weight: 7.9990 chunk 204 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.067470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.057477 restraints weight = 59063.519| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.05 r_work: 0.2846 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2963 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= 0.145 Angle : 0.577 10.806 26408 Z= 0.290 Chirality : 0.042 0.226 2908 Planarity : 0.004 0.051 3486 Dihedral : 4.942 47.853 2819 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.84 % Allowed : 13.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2479 helix: 1.62 (0.15), residues: 1237 sheet: -0.45 (0.52), residues: 107 loop : -0.39 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 447 HIS 0.007 0.001 HIS B 454 PHE 0.015 0.001 PHE F 101 TYR 0.026 0.001 TYR B 102 ARG 0.002 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 961) hydrogen bonds : angle 4.39317 ( 2763) covalent geometry : bond 0.00330 (19492) covalent geometry : angle 0.57697 (26408) *********************** 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 160 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8507 (tptt) REVERT: A 125 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8168 (tmm) REVERT: A 168 HIS cc_start: 0.8608 (t-90) cc_final: 0.8260 (t-90) REVERT: A 243 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7929 (ptt) REVERT: A 291 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: A 346 TYR cc_start: 0.8397 (m-10) cc_final: 0.8189 (m-10) REVERT: B 451 MET cc_start: 0.9353 (tpp) cc_final: 0.9043 (mtp) REVERT: C 403 MET cc_start: 0.8995 (tpt) cc_final: 0.8761 (ttt) REVERT: D 59 MET cc_start: 0.9171 (ptp) cc_final: 0.8942 (ptm) REVERT: D 223 MET cc_start: 0.8344 (mtp) cc_final: 0.7940 (mtm) REVERT: E 100 TYR cc_start: 0.8854 (m-80) cc_final: 0.8364 (m-80) REVERT: F 100 TYR cc_start: 0.8798 (m-80) cc_final: 0.8519 (m-80) REVERT: F 172 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7709 (ttt) REVERT: F 184 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9071 (mp) REVERT: F 185 MET cc_start: 0.9083 (ttt) cc_final: 0.8555 (tpp) REVERT: X 44 MET cc_start: 0.8387 (ttt) cc_final: 0.8017 (tpp) REVERT: X 70 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8179 (mmtm) REVERT: X 100 LYS cc_start: 0.9223 (ptmm) cc_final: 0.8986 (ptpp) outliers start: 36 outliers final: 17 residues processed: 148 average time/residue: 1.3393 time to fit residues: 225.1748 Evaluate side-chains 143 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 2.313 ------------------------------------------------------------------------------- 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 143 ILE 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 325 CYS 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 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 F residue 123 ILE Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain X residue 72 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 79 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** ** 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 = 0.3215 r_free = 0.3215 target = 0.066935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.056768 restraints weight = 59257.283| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.09 r_work: 0.2826 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19492 Z= 0.172 Angle : 0.593 11.996 26408 Z= 0.297 Chirality : 0.043 0.232 2908 Planarity : 0.004 0.050 3486 Dihedral : 4.966 47.913 2819 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.99 % Allowed : 13.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2479 helix: 1.61 (0.15), residues: 1243 sheet: -0.48 (0.52), residues: 107 loop : -0.36 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 447 HIS 0.007 0.001 HIS B 454 PHE 0.016 0.001 PHE F 101 TYR 0.027 0.001 TYR B 102 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 961) hydrogen bonds : angle 4.39588 ( 2763) covalent geometry : bond 0.00390 (19492) covalent geometry : angle 0.59267 (26408) *********************** 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 159 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8492 (tptt) REVERT: A 125 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8221 (tmm) REVERT: A 168 HIS cc_start: 0.8546 (t-90) cc_final: 0.8195 (t-90) REVERT: A 243 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7949 (ptt) REVERT: A 291 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: A 346 TYR cc_start: 0.8400 (m-10) cc_final: 0.8131 (m-10) REVERT: B 205 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: B 451 MET cc_start: 0.9402 (tpp) cc_final: 0.9058 (mtp) REVERT: D 59 MET cc_start: 0.9203 (ptp) cc_final: 0.8975 (ptm) REVERT: D 223 MET cc_start: 0.8380 (mtp) cc_final: 0.8126 (mtm) REVERT: E 100 TYR cc_start: 0.8879 (m-80) cc_final: 0.8428 (m-80) REVERT: F 100 TYR cc_start: 0.8851 (m-80) cc_final: 0.8578 (m-80) REVERT: F 169 MET cc_start: 0.8175 (ttm) cc_final: 0.7934 (ttm) REVERT: F 172 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7731 (ttt) REVERT: F 184 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9084 (mp) REVERT: X 44 MET cc_start: 0.8425 (ttt) cc_final: 0.8013 (tpp) REVERT: X 70 LYS cc_start: 0.8510 (mmtm) cc_final: 0.8192 (mmtm) REVERT: X 74 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8822 (pp) REVERT: X 100 LYS cc_start: 0.9214 (ptmm) cc_final: 0.8971 (ptpp) outliers start: 39 outliers final: 17 residues processed: 147 average time/residue: 1.6203 time to fit residues: 270.0918 Evaluate side-chains 141 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 2.137 ------------------------------------------------------------------------------- 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 143 ILE 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 325 CYS Chi-restraints excluded: chain A residue 389 VAL 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 205 GLU 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 172 MET Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 117 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.067597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.057555 restraints weight = 59286.607| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.07 r_work: 0.2848 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19492 Z= 0.145 Angle : 0.595 12.693 26408 Z= 0.294 Chirality : 0.042 0.228 2908 Planarity : 0.004 0.050 3486 Dihedral : 4.927 47.353 2819 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.73 % Allowed : 13.97 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2479 helix: 1.68 (0.15), residues: 1243 sheet: -0.43 (0.52), residues: 109 loop : -0.35 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 447 HIS 0.007 0.001 HIS B 454 PHE 0.015 0.001 PHE F 101 TYR 0.031 0.001 TYR B 102 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 961) hydrogen bonds : angle 4.38054 ( 2763) covalent geometry : bond 0.00331 (19492) covalent geometry : angle 0.59475 (26408) *********************** 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 154 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 2.715 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8513 (tptt) REVERT: A 125 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8201 (tmm) REVERT: A 168 HIS cc_start: 0.8534 (t-90) cc_final: 0.8196 (t-90) REVERT: A 243 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7939 (ptt) REVERT: A 245 ILE cc_start: 0.9050 (mp) cc_final: 0.8798 (pp) REVERT: A 291 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: A 346 TYR cc_start: 0.8403 (m-10) cc_final: 0.8180 (m-10) REVERT: B 205 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: B 451 MET cc_start: 0.9391 (tpp) cc_final: 0.9051 (mtp) REVERT: D 223 MET cc_start: 0.8375 (mtp) cc_final: 0.8125 (mtm) REVERT: E 100 TYR cc_start: 0.8824 (m-80) cc_final: 0.8301 (m-80) REVERT: F 100 TYR cc_start: 0.8819 (m-80) cc_final: 0.8555 (m-80) REVERT: F 169 MET cc_start: 0.8149 (ttm) cc_final: 0.7914 (ttm) REVERT: F 172 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7744 (ttt) REVERT: F 184 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9073 (mp) REVERT: F 185 MET cc_start: 0.9102 (ttt) cc_final: 0.8608 (tpp) REVERT: X 44 MET cc_start: 0.8412 (ttt) cc_final: 0.8005 (tpp) REVERT: X 70 LYS cc_start: 0.8496 (mmtm) cc_final: 0.8174 (mmtm) REVERT: X 77 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7378 (mt0) outliers start: 34 outliers final: 17 residues processed: 145 average time/residue: 1.6816 time to fit residues: 275.9996 Evaluate side-chains 143 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 2.865 ------------------------------------------------------------------------------- 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 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 389 VAL 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 205 GLU 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 86 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain X residue 72 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 47 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 56 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 133 optimal weight: 0.2980 chunk 124 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** B 501 ASN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.069550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.059520 restraints weight = 58446.010| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.07 r_work: 0.2898 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19492 Z= 0.108 Angle : 0.587 12.626 26408 Z= 0.289 Chirality : 0.041 0.214 2908 Planarity : 0.004 0.052 3486 Dihedral : 4.818 44.838 2819 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.17 % Allowed : 14.48 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2479 helix: 1.78 (0.15), residues: 1234 sheet: -0.07 (0.51), residues: 119 loop : -0.33 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 447 HIS 0.007 0.001 HIS B 454 PHE 0.012 0.001 PHE F 101 TYR 0.022 0.001 TYR E 104 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 961) hydrogen bonds : angle 4.34341 ( 2763) covalent geometry : bond 0.00242 (19492) covalent geometry : angle 0.58737 (26408) ********************** 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 155 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 2.399 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8952 (mmm) cc_final: 0.8709 (mtp) REVERT: A 72 MET cc_start: 0.8187 (mtp) cc_final: 0.7773 (mmt) REVERT: A 125 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8224 (tmm) REVERT: A 168 HIS cc_start: 0.8551 (t-90) cc_final: 0.8218 (t-90) REVERT: A 243 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7892 (ptt) REVERT: A 291 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 346 TYR cc_start: 0.8376 (m-10) cc_final: 0.8135 (m-10) REVERT: B 205 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: B 451 MET cc_start: 0.9390 (tpp) cc_final: 0.9041 (mtp) REVERT: C 337 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8489 (mm-30) REVERT: D 223 MET cc_start: 0.8303 (mtp) cc_final: 0.8074 (mtm) REVERT: E 22 MET cc_start: 0.8842 (mtm) cc_final: 0.8543 (mtm) REVERT: E 125 GLU cc_start: 0.8161 (tt0) cc_final: 0.7731 (tt0) REVERT: E 144 THR cc_start: 0.8958 (m) cc_final: 0.8725 (p) REVERT: E 202 LYS cc_start: 0.8970 (tmmt) cc_final: 0.8646 (tptp) REVERT: F 100 TYR cc_start: 0.8720 (m-80) cc_final: 0.8441 (m-80) REVERT: F 169 MET cc_start: 0.8156 (ttm) cc_final: 0.7876 (ttm) REVERT: F 184 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9069 (mp) REVERT: X 44 MET cc_start: 0.8358 (ttt) cc_final: 0.7976 (tpp) REVERT: X 70 LYS cc_start: 0.8424 (mmtm) cc_final: 0.8157 (mmtm) REVERT: X 77 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7795 (mt0) outliers start: 23 outliers final: 14 residues processed: 148 average time/residue: 1.6928 time to fit residues: 286.7864 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 : 2.367 ------------------------------------------------------------------------------- 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 243 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 205 GLU 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 86 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 194 optimal weight: 0.0170 chunk 137 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.069729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.059579 restraints weight = 58558.676| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.10 r_work: 0.2892 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3432 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= 0.113 Angle : 0.590 13.763 26408 Z= 0.290 Chirality : 0.042 0.210 2908 Planarity : 0.004 0.054 3486 Dihedral : 4.778 44.430 2819 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.53 % Allowed : 14.43 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2479 helix: 1.81 (0.15), residues: 1244 sheet: -0.03 (0.51), residues: 119 loop : -0.30 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 447 HIS 0.007 0.001 HIS B 454 PHE 0.012 0.001 PHE E 101 TYR 0.021 0.001 TYR E 104 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 961) hydrogen bonds : angle 4.33568 ( 2763) covalent geometry : bond 0.00256 (19492) covalent geometry : angle 0.59000 (26408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9832.85 seconds wall clock time: 177 minutes 6.15 seconds (10626.15 seconds total)