Starting phenix.real_space_refine on Mon May 19 22:47:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gf5_29978/05_2025/8gf5_29978_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gf5_29978/05_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_29978/05_2025/8gf5_29978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gf5_29978/05_2025/8gf5_29978.map" model { file = "/net/cci-nas-00/data/ceres_data/8gf5_29978/05_2025/8gf5_29978_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gf5_29978/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.52, per 1000 atoms: 0.55 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: 4.67 Conformation dependent library (CDL) restraints added in 2.4 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: 2.16 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: 6.14 Time building geometry restraints manager: 5.27 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: 0.570 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 40.970 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.600 ------------------------------------------------------------------------------- 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 : 1.996 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: 1.4727 time to fit residues: 322.6598 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 : 1.972 ------------------------------------------------------------------------------- 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 = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.058427 restraints weight = 58697.445| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.01 r_work: 0.2859 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 11.219 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 4.94655 ( 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 : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8313 (mmm) REVERT: A 243 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7887 (ptp) REVERT: A 346 TYR cc_start: 0.8459 (m-10) cc_final: 0.8189 (m-10) REVERT: B 277 MET cc_start: 0.9323 (mmp) cc_final: 0.8888 (mmp) REVERT: B 280 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8588 (ppp) REVERT: B 316 ILE cc_start: 0.9070 (mm) cc_final: 0.8828 (mp) REVERT: C 337 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8513 (mm-30) REVERT: D 223 MET cc_start: 0.8519 (mtp) cc_final: 0.8138 (mtm) REVERT: E 100 TYR cc_start: 0.8758 (m-80) cc_final: 0.8345 (m-80) REVERT: X 29 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8098 (pttt) REVERT: X 100 LYS cc_start: 0.9199 (mtpp) cc_final: 0.8875 (ptpp) REVERT: X 111 PHE cc_start: 0.6434 (p90) cc_final: 0.6225 (p90) outliers start: 34 outliers final: 6 residues processed: 163 average time/residue: 1.4095 time to fit residues: 258.3291 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 : 2.190 ------------------------------------------------------------------------------- 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: 1.9990 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 56 optimal weight: 0.0770 chunk 125 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN X 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.069186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.058840 restraints weight = 58170.187| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.10 r_work: 0.2876 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19492 Z= 0.125 Angle : 0.562 10.392 26408 Z= 0.289 Chirality : 0.042 0.245 2908 Planarity : 0.004 0.063 3486 Dihedral : 5.134 58.780 2819 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.89 % Allowed : 10.15 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.17), residues: 2479 helix: 1.22 (0.15), residues: 1259 sheet: -0.41 (0.46), residues: 129 loop : -0.56 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 447 HIS 0.006 0.001 HIS B 454 PHE 0.015 0.001 PHE F 101 TYR 0.014 0.001 TYR D 365 ARG 0.004 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 961) hydrogen bonds : angle 4.61849 ( 2763) covalent geometry : bond 0.00281 (19492) covalent geometry : angle 0.56163 (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 180 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8207 (mmm) REVERT: A 168 HIS cc_start: 0.8761 (t-90) cc_final: 0.8373 (t-90) REVERT: A 291 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: A 346 TYR cc_start: 0.8390 (m-10) cc_final: 0.8177 (m-10) REVERT: B 316 ILE cc_start: 0.9089 (mm) cc_final: 0.8886 (mp) REVERT: C 403 MET cc_start: 0.8930 (tpt) cc_final: 0.8506 (ttt) REVERT: D 191 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7659 (p0) REVERT: D 222 GLU cc_start: 0.8664 (tp30) cc_final: 0.8443 (tp30) REVERT: D 223 MET cc_start: 0.8478 (mtp) cc_final: 0.8253 (mtm) REVERT: E 100 TYR cc_start: 0.8726 (m-80) cc_final: 0.8239 (m-80) REVERT: F 28 LYS cc_start: 0.8901 (tttm) cc_final: 0.8673 (tptp) REVERT: F 100 TYR cc_start: 0.8716 (m-80) cc_final: 0.8329 (m-80) REVERT: F 184 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9058 (mp) REVERT: X 29 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8076 (mtmm) REVERT: X 38 ASP cc_start: 0.8411 (p0) cc_final: 0.8195 (p0) REVERT: X 70 LYS cc_start: 0.8453 (mmtm) cc_final: 0.7994 (mmtm) REVERT: X 111 PHE cc_start: 0.6456 (p90) cc_final: 0.6156 (p90) outliers start: 37 outliers final: 7 residues processed: 166 average time/residue: 1.2918 time to fit residues: 242.5425 Evaluate side-chains 139 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 192 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 93 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 chunk 247 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** 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** X 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.065733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.055474 restraints weight = 59815.767| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.08 r_work: 0.2795 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 19492 Z= 0.252 Angle : 0.636 11.210 26408 Z= 0.327 Chirality : 0.045 0.244 2908 Planarity : 0.005 0.063 3486 Dihedral : 5.271 56.648 2819 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.94 % Allowed : 11.47 % Favored : 86.59 % 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: 0.56 (0.17), residues: 2479 helix: 1.29 (0.15), residues: 1244 sheet: -0.61 (0.51), residues: 108 loop : -0.52 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 158 HIS 0.007 0.001 HIS B 504 PHE 0.019 0.002 PHE E 101 TYR 0.026 0.002 TYR B 102 ARG 0.004 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 961) hydrogen bonds : angle 4.60747 ( 2763) covalent geometry : bond 0.00569 (19492) covalent geometry : angle 0.63606 (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 161 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8504 (tptt) REVERT: A 125 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8217 (mmm) REVERT: A 168 HIS cc_start: 0.8685 (t-90) cc_final: 0.8295 (t-90) REVERT: A 280 MET cc_start: 0.7527 (pmm) cc_final: 0.7077 (pmm) REVERT: A 346 TYR cc_start: 0.8487 (m-10) cc_final: 0.8244 (m-10) REVERT: B 83 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6531 (pp) REVERT: B 277 MET cc_start: 0.9303 (mmp) cc_final: 0.8915 (mmp) REVERT: B 484 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: C 403 MET cc_start: 0.9030 (tpt) cc_final: 0.8578 (ttt) REVERT: D 223 MET cc_start: 0.8611 (mtp) cc_final: 0.8403 (mtp) REVERT: E 100 TYR cc_start: 0.8976 (m-80) cc_final: 0.8522 (m-80) REVERT: F 184 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9058 (mp) REVERT: X 13 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7275 (mt0) REVERT: X 44 MET cc_start: 0.8312 (ttt) cc_final: 0.8046 (tpp) REVERT: X 70 LYS cc_start: 0.8515 (mmtm) cc_final: 0.8084 (mmtm) outliers start: 38 outliers final: 10 residues processed: 148 average time/residue: 1.3385 time to fit residues: 223.8585 Evaluate side-chains 126 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.943 ------------------------------------------------------------------------------- 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 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 484 GLU 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 Chi-restraints excluded: chain X residue 13 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 107 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.067421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.057312 restraints weight = 59360.045| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.09 r_work: 0.2841 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19492 Z= 0.140 Angle : 0.570 10.714 26408 Z= 0.290 Chirality : 0.042 0.239 2908 Planarity : 0.004 0.059 3486 Dihedral : 5.078 52.160 2819 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.84 % Allowed : 11.93 % Favored : 86.23 % 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: 0.72 (0.17), residues: 2479 helix: 1.46 (0.15), residues: 1240 sheet: -0.59 (0.52), residues: 107 loop : -0.48 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 447 HIS 0.007 0.001 HIS B 454 PHE 0.015 0.001 PHE F 101 TYR 0.022 0.001 TYR B 102 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 961) hydrogen bonds : angle 4.46528 ( 2763) covalent geometry : bond 0.00318 (19492) covalent geometry : angle 0.57023 (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 164 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8569 (tptt) REVERT: A 125 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: A 168 HIS cc_start: 0.8749 (t-90) cc_final: 0.8376 (t-90) REVERT: A 243 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7981 (ptt) REVERT: A 280 MET cc_start: 0.7528 (pmm) cc_final: 0.7015 (pmm) REVERT: A 291 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: A 346 TYR cc_start: 0.8423 (m-10) cc_final: 0.8196 (m-10) REVERT: C 403 MET cc_start: 0.9001 (tpt) cc_final: 0.8705 (ttt) REVERT: E 100 TYR cc_start: 0.8847 (m-80) cc_final: 0.8402 (m-80) REVERT: F 100 TYR cc_start: 0.8757 (m-80) cc_final: 0.8444 (m-80) REVERT: F 169 MET cc_start: 0.8183 (ttm) cc_final: 0.7954 (ttm) REVERT: F 184 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9043 (mp) REVERT: X 44 MET cc_start: 0.8380 (ttt) cc_final: 0.7993 (tpp) REVERT: X 70 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8096 (mmtm) REVERT: X 100 LYS cc_start: 0.9204 (ptpp) cc_final: 0.8899 (pttm) outliers start: 36 outliers final: 13 residues processed: 152 average time/residue: 1.2925 time to fit residues: 222.4333 Evaluate side-chains 136 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.948 ------------------------------------------------------------------------------- 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 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 184 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 25 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** F 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.067272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.057057 restraints weight = 59537.796| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.12 r_work: 0.2834 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19492 Z= 0.154 Angle : 0.577 10.602 26408 Z= 0.291 Chirality : 0.042 0.234 2908 Planarity : 0.004 0.057 3486 Dihedral : 5.023 50.807 2819 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.78 % Allowed : 13.00 % Favored : 85.21 % 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: 0.85 (0.17), residues: 2479 helix: 1.57 (0.15), residues: 1238 sheet: -0.49 (0.52), residues: 107 loop : -0.42 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 447 HIS 0.007 0.001 HIS B 454 PHE 0.016 0.001 PHE F 101 TYR 0.020 0.001 TYR B 102 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 961) hydrogen bonds : angle 4.41593 ( 2763) covalent geometry : bond 0.00350 (19492) covalent geometry : angle 0.57699 (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 157 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8553 (tptt) REVERT: A 125 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8192 (mmm) REVERT: A 168 HIS cc_start: 0.8659 (t-90) cc_final: 0.8294 (t-90) REVERT: A 243 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7882 (ptt) REVERT: A 247 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8853 (mtm) REVERT: A 291 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: A 346 TYR cc_start: 0.8379 (m-10) cc_final: 0.8151 (m-10) REVERT: C 403 MET cc_start: 0.9031 (tpt) cc_final: 0.8745 (ttt) REVERT: D 223 MET cc_start: 0.8336 (mtp) cc_final: 0.7847 (mtm) REVERT: E 100 TYR cc_start: 0.8878 (m-80) cc_final: 0.8367 (m-80) REVERT: F 100 TYR cc_start: 0.8810 (m-80) cc_final: 0.8503 (m-80) REVERT: F 169 MET cc_start: 0.8171 (ttm) cc_final: 0.7945 (ttm) REVERT: F 184 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9062 (mp) REVERT: F 185 MET cc_start: 0.9114 (ttt) cc_final: 0.8573 (tpp) REVERT: X 44 MET cc_start: 0.8373 (ttt) cc_final: 0.7979 (tpp) REVERT: X 70 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8076 (mmtm) outliers start: 35 outliers final: 16 residues processed: 145 average time/residue: 1.2908 time to fit residues: 212.9353 Evaluate side-chains 137 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 184 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 145 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 157 optimal weight: 0.0770 overall best weight: 2.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.066810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.056844 restraints weight = 59350.200| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.03 r_work: 0.2830 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19492 Z= 0.170 Angle : 0.587 11.284 26408 Z= 0.294 Chirality : 0.043 0.233 2908 Planarity : 0.004 0.055 3486 Dihedral : 5.015 48.725 2819 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.04 % Allowed : 13.11 % Favored : 84.85 % 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: 0.86 (0.17), residues: 2479 helix: 1.57 (0.15), residues: 1243 sheet: -0.51 (0.52), residues: 107 loop : -0.40 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 447 HIS 0.007 0.001 HIS B 454 PHE 0.016 0.001 PHE F 101 TYR 0.019 0.001 TYR B 102 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 961) hydrogen bonds : angle 4.41273 ( 2763) covalent geometry : bond 0.00387 (19492) covalent geometry : angle 0.58664 (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 159 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8570 (tptt) REVERT: A 125 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8197 (mmm) REVERT: A 168 HIS cc_start: 0.8624 (t-90) cc_final: 0.8279 (t-90) REVERT: A 243 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7862 (ptt) REVERT: A 291 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: A 346 TYR cc_start: 0.8421 (m-10) cc_final: 0.8216 (m-10) REVERT: C 403 MET cc_start: 0.9027 (tpt) cc_final: 0.8773 (ttt) REVERT: D 165 MET cc_start: 0.8221 (mpt) cc_final: 0.7998 (mpp) REVERT: D 223 MET cc_start: 0.8370 (mtp) cc_final: 0.7858 (mtm) REVERT: E 100 TYR cc_start: 0.8903 (m-80) cc_final: 0.8450 (m-80) REVERT: F 100 TYR cc_start: 0.8843 (m-80) cc_final: 0.8570 (m-80) REVERT: F 169 MET cc_start: 0.8164 (ttm) cc_final: 0.7944 (ttm) REVERT: F 172 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7706 (ttt) REVERT: F 184 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9085 (mp) REVERT: X 44 MET cc_start: 0.8386 (ttt) cc_final: 0.7973 (tpp) REVERT: X 70 LYS cc_start: 0.8509 (mmtm) cc_final: 0.8112 (mmtm) outliers start: 40 outliers final: 15 residues processed: 144 average time/residue: 1.2588 time to fit residues: 206.5692 Evaluate side-chains 138 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 79 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.068342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.058363 restraints weight = 58743.027| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.07 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: 0.8476 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19492 Z= 0.119 Angle : 0.566 12.093 26408 Z= 0.281 Chirality : 0.042 0.225 2908 Planarity : 0.004 0.052 3486 Dihedral : 4.870 46.220 2819 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.53 % Allowed : 13.56 % Favored : 84.91 % 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: 1.00 (0.17), residues: 2479 helix: 1.71 (0.15), residues: 1237 sheet: -0.53 (0.52), residues: 107 loop : -0.35 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 447 HIS 0.007 0.001 HIS B 454 PHE 0.014 0.001 PHE F 101 TYR 0.017 0.001 TYR B 102 ARG 0.002 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 961) hydrogen bonds : angle 4.35463 ( 2763) covalent geometry : bond 0.00269 (19492) covalent geometry : angle 0.56570 (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 156 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8534 (tptt) REVERT: A 125 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8262 (tmm) REVERT: A 168 HIS cc_start: 0.8568 (t-90) cc_final: 0.8228 (t-90) REVERT: A 243 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7895 (ptt) REVERT: A 245 ILE cc_start: 0.9036 (mp) cc_final: 0.8750 (pp) REVERT: A 291 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: A 346 TYR cc_start: 0.8360 (m-10) cc_final: 0.8153 (m-10) REVERT: B 451 MET cc_start: 0.9391 (tpp) cc_final: 0.9115 (mtp) REVERT: D 223 MET cc_start: 0.8251 (mtp) cc_final: 0.7908 (mtm) REVERT: E 100 TYR cc_start: 0.8788 (m-80) cc_final: 0.8376 (m-80) REVERT: E 125 GLU cc_start: 0.8189 (tt0) cc_final: 0.7778 (tt0) REVERT: F 100 TYR cc_start: 0.8773 (m-80) cc_final: 0.8506 (m-80) REVERT: F 184 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9102 (mp) REVERT: X 44 MET cc_start: 0.8378 (ttt) cc_final: 0.8011 (tpp) outliers start: 30 outliers final: 14 residues processed: 143 average time/residue: 1.2931 time to fit residues: 209.5562 Evaluate side-chains 137 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.948 ------------------------------------------------------------------------------- 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 467 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 184 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 117 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 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: 9.9990 chunk 114 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** F 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.068017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.057836 restraints weight = 59463.979| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.06 r_work: 0.2876 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19492 Z= 0.121 Angle : 0.576 12.455 26408 Z= 0.285 Chirality : 0.042 0.219 2908 Planarity : 0.004 0.053 3486 Dihedral : 4.839 45.091 2819 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.58 % Allowed : 13.77 % Favored : 84.65 % 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: 1.04 (0.17), residues: 2479 helix: 1.71 (0.15), residues: 1249 sheet: -0.46 (0.52), residues: 109 loop : -0.32 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 447 HIS 0.007 0.001 HIS B 454 PHE 0.014 0.001 PHE F 101 TYR 0.019 0.001 TYR B 102 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 961) hydrogen bonds : angle 4.34286 ( 2763) covalent geometry : bond 0.00274 (19492) covalent geometry : angle 0.57619 (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 157 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8547 (tptt) REVERT: A 125 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8218 (tmm) REVERT: A 168 HIS cc_start: 0.8543 (t-90) cc_final: 0.8201 (t-90) REVERT: A 243 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7888 (ptt) REVERT: A 245 ILE cc_start: 0.9045 (mp) cc_final: 0.8734 (pp) REVERT: A 291 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: A 326 MET cc_start: 0.9158 (tmt) cc_final: 0.8958 (tmm) REVERT: A 346 TYR cc_start: 0.8374 (m-10) cc_final: 0.8149 (m-10) REVERT: B 451 MET cc_start: 0.9388 (tpp) cc_final: 0.9147 (mtp) REVERT: E 100 TYR cc_start: 0.8736 (m-80) cc_final: 0.8296 (m-80) REVERT: E 125 GLU cc_start: 0.8162 (tt0) cc_final: 0.7748 (tt0) REVERT: E 144 THR cc_start: 0.9006 (m) cc_final: 0.8788 (p) REVERT: F 100 TYR cc_start: 0.8771 (m-80) cc_final: 0.8470 (m-80) REVERT: F 172 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7361 (ttp) REVERT: F 184 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9094 (mp) REVERT: X 44 MET cc_start: 0.8384 (ttt) cc_final: 0.7996 (tpp) outliers start: 31 outliers final: 16 residues processed: 147 average time/residue: 1.3273 time to fit residues: 221.2128 Evaluate side-chains 141 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 2.022 ------------------------------------------------------------------------------- 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 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 111 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 47 optimal weight: 0.9980 chunk 239 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 104 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3258 r_free = 0.3258 target = 0.068551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.058601 restraints weight = 58905.830| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.03 r_work: 0.2877 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3243 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= 0.125 Angle : 0.589 12.893 26408 Z= 0.289 Chirality : 0.042 0.215 2908 Planarity : 0.004 0.053 3486 Dihedral : 4.828 44.370 2819 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.53 % Allowed : 14.07 % Favored : 84.40 % 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: 1.08 (0.17), residues: 2479 helix: 1.75 (0.15), residues: 1249 sheet: -0.23 (0.49), residues: 125 loop : -0.33 (0.19), residues: 1105 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 0.014 0.001 PHE F 101 TYR 0.030 0.001 TYR B 102 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 961) hydrogen bonds : angle 4.34181 ( 2763) covalent geometry : bond 0.00286 (19492) covalent geometry : angle 0.58866 (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 156 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8333 (tmtp) REVERT: A 125 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8138 (tmm) REVERT: A 168 HIS cc_start: 0.8520 (t-90) cc_final: 0.8185 (t-90) REVERT: A 243 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7887 (ptt) REVERT: A 245 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8724 (pp) REVERT: A 291 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: A 326 MET cc_start: 0.9131 (tmt) cc_final: 0.8883 (tmm) REVERT: A 346 TYR cc_start: 0.8376 (m-10) cc_final: 0.8152 (m-10) REVERT: B 125 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8504 (mtp) REVERT: B 451 MET cc_start: 0.9379 (tpp) cc_final: 0.9137 (mtp) REVERT: E 22 MET cc_start: 0.8866 (mtm) cc_final: 0.8571 (mtm) REVERT: E 125 GLU cc_start: 0.8155 (tt0) cc_final: 0.7740 (tt0) REVERT: E 144 THR cc_start: 0.8972 (m) cc_final: 0.8741 (p) REVERT: F 100 TYR cc_start: 0.8797 (m-80) cc_final: 0.8521 (m-80) REVERT: F 184 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9084 (mp) REVERT: X 44 MET cc_start: 0.8390 (ttt) cc_final: 0.8003 (tpp) REVERT: X 72 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7900 (mp) outliers start: 30 outliers final: 17 residues processed: 146 average time/residue: 1.3006 time to fit residues: 217.2922 Evaluate side-chains 149 residues out of total 1961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 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 102 TYR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 501 ASN 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 111 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 194 optimal weight: 0.0070 chunk 137 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN ** B 501 ASN ** 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.067989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.057738 restraints weight = 59323.485| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.07 r_work: 0.2869 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19492 Z= 0.132 Angle : 0.582 11.997 26408 Z= 0.288 Chirality : 0.042 0.213 2908 Planarity : 0.004 0.052 3486 Dihedral : 4.855 44.093 2819 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.58 % Allowed : 14.07 % 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: 1.08 (0.17), residues: 2479 helix: 1.74 (0.15), residues: 1247 sheet: -0.26 (0.49), residues: 125 loop : -0.31 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 447 HIS 0.007 0.001 HIS B 454 PHE 0.014 0.001 PHE F 101 TYR 0.034 0.001 TYR B 102 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 961) hydrogen bonds : angle 4.37068 ( 2763) covalent geometry : bond 0.00299 (19492) covalent geometry : angle 0.58231 (26408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8163.22 seconds wall clock time: 143 minutes 7.88 seconds (8587.88 seconds total)