Starting phenix.real_space_refine on Thu Feb 5 08:25:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hip_52197/02_2026/9hip_52197_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hip_52197/02_2026/9hip_52197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hip_52197/02_2026/9hip_52197_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hip_52197/02_2026/9hip_52197_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hip_52197/02_2026/9hip_52197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hip_52197/02_2026/9hip_52197.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 56 5.16 5 C 9886 2.51 5 N 2832 2.21 5 O 3038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15820 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3458 Classifications: {'peptide': 454} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 436} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3418 Classifications: {'peptide': 451} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 4846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4846 Classifications: {'peptide': 624} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 589} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3981 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.91, per 1000 atoms: 0.25 Number of scatterers: 15820 At special positions: 0 Unit cell: (116.978, 98.748, 217.246, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 8 15.00 O 3038 8.00 N 2832 7.00 C 9886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 763.5 milliseconds 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 15 sheets defined 46.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 86 through 100 removed outlier: 3.590A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 removed outlier: 3.587A pdb=" N ALA A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.610A pdb=" N ALA A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.677A pdb=" N GLY A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 175 removed outlier: 3.587A pdb=" N ALA A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 4.082A pdb=" N ILE A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ASP A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 210 Processing helix chain 'A' and resid 211 through 216 removed outlier: 4.025A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 Processing helix chain 'A' and resid 279 through 296 removed outlier: 4.410A pdb=" N GLU A 294 " --> pdb=" O TRP A 290 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.519A pdb=" N ILE A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 317' Processing helix chain 'A' and resid 317 through 324 removed outlier: 3.858A pdb=" N ILE A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 322 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.711A pdb=" N THR A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 3.723A pdb=" N MET A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 413 Processing helix chain 'A' and resid 415 through 432 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 439 through 449 removed outlier: 3.594A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 38 Processing helix chain 'B' and resid 86 through 99 removed outlier: 3.576A pdb=" N THR B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.816A pdb=" N GLU B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 143 removed outlier: 3.657A pdb=" N ASP B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 176 removed outlier: 3.693A pdb=" N ARG B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA B 173 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 207 removed outlier: 3.759A pdb=" N ALA B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 196 " --> pdb=" O GLN B 192 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 279 through 296 removed outlier: 3.522A pdb=" N GLU B 294 " --> pdb=" O TRP B 290 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 364 through 376 removed outlier: 3.505A pdb=" N LEU B 368 " --> pdb=" O GLY B 364 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 396 removed outlier: 3.657A pdb=" N ARG B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 411 removed outlier: 3.771A pdb=" N ALA B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N HIS B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 removed outlier: 3.794A pdb=" N LEU B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 450 removed outlier: 3.612A pdb=" N LEU B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 56 through 66 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.584A pdb=" N TYR C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 190 removed outlier: 3.887A pdb=" N SER C 184 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.579A pdb=" N VAL C 214 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 215 " --> pdb=" O PHE C 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 211 through 215' Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.729A pdb=" N GLN C 235 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS C 236 " --> pdb=" O ALA C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 236' Processing helix chain 'C' and resid 248 through 259 Processing helix chain 'C' and resid 280 through 287 removed outlier: 3.506A pdb=" N PHE C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 326 Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 377 through 396 removed outlier: 4.089A pdb=" N ALA C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 419 removed outlier: 3.551A pdb=" N VAL C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 433 Processing helix chain 'C' and resid 443 through 456 removed outlier: 6.269A pdb=" N GLU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ILE C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 481 Processing helix chain 'C' and resid 491 through 498 removed outlier: 3.879A pdb=" N VAL C 495 " --> pdb=" O ALA C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 513 Processing helix chain 'C' and resid 519 through 525 removed outlier: 3.746A pdb=" N LEU C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 562 removed outlier: 4.312A pdb=" N GLN C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLY C 550 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR C 551 " --> pdb=" O LYS C 547 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 561 " --> pdb=" O ASP C 557 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 Processing helix chain 'C' and resid 575 through 579 Processing helix chain 'C' and resid 583 through 594 Processing helix chain 'C' and resid 597 through 603 Processing helix chain 'C' and resid 608 through 623 Processing helix chain 'D' and resid 15 through 29 removed outlier: 3.503A pdb=" N THR D 19 " --> pdb=" O GLY D 15 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 20 " --> pdb=" O HIS D 16 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 42 Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 69 through 77 removed outlier: 4.157A pdb=" N GLN D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.538A pdb=" N VAL D 92 " --> pdb=" O GLY D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 114 removed outlier: 3.603A pdb=" N ASN D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 188 removed outlier: 3.789A pdb=" N SER D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D 185 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG D 188 " --> pdb=" O SER D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 232 through 236 removed outlier: 3.994A pdb=" N GLN D 235 " --> pdb=" O ASN D 232 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS D 236 " --> pdb=" O ALA D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 232 through 236' Processing helix chain 'D' and resid 248 through 255 removed outlier: 3.853A pdb=" N HIS D 252 " --> pdb=" O ASN D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 326 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 377 through 397 removed outlier: 3.579A pdb=" N ALA D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 419 Processing helix chain 'D' and resid 443 through 456 removed outlier: 3.583A pdb=" N ARG D 447 " --> pdb=" O ASN D 443 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE D 451 " --> pdb=" O ARG D 447 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 455 " --> pdb=" O ILE D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 482 Processing helix chain 'D' and resid 491 through 499 Processing helix chain 'D' and resid 509 through 514 Processing helix chain 'D' and resid 519 through 525 Processing helix chain 'D' and resid 535 through 548 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.971A pdb=" N ASP A 47 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE A 63 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU A 49 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLN A 61 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 51 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 259 removed outlier: 3.749A pdb=" N LEU A 255 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 219 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LYS A 218 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU A 300 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 220 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N MET A 302 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA A 222 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N ASP A 304 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 299 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL A 333 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 301 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN A 335 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL A 303 " --> pdb=" O ASN A 335 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 353 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.826A pdb=" N ASP B 47 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE B 63 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU B 49 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLN B 61 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE B 51 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 7 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 261 removed outlier: 6.669A pdb=" N MET B 217 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE B 269 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 219 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 298 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA B 222 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 299 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL B 333 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 301 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN B 335 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 303 " --> pdb=" O ASN B 335 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA B 353 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 356 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B 345 " --> pdb=" O ARG B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 122 removed outlier: 6.341A pdb=" N THR C 32 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE C 121 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU C 34 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 50 through 52 removed outlier: 6.215A pdb=" N ALA C 94 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE C 83 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG C 96 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE C 81 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN C 98 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 130 removed outlier: 6.821A pdb=" N VAL C 139 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU C 128 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N GLY C 137 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 130 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL C 135 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 168 through 171 Processing sheet with id=AA9, first strand: chain 'C' and resid 216 through 218 removed outlier: 3.700A pdb=" N ALA C 216 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG C 204 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 122 removed outlier: 6.439A pdb=" N THR D 32 " --> pdb=" O MET D 119 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE D 121 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU D 34 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL D 151 " --> pdb=" O PHE D 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 50 through 53 removed outlier: 4.194A pdb=" N THR D 95 " --> pdb=" O GLY D 53 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA D 94 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE D 83 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG D 96 " --> pdb=" O PHE D 81 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE D 81 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLN D 98 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 125 through 130 removed outlier: 6.070A pdb=" N VAL D 125 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR D 140 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP D 127 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA D 138 " --> pdb=" O ASP D 127 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE D 129 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 168 through 171 removed outlier: 3.828A pdb=" N LEU D 197 " --> pdb=" O TYR D 345 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 216 through 218 removed outlier: 3.742A pdb=" N ALA D 216 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR D 243 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE D 296 " --> pdb=" O ASN D 310 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG D 204 " --> pdb=" O VAL D 337 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 484 through 485 680 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3818 1.33 - 1.45: 2992 1.45 - 1.57: 9161 1.57 - 1.69: 17 1.69 - 1.81: 107 Bond restraints: 16095 Sorted by residual: bond pdb=" O3A GNP B 501 " pdb=" PB GNP B 501 " ideal model delta sigma weight residual 1.687 1.576 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" O2B GNP A 501 " pdb=" PB GNP A 501 " ideal model delta sigma weight residual 1.505 1.601 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" O3A GNP A 501 " pdb=" PB GNP A 501 " ideal model delta sigma weight residual 1.687 1.592 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" O2B GNP B 501 " pdb=" PB GNP B 501 " ideal model delta sigma weight residual 1.505 1.600 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C6 GNP B 501 " pdb=" N1 GNP B 501 " ideal model delta sigma weight residual 1.403 1.314 0.089 2.00e-02 2.50e+03 2.00e+01 ... (remaining 16090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 21760 3.55 - 7.09: 46 7.09 - 10.64: 10 10.64 - 14.19: 6 14.19 - 17.74: 1 Bond angle restraints: 21823 Sorted by residual: angle pdb=" PA GNP A 501 " pdb=" O3A GNP A 501 " pdb=" PB GNP A 501 " ideal model delta sigma weight residual 126.68 108.94 17.74 3.00e+00 1.11e-01 3.49e+01 angle pdb=" N ILE D 312 " pdb=" CA ILE D 312 " pdb=" C ILE D 312 " ideal model delta sigma weight residual 113.20 107.95 5.25 9.60e-01 1.09e+00 2.99e+01 angle pdb=" PA GNP B 501 " pdb=" O3A GNP B 501 " pdb=" PB GNP B 501 " ideal model delta sigma weight residual 126.68 112.93 13.75 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N3B GNP A 501 " pdb=" PB GNP A 501 " pdb=" O3A GNP A 501 " ideal model delta sigma weight residual 100.48 114.19 -13.71 3.00e+00 1.11e-01 2.09e+01 angle pdb=" O3A GNP A 501 " pdb=" PA GNP A 501 " pdb=" O5' GNP A 501 " ideal model delta sigma weight residual 97.31 109.13 -11.82 3.00e+00 1.11e-01 1.55e+01 ... (remaining 21818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 9056 17.38 - 34.76: 600 34.76 - 52.14: 122 52.14 - 69.53: 42 69.53 - 86.91: 14 Dihedral angle restraints: 9834 sinusoidal: 4022 harmonic: 5812 Sorted by residual: dihedral pdb=" CA ASN C 222 " pdb=" C ASN C 222 " pdb=" N PRO C 223 " pdb=" CA PRO C 223 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA THR C 527 " pdb=" C THR C 527 " pdb=" N PRO C 528 " pdb=" CA PRO C 528 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA LEU B 145 " pdb=" C LEU B 145 " pdb=" N ASN B 146 " pdb=" CA ASN B 146 " ideal model delta harmonic sigma weight residual 180.00 162.91 17.09 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 9831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1749 0.033 - 0.065: 491 0.065 - 0.098: 138 0.098 - 0.130: 75 0.130 - 0.163: 4 Chirality restraints: 2457 Sorted by residual: chirality pdb=" C1' GNP A 501 " pdb=" C2' GNP A 501 " pdb=" N9 GNP A 501 " pdb=" O4' GNP A 501 " both_signs ideal model delta sigma weight residual False 2.36 2.52 -0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" C3' GNP A 501 " pdb=" C2' GNP A 501 " pdb=" C4' GNP A 501 " pdb=" O3' GNP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.55 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" C3' GNP B 501 " pdb=" C2' GNP B 501 " pdb=" C4' GNP B 501 " pdb=" O3' GNP B 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.56 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 2454 not shown) Planarity restraints: 2887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 222 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO C 223 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO C 223 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 223 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 462 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C ARG D 462 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG D 462 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP D 463 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GNP A 501 " 0.020 2.00e-02 2.50e+03 8.43e-03 2.13e+00 pdb=" C2 GNP A 501 " -0.001 2.00e-02 2.50e+03 pdb=" C4 GNP A 501 " -0.002 2.00e-02 2.50e+03 pdb=" C5 GNP A 501 " 0.002 2.00e-02 2.50e+03 pdb=" C6 GNP A 501 " 0.004 2.00e-02 2.50e+03 pdb=" C8 GNP A 501 " -0.003 2.00e-02 2.50e+03 pdb=" N1 GNP A 501 " 0.004 2.00e-02 2.50e+03 pdb=" N2 GNP A 501 " -0.005 2.00e-02 2.50e+03 pdb=" N3 GNP A 501 " -0.001 2.00e-02 2.50e+03 pdb=" N7 GNP A 501 " -0.002 2.00e-02 2.50e+03 pdb=" N9 GNP A 501 " -0.019 2.00e-02 2.50e+03 pdb=" O6 GNP A 501 " 0.003 2.00e-02 2.50e+03 ... (remaining 2884 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 286 2.60 - 3.18: 15421 3.18 - 3.75: 24150 3.75 - 4.33: 33525 4.33 - 4.90: 54720 Nonbonded interactions: 128102 Sorted by model distance: nonbonded pdb=" OH TYR B 48 " pdb=" OE1 GLN B 61 " model vdw 2.031 3.040 nonbonded pdb=" OG SER B 431 " pdb=" O GLY B 435 " model vdw 2.055 3.040 nonbonded pdb=" O ARG A 96 " pdb=" OG1 THR A 99 " model vdw 2.062 3.040 nonbonded pdb=" OD1 ASP B 440 " pdb=" NH2 ARG C 275 " model vdw 2.085 3.120 nonbonded pdb=" N GLN B 125 " pdb=" OE1 GLN B 125 " model vdw 2.091 3.120 ... (remaining 128097 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 'A' and (resid 1 through 142 or (resid 143 through 144 and (name N or nam \ e CA or name C or name O or name CB )) or resid 145 through 170 or (resid 171 th \ rough 173 and (name N or name CA or name C or name O or name CB )) or resid 174 \ through 212 or (resid 213 through 214 and (name N or name CA or name C or name O \ or name CB )) or resid 215 through 217 or (resid 218 and (name N or name CA or \ name C or name O or name CB )) or resid 219 through 376 or resid 380 through 382 \ or (resid 383 and (name N or name CA or name C or name O or name CB )) or resid \ 384 through 408 or (resid 409 and (name N or name CA or name C or name O or nam \ e CB )) or resid 410 through 501)) selection = (chain 'B' and (resid 1 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 232 or (resid 233 and (name \ N or name CA or name C or name O or name CB )) or resid 234 through 294 or (res \ id 295 through 296 and (name N or name CA or name C or name O or name CB )) or r \ esid 297 through 501)) } 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: 12.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.200 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.004 0.111 16095 Z= 0.174 Angle : 0.556 17.735 21823 Z= 0.255 Chirality : 0.037 0.163 2457 Planarity : 0.004 0.108 2887 Dihedral : 12.851 86.906 6094 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 44.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.96 % Favored : 93.94 % Rotamer: Outliers : 0.55 % Allowed : 11.14 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 2029 helix: 1.75 (0.19), residues: 799 sheet: 0.45 (0.31), residues: 324 loop : -1.34 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 82 TYR 0.009 0.001 TYR C 341 PHE 0.010 0.001 PHE A 320 TRP 0.005 0.001 TRP C 484 HIS 0.002 0.000 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00356 (16095) covalent geometry : angle 0.55612 (21823) hydrogen bonds : bond 0.18183 ( 680) hydrogen bonds : angle 6.57249 ( 1950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 318 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7334 (mmtp) cc_final: 0.7052 (mmtt) REVERT: A 110 GLU cc_start: 0.7155 (tp30) cc_final: 0.6683 (tp30) REVERT: A 232 LEU cc_start: 0.8844 (tp) cc_final: 0.8538 (tp) REVERT: B 1 MET cc_start: 0.0487 (ttp) cc_final: -0.0136 (ttp) REVERT: B 188 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.7862 (ptpp) REVERT: C 37 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.7605 (t70) REVERT: C 440 ARG cc_start: 0.8437 (mtm-85) cc_final: 0.7962 (mtm-85) REVERT: C 474 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7230 (tm-30) REVERT: C 518 MET cc_start: 0.6603 (mmt) cc_final: 0.6304 (mmt) REVERT: D 343 ILE cc_start: 0.8882 (tt) cc_final: 0.8495 (mm) REVERT: D 409 TYR cc_start: 0.7554 (m-80) cc_final: 0.7136 (m-10) REVERT: D 522 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8222 (mtmm) outliers start: 9 outliers final: 5 residues processed: 324 average time/residue: 0.1571 time to fit residues: 71.9446 Evaluate side-chains 276 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 269 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 529 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0020 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS B 149 GLN B 226 ASN B 370 ASN B 402 HIS C 390 ASN C 600 GLN D 37 HIS ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN ** D 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.203760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.147932 restraints weight = 22041.629| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.02 r_work: 0.3473 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16095 Z= 0.167 Angle : 0.693 9.666 21823 Z= 0.345 Chirality : 0.044 0.210 2457 Planarity : 0.005 0.104 2887 Dihedral : 7.444 66.146 2347 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 2.57 % Allowed : 14.50 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 2029 helix: 1.40 (0.19), residues: 816 sheet: 0.45 (0.31), residues: 310 loop : -1.26 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 208 TYR 0.022 0.001 TYR D 409 PHE 0.025 0.002 PHE A 378 TRP 0.008 0.001 TRP D 401 HIS 0.004 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00372 (16095) covalent geometry : angle 0.69251 (21823) hydrogen bonds : bond 0.04551 ( 680) hydrogen bonds : angle 5.33872 ( 1950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8008 (tp30) cc_final: 0.7366 (tp30) REVERT: A 127 GLU cc_start: 0.6747 (mp0) cc_final: 0.6537 (mp0) REVERT: A 146 ASN cc_start: 0.8671 (m-40) cc_final: 0.8463 (m-40) REVERT: A 214 ARG cc_start: 0.7529 (mtp180) cc_final: 0.7314 (mtp180) REVERT: A 267 HIS cc_start: 0.6279 (m90) cc_final: 0.5453 (m-70) REVERT: A 282 GLU cc_start: 0.7369 (tt0) cc_final: 0.6986 (pt0) REVERT: A 301 PHE cc_start: 0.7124 (t80) cc_final: 0.6862 (t80) REVERT: A 317 TRP cc_start: 0.6709 (t-100) cc_final: 0.6437 (t-100) REVERT: A 405 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7892 (mm-40) REVERT: A 429 ASN cc_start: 0.8645 (m-40) cc_final: 0.8172 (m-40) REVERT: A 432 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7496 (tm-30) REVERT: B 264 MET cc_start: 0.5686 (ttt) cc_final: 0.5447 (ttt) REVERT: B 369 ARG cc_start: 0.7579 (tpt90) cc_final: 0.7196 (ttp-110) REVERT: C 37 HIS cc_start: 0.8511 (OUTLIER) cc_final: 0.7694 (t70) REVERT: C 518 MET cc_start: 0.7429 (mmt) cc_final: 0.6685 (mtp) REVERT: C 545 GLN cc_start: 0.8377 (mt0) cc_final: 0.8126 (mt0) REVERT: D 343 ILE cc_start: 0.8811 (tt) cc_final: 0.8424 (mm) REVERT: D 409 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7384 (m-80) outliers start: 42 outliers final: 30 residues processed: 319 average time/residue: 0.1438 time to fit residues: 65.8947 Evaluate side-chains 284 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 66 TRP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 520 TYR Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 409 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 174 optimal weight: 0.0030 chunk 29 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 146 optimal weight: 0.2980 chunk 189 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 149 GLN ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 HIS C 600 GLN ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.204981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149350 restraints weight = 22333.945| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.01 r_work: 0.3473 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16095 Z= 0.132 Angle : 0.617 14.840 21823 Z= 0.306 Chirality : 0.042 0.184 2457 Planarity : 0.005 0.106 2887 Dihedral : 6.877 64.496 2340 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 3.12 % Allowed : 14.99 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.19), residues: 2029 helix: 1.27 (0.19), residues: 826 sheet: 0.52 (0.30), residues: 316 loop : -1.21 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 16 TYR 0.011 0.001 TYR D 308 PHE 0.035 0.001 PHE A 378 TRP 0.010 0.001 TRP D 401 HIS 0.004 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00307 (16095) covalent geometry : angle 0.61729 (21823) hydrogen bonds : bond 0.03956 ( 680) hydrogen bonds : angle 5.01834 ( 1950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 283 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8632 (tp) cc_final: 0.8364 (tt) REVERT: A 110 GLU cc_start: 0.7945 (tp30) cc_final: 0.7295 (tp30) REVERT: A 146 ASN cc_start: 0.8581 (m-40) cc_final: 0.8312 (m-40) REVERT: A 214 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7326 (mtp180) REVERT: A 373 LYS cc_start: 0.8223 (tptp) cc_final: 0.7996 (tptp) REVERT: A 401 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8068 (pp20) REVERT: A 405 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7252 (pt0) REVERT: A 429 ASN cc_start: 0.8733 (m-40) cc_final: 0.8288 (m-40) REVERT: A 432 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7513 (tm-30) REVERT: B 346 MET cc_start: 0.5031 (mpp) cc_final: 0.3993 (tpt) REVERT: B 357 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5931 (pp) REVERT: B 369 ARG cc_start: 0.7571 (tpt90) cc_final: 0.7262 (ttm-80) REVERT: B 370 ASN cc_start: 0.8235 (m110) cc_final: 0.7904 (m110) REVERT: B 398 GLN cc_start: 0.7887 (pt0) cc_final: 0.7610 (pt0) REVERT: C 37 HIS cc_start: 0.8467 (OUTLIER) cc_final: 0.7675 (t70) REVERT: C 518 MET cc_start: 0.7425 (mmt) cc_final: 0.6686 (mtp) REVERT: C 603 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8016 (mtm180) REVERT: D 343 ILE cc_start: 0.8714 (tt) cc_final: 0.8381 (mm) REVERT: D 409 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7600 (m-80) outliers start: 51 outliers final: 30 residues processed: 316 average time/residue: 0.1298 time to fit residues: 60.0932 Evaluate side-chains 287 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 520 TYR Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 603 ARG Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 409 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 194 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 176 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 149 GLN C 600 GLN ** D 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN D 472 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.199803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144969 restraints weight = 22278.632| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.69 r_work: 0.3413 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 16095 Z= 0.276 Angle : 0.725 12.588 21823 Z= 0.364 Chirality : 0.046 0.210 2457 Planarity : 0.006 0.111 2887 Dihedral : 7.248 68.140 2340 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer: Outliers : 4.04 % Allowed : 16.22 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.19), residues: 2029 helix: 0.81 (0.18), residues: 824 sheet: 0.31 (0.30), residues: 318 loop : -1.43 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 440 TYR 0.017 0.002 TYR D 308 PHE 0.034 0.002 PHE A 378 TRP 0.013 0.001 TRP D 401 HIS 0.007 0.001 HIS D 246 Details of bonding type rmsd covalent geometry : bond 0.00653 (16095) covalent geometry : angle 0.72508 (21823) hydrogen bonds : bond 0.05507 ( 680) hydrogen bonds : angle 5.28607 ( 1950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 269 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: A 110 GLU cc_start: 0.7884 (tp30) cc_final: 0.7364 (tp30) REVERT: A 146 ASN cc_start: 0.8612 (m-40) cc_final: 0.8334 (m-40) REVERT: A 155 ARG cc_start: 0.7849 (mmm160) cc_final: 0.7633 (mmm160) REVERT: A 275 ARG cc_start: 0.7535 (mtm110) cc_final: 0.7305 (mtm110) REVERT: A 282 GLU cc_start: 0.7509 (tt0) cc_final: 0.6982 (pt0) REVERT: A 373 LYS cc_start: 0.8217 (tptp) cc_final: 0.7964 (tptp) REVERT: A 401 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 405 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7196 (pt0) REVERT: A 429 ASN cc_start: 0.8696 (m-40) cc_final: 0.8289 (m-40) REVERT: A 432 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7642 (tm-30) REVERT: B 30 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7767 (ptp-110) REVERT: B 39 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7631 (ptmm) REVERT: B 288 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7467 (tpp80) REVERT: B 346 MET cc_start: 0.4941 (mpp) cc_final: 0.3897 (tpt) REVERT: B 398 GLN cc_start: 0.7986 (pt0) cc_final: 0.7721 (pt0) REVERT: B 403 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8222 (mp) REVERT: C 37 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.7657 (t70) REVERT: C 66 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8417 (mp) REVERT: C 160 ASP cc_start: 0.7664 (t0) cc_final: 0.7419 (t0) REVERT: C 450 GLU cc_start: 0.7963 (tp30) cc_final: 0.7724 (pm20) REVERT: C 474 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7831 (tm-30) REVERT: C 560 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7818 (tm-30) REVERT: C 603 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8215 (mtm180) REVERT: D 343 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8405 (mm) REVERT: D 409 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7578 (m-80) REVERT: D 471 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7546 (tm-30) REVERT: D 518 MET cc_start: 0.6944 (tmm) cc_final: 0.6662 (tmm) outliers start: 66 outliers final: 42 residues processed: 311 average time/residue: 0.1295 time to fit residues: 58.0140 Evaluate side-chains 310 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 258 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 520 TYR Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 603 ARG Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 409 TYR Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 140 optimal weight: 5.9990 chunk 129 optimal weight: 0.3980 chunk 173 optimal weight: 0.2980 chunk 112 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 149 GLN ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN C 600 GLN D 58 HIS ** D 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.204348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.147524 restraints weight = 22315.127| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.08 r_work: 0.3450 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16095 Z= 0.132 Angle : 0.604 12.078 21823 Z= 0.301 Chirality : 0.041 0.197 2457 Planarity : 0.005 0.110 2887 Dihedral : 6.802 66.572 2340 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.34 % Favored : 95.61 % Rotamer: Outliers : 3.73 % Allowed : 17.20 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 2029 helix: 1.07 (0.19), residues: 824 sheet: 0.37 (0.29), residues: 314 loop : -1.29 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 16 TYR 0.011 0.001 TYR D 308 PHE 0.028 0.001 PHE A 378 TRP 0.013 0.001 TRP D 401 HIS 0.004 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00308 (16095) covalent geometry : angle 0.60397 (21823) hydrogen bonds : bond 0.03898 ( 680) hydrogen bonds : angle 4.93430 ( 1950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 273 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8693 (tp) cc_final: 0.8332 (tt) REVERT: A 110 GLU cc_start: 0.7847 (tp30) cc_final: 0.7474 (mm-30) REVERT: A 146 ASN cc_start: 0.8559 (m-40) cc_final: 0.8280 (m-40) REVERT: A 214 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7336 (mtp-110) REVERT: A 267 HIS cc_start: 0.6392 (m90) cc_final: 0.5573 (m-70) REVERT: A 275 ARG cc_start: 0.7625 (mtm110) cc_final: 0.7353 (mtm110) REVERT: A 360 ARG cc_start: 0.7910 (ttm110) cc_final: 0.7657 (mtt90) REVERT: A 405 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7208 (pt0) REVERT: A 429 ASN cc_start: 0.8696 (m-40) cc_final: 0.8325 (m-40) REVERT: A 432 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7584 (tm-30) REVERT: B 66 TRP cc_start: 0.8792 (OUTLIER) cc_final: 0.8546 (t-100) REVERT: B 346 MET cc_start: 0.4965 (mpp) cc_final: 0.4033 (tpt) REVERT: C 37 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.7690 (t70) REVERT: C 66 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8264 (mp) REVERT: C 160 ASP cc_start: 0.7375 (t0) cc_final: 0.7167 (t0) REVERT: C 518 MET cc_start: 0.7333 (mmt) cc_final: 0.6663 (mtp) REVERT: C 603 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8073 (mtm180) REVERT: D 409 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: D 471 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7547 (tm-30) REVERT: D 518 MET cc_start: 0.7087 (tmm) cc_final: 0.6882 (tmm) outliers start: 61 outliers final: 37 residues processed: 316 average time/residue: 0.1284 time to fit residues: 59.2576 Evaluate side-chains 296 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 254 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 66 TRP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 560 GLU Chi-restraints excluded: chain C residue 603 ARG Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 409 TYR Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 156 optimal weight: 0.0670 chunk 42 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 84 HIS B 149 GLN ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN B 429 ASN C 600 GLN ** D 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.204403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.146911 restraints weight = 22257.744| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.47 r_work: 0.3453 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16095 Z= 0.136 Angle : 0.597 10.949 21823 Z= 0.298 Chirality : 0.042 0.185 2457 Planarity : 0.005 0.111 2887 Dihedral : 6.666 65.076 2340 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.03 % Favored : 94.92 % Rotamer: Outliers : 3.55 % Allowed : 17.75 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 2029 helix: 1.13 (0.18), residues: 829 sheet: 0.38 (0.29), residues: 314 loop : -1.28 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 16 TYR 0.011 0.001 TYR D 308 PHE 0.027 0.001 PHE A 378 TRP 0.017 0.001 TRP A 317 HIS 0.004 0.001 HIS D 246 Details of bonding type rmsd covalent geometry : bond 0.00322 (16095) covalent geometry : angle 0.59714 (21823) hydrogen bonds : bond 0.03868 ( 680) hydrogen bonds : angle 4.78468 ( 1950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 268 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.8452 (mtm110) cc_final: 0.8121 (mtp85) REVERT: A 80 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: A 94 LEU cc_start: 0.8692 (tp) cc_final: 0.8307 (tt) REVERT: A 110 GLU cc_start: 0.7753 (tp30) cc_final: 0.7396 (mm-30) REVERT: A 146 ASN cc_start: 0.8495 (m-40) cc_final: 0.8195 (m-40) REVERT: A 208 ARG cc_start: 0.7951 (tmt170) cc_final: 0.7443 (tmt-80) REVERT: A 214 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7374 (mtp-110) REVERT: A 267 HIS cc_start: 0.6397 (m90) cc_final: 0.5565 (m-70) REVERT: A 356 ARG cc_start: 0.6409 (mtt90) cc_final: 0.6192 (mtt90) REVERT: A 401 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8015 (pp20) REVERT: A 405 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7413 (pt0) REVERT: A 429 ASN cc_start: 0.8683 (m-40) cc_final: 0.8265 (m-40) REVERT: A 432 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7598 (tm-30) REVERT: A 445 ARG cc_start: 0.7982 (ptp-110) cc_final: 0.7747 (ptp90) REVERT: B 256 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7612 (mtt180) REVERT: B 346 MET cc_start: 0.5009 (mpp) cc_final: 0.4022 (tpt) REVERT: B 429 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8584 (m110) REVERT: C 37 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.7732 (t70) REVERT: C 66 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8277 (mp) REVERT: C 160 ASP cc_start: 0.7433 (t0) cc_final: 0.7231 (t0) REVERT: C 518 MET cc_start: 0.7276 (mmt) cc_final: 0.6560 (mtp) REVERT: C 603 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8066 (mtm180) REVERT: D 409 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7423 (m-80) REVERT: D 455 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8419 (mp) REVERT: D 471 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7566 (tm-30) outliers start: 58 outliers final: 40 residues processed: 309 average time/residue: 0.1322 time to fit residues: 59.1319 Evaluate side-chains 303 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 256 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 520 TYR Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 603 ARG Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 409 TYR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN B 84 HIS ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN C 600 GLN ** D 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.203155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147166 restraints weight = 22153.559| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.14 r_work: 0.3441 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16095 Z= 0.168 Angle : 0.618 10.547 21823 Z= 0.309 Chirality : 0.042 0.156 2457 Planarity : 0.005 0.112 2887 Dihedral : 6.788 65.793 2340 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.23 % Rotamer: Outliers : 3.92 % Allowed : 18.24 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 2029 helix: 1.08 (0.18), residues: 829 sheet: 0.31 (0.29), residues: 314 loop : -1.30 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 275 TYR 0.013 0.001 TYR D 308 PHE 0.023 0.001 PHE A 378 TRP 0.015 0.001 TRP D 401 HIS 0.005 0.001 HIS D 246 Details of bonding type rmsd covalent geometry : bond 0.00401 (16095) covalent geometry : angle 0.61789 (21823) hydrogen bonds : bond 0.04197 ( 680) hydrogen bonds : angle 4.82313 ( 1950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 264 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.8436 (mtm110) cc_final: 0.8104 (mtp85) REVERT: A 80 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: A 110 GLU cc_start: 0.7763 (tp30) cc_final: 0.7412 (mm-30) REVERT: A 146 ASN cc_start: 0.8493 (m-40) cc_final: 0.8195 (m-40) REVERT: A 214 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7408 (mtp-110) REVERT: A 267 HIS cc_start: 0.6467 (m90) cc_final: 0.5595 (m-70) REVERT: A 356 ARG cc_start: 0.6467 (mtt90) cc_final: 0.6231 (mtt90) REVERT: A 401 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8027 (pp20) REVERT: A 405 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7426 (pt0) REVERT: A 429 ASN cc_start: 0.8688 (m-40) cc_final: 0.8258 (m-40) REVERT: A 432 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7639 (tm-30) REVERT: A 445 ARG cc_start: 0.7980 (ptp-110) cc_final: 0.7706 (ptp90) REVERT: B 39 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.7599 (ptmm) REVERT: B 66 TRP cc_start: 0.8816 (OUTLIER) cc_final: 0.8554 (t-100) REVERT: B 256 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7625 (mtt180) REVERT: C 37 HIS cc_start: 0.8575 (OUTLIER) cc_final: 0.7633 (t70) REVERT: C 66 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8348 (mp) REVERT: C 160 ASP cc_start: 0.7486 (t0) cc_final: 0.7233 (t0) REVERT: C 518 MET cc_start: 0.7241 (mmt) cc_final: 0.6497 (mtp) REVERT: C 603 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8123 (mtm180) REVERT: D 409 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: D 455 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8413 (mp) REVERT: D 471 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7576 (tm-30) outliers start: 64 outliers final: 41 residues processed: 310 average time/residue: 0.1289 time to fit residues: 57.7915 Evaluate side-chains 310 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 261 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 66 TRP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 520 TYR Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 603 ARG Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 409 TYR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 40 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 111 optimal weight: 0.0020 chunk 51 optimal weight: 3.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 84 HIS ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 HIS B 429 ASN C 600 GLN ** D 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.204380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148386 restraints weight = 22291.324| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.50 r_work: 0.3460 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16095 Z= 0.142 Angle : 0.608 10.106 21823 Z= 0.304 Chirality : 0.041 0.155 2457 Planarity : 0.005 0.112 2887 Dihedral : 6.698 64.443 2340 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 3.49 % Allowed : 18.91 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 2029 helix: 1.10 (0.18), residues: 829 sheet: 0.26 (0.29), residues: 317 loop : -1.24 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 275 TYR 0.011 0.001 TYR D 308 PHE 0.020 0.001 PHE A 378 TRP 0.018 0.001 TRP D 401 HIS 0.004 0.001 HIS D 246 Details of bonding type rmsd covalent geometry : bond 0.00337 (16095) covalent geometry : angle 0.60823 (21823) hydrogen bonds : bond 0.03885 ( 680) hydrogen bonds : angle 4.72897 ( 1950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 259 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.8490 (mtm110) cc_final: 0.8185 (mtp85) REVERT: A 80 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: A 94 LEU cc_start: 0.8714 (tp) cc_final: 0.8314 (tt) REVERT: A 110 GLU cc_start: 0.7743 (tp30) cc_final: 0.7380 (mm-30) REVERT: A 146 ASN cc_start: 0.8471 (m-40) cc_final: 0.8171 (m-40) REVERT: A 208 ARG cc_start: 0.7919 (tmt170) cc_final: 0.7442 (tmt-80) REVERT: A 214 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7333 (mtp-110) REVERT: A 267 HIS cc_start: 0.6495 (m90) cc_final: 0.5596 (m-70) REVERT: A 301 PHE cc_start: 0.6814 (t80) cc_final: 0.6470 (t80) REVERT: A 356 ARG cc_start: 0.6458 (mtt90) cc_final: 0.6202 (mtt90) REVERT: A 401 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7919 (pp20) REVERT: A 405 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7562 (pt0) REVERT: A 429 ASN cc_start: 0.8657 (m-40) cc_final: 0.8268 (m-40) REVERT: A 432 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7666 (tm-30) REVERT: A 445 ARG cc_start: 0.7994 (ptp-110) cc_final: 0.7713 (ptp90) REVERT: B 39 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7534 (ptmm) REVERT: B 256 ARG cc_start: 0.7861 (mtt180) cc_final: 0.7648 (mtt180) REVERT: C 37 HIS cc_start: 0.8574 (OUTLIER) cc_final: 0.7548 (t70) REVERT: C 66 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8295 (mp) REVERT: C 328 MET cc_start: 0.8286 (mtp) cc_final: 0.8068 (mtp) REVERT: C 454 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7584 (tm-30) REVERT: C 518 MET cc_start: 0.7215 (mmt) cc_final: 0.6544 (mtp) REVERT: C 603 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8056 (mtm180) REVERT: D 409 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7403 (m-80) REVERT: D 455 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8413 (mp) REVERT: D 471 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7623 (tm-30) outliers start: 57 outliers final: 41 residues processed: 302 average time/residue: 0.1340 time to fit residues: 58.2727 Evaluate side-chains 299 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 251 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 520 TYR Chi-restraints excluded: chain C residue 603 ARG Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 409 TYR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 31 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 116 optimal weight: 0.0980 chunk 148 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 HIS B 226 ASN ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN ** D 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.202671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.145866 restraints weight = 22122.496| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.06 r_work: 0.3438 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16095 Z= 0.181 Angle : 0.641 10.240 21823 Z= 0.321 Chirality : 0.042 0.152 2457 Planarity : 0.005 0.113 2887 Dihedral : 6.801 65.320 2338 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 3.55 % Allowed : 18.85 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 2029 helix: 0.97 (0.18), residues: 829 sheet: 0.21 (0.29), residues: 322 loop : -1.29 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 275 TYR 0.013 0.001 TYR D 308 PHE 0.019 0.001 PHE A 378 TRP 0.017 0.001 TRP D 401 HIS 0.005 0.001 HIS D 246 Details of bonding type rmsd covalent geometry : bond 0.00429 (16095) covalent geometry : angle 0.64125 (21823) hydrogen bonds : bond 0.04434 ( 680) hydrogen bonds : angle 4.83807 ( 1950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 259 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.8453 (mtm110) cc_final: 0.8156 (mtp85) REVERT: A 80 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: A 110 GLU cc_start: 0.7734 (tp30) cc_final: 0.7368 (mm-30) REVERT: A 146 ASN cc_start: 0.8476 (m-40) cc_final: 0.8167 (m-40) REVERT: A 208 ARG cc_start: 0.7947 (tmt170) cc_final: 0.7445 (tmt-80) REVERT: A 214 ARG cc_start: 0.7754 (mtp180) cc_final: 0.7380 (mtp-110) REVERT: A 275 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7332 (mtm180) REVERT: A 301 PHE cc_start: 0.6765 (t80) cc_final: 0.6538 (t80) REVERT: A 356 ARG cc_start: 0.6519 (mtt90) cc_final: 0.6244 (mtt90) REVERT: A 401 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8019 (pp20) REVERT: A 405 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7528 (pt0) REVERT: A 429 ASN cc_start: 0.8683 (m-40) cc_final: 0.8284 (m-40) REVERT: A 432 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7679 (tm-30) REVERT: A 445 ARG cc_start: 0.7998 (ptp-110) cc_final: 0.7721 (ptp90) REVERT: B 39 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7566 (ptmm) REVERT: B 256 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7603 (mtt180) REVERT: C 37 HIS cc_start: 0.8682 (OUTLIER) cc_final: 0.7581 (t70) REVERT: C 66 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8368 (mp) REVERT: C 160 ASP cc_start: 0.7601 (t0) cc_final: 0.7361 (t0) REVERT: C 328 MET cc_start: 0.8387 (mtp) cc_final: 0.8179 (mtp) REVERT: C 454 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7603 (tm-30) REVERT: C 518 MET cc_start: 0.7178 (mmt) cc_final: 0.6440 (mtp) REVERT: C 603 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8121 (mtm180) REVERT: D 409 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: D 455 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8406 (mp) REVERT: D 471 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7581 (tm-30) outliers start: 58 outliers final: 44 residues processed: 299 average time/residue: 0.1313 time to fit residues: 56.5941 Evaluate side-chains 307 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 520 TYR Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 603 ARG Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 409 TYR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 22 optimal weight: 0.7980 chunk 116 optimal weight: 0.0060 chunk 157 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 177 optimal weight: 0.0070 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.5414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS B 84 HIS ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN ** D 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.205658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150412 restraints weight = 22212.527| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.86 r_work: 0.3479 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16095 Z= 0.124 Angle : 0.598 10.013 21823 Z= 0.299 Chirality : 0.041 0.158 2457 Planarity : 0.005 0.112 2887 Dihedral : 6.625 62.846 2338 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 3.12 % Allowed : 19.22 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 2029 helix: 1.12 (0.19), residues: 827 sheet: 0.32 (0.29), residues: 323 loop : -1.17 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 275 TYR 0.008 0.001 TYR D 308 PHE 0.020 0.001 PHE A 386 TRP 0.019 0.001 TRP D 401 HIS 0.005 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00294 (16095) covalent geometry : angle 0.59781 (21823) hydrogen bonds : bond 0.03597 ( 680) hydrogen bonds : angle 4.67410 ( 1950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 257 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.8374 (mtm110) cc_final: 0.8082 (mtp85) REVERT: A 80 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: A 94 LEU cc_start: 0.8706 (tp) cc_final: 0.8308 (tt) REVERT: A 110 GLU cc_start: 0.7731 (tp30) cc_final: 0.7410 (mm-30) REVERT: A 146 ASN cc_start: 0.8394 (m-40) cc_final: 0.8081 (m-40) REVERT: A 208 ARG cc_start: 0.7930 (tmt170) cc_final: 0.7394 (tpt90) REVERT: A 214 ARG cc_start: 0.7691 (mtp180) cc_final: 0.7326 (mtp-110) REVERT: A 267 HIS cc_start: 0.6428 (m90) cc_final: 0.5514 (m-70) REVERT: A 275 ARG cc_start: 0.7609 (mtm110) cc_final: 0.7355 (mtm180) REVERT: A 356 ARG cc_start: 0.6480 (mtt90) cc_final: 0.6175 (mtt90) REVERT: A 361 THR cc_start: 0.9010 (m) cc_final: 0.8758 (p) REVERT: A 401 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7962 (pp20) REVERT: A 405 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7546 (pt0) REVERT: A 429 ASN cc_start: 0.8711 (m-40) cc_final: 0.8303 (m-40) REVERT: A 432 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7663 (tm-30) REVERT: A 445 ARG cc_start: 0.7999 (ptp-110) cc_final: 0.7732 (ptp90) REVERT: B 39 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7529 (ptmm) REVERT: B 256 ARG cc_start: 0.7872 (mtt180) cc_final: 0.7664 (mtt180) REVERT: C 37 HIS cc_start: 0.8628 (OUTLIER) cc_final: 0.7670 (t70) REVERT: C 66 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8266 (mp) REVERT: C 454 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7539 (tm-30) REVERT: C 518 MET cc_start: 0.7206 (mmt) cc_final: 0.6506 (mtp) REVERT: C 562 GLN cc_start: 0.7967 (mp10) cc_final: 0.7761 (tt0) REVERT: C 603 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8114 (mtm180) REVERT: D 351 ARG cc_start: 0.8496 (ttm170) cc_final: 0.7968 (mtt180) REVERT: D 409 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: D 471 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7598 (tm-30) outliers start: 51 outliers final: 38 residues processed: 293 average time/residue: 0.1324 time to fit residues: 56.3542 Evaluate side-chains 298 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 603 ARG Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 409 TYR Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 90 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN ** D 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.203282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.147612 restraints weight = 22202.362| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.14 r_work: 0.3422 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16095 Z= 0.174 Angle : 0.638 10.062 21823 Z= 0.319 Chirality : 0.042 0.155 2457 Planarity : 0.005 0.113 2887 Dihedral : 6.761 63.379 2338 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 2.82 % Allowed : 20.01 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 2029 helix: 1.01 (0.18), residues: 829 sheet: 0.27 (0.29), residues: 322 loop : -1.24 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 275 TYR 0.014 0.001 TYR D 308 PHE 0.022 0.001 PHE A 386 TRP 0.019 0.001 TRP D 401 HIS 0.005 0.001 HIS D 246 Details of bonding type rmsd covalent geometry : bond 0.00414 (16095) covalent geometry : angle 0.63829 (21823) hydrogen bonds : bond 0.04337 ( 680) hydrogen bonds : angle 4.78671 ( 1950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4253.06 seconds wall clock time: 73 minutes 27.27 seconds (4407.27 seconds total)