Starting phenix.real_space_refine on Sat Jul 4 19:40:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tjt_25931/07_2026/7tjt_25931.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjt_25931/07_2026/7tjt_25931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7tjt_25931/07_2026/7tjt_25931.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tjt_25931/07_2026/7tjt_25931.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tjt_25931/07_2026/7tjt_25931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjt_25931/07_2026/7tjt_25931.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjt_25931/07_2026/7tjt_25931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjt_25931/07_2026/7tjt_25931.cif" } resolution = 3.2 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= 0.004 sd= 0.246 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 3 5.21 5 S 33 5.16 5 C 14610 2.51 5 N 4038 2.21 5 O 4435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23129 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3607 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 459} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3606 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 458} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3642 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 462} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3433 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "E" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3483 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3497 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1760 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.15, per 1000 atoms: 0.22 Number of scatterers: 23129 At special positions: 0 Unit cell: (128.135, 128.135, 147.748, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 10 15.00 Mg 3 11.99 O 4435 8.00 N 4038 7.00 C 14610 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: 1.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5630 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 20 sheets defined 51.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.897A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.627A pdb=" N ASN A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 226 through 229 removed outlier: 3.905A pdb=" N LYS A 229 " --> pdb=" O ASP A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 241 through 262 Proline residue: A 249 - end of helix removed outlier: 3.623A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.564A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 332 through 335 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.576A pdb=" N ALA A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 404 removed outlier: 3.681A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 removed outlier: 5.671A pdb=" N SER A 410 " --> pdb=" O GLN A 407 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 412 " --> pdb=" O GLY A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.551A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.914A pdb=" N GLY A 457 " --> pdb=" O HIS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 475 Processing helix chain 'A' and resid 478 through 489 removed outlier: 3.644A pdb=" N LEU A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.593A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.912A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 removed outlier: 3.535A pdb=" N ASN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 226 through 229 removed outlier: 3.828A pdb=" N LYS B 229 " --> pdb=" O ASP B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 229' Processing helix chain 'B' and resid 241 through 262 Proline residue: B 249 - end of helix removed outlier: 4.073A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.865A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 297 through 298 No H-bonds generated for 'chain 'B' and resid 297 through 298' Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.665A pdb=" N HIS B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.542A pdb=" N ALA B 379 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 392 through 407 removed outlier: 3.773A pdb=" N ALA B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.536A pdb=" N ARG B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.783A pdb=" N GLY B 457 " --> pdb=" O HIS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 478 removed outlier: 3.685A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 489 Processing helix chain 'B' and resid 492 through 509 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.519A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.991A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 removed outlier: 3.737A pdb=" N ASN C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.689A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.954A pdb=" N ALA C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 391 through 408 removed outlier: 4.533A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 430 removed outlier: 3.605A pdb=" N ARG C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 478 Processing helix chain 'C' and resid 478 through 489 removed outlier: 3.736A pdb=" N LEU C 482 " --> pdb=" O HIS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 508 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 225 through 246 removed outlier: 5.016A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 272 Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 327 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.798A pdb=" N LEU D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 392 removed outlier: 4.950A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 Processing helix chain 'D' and resid 397 through 414 removed outlier: 3.768A pdb=" N ARG D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 462 through 475 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 178 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 225 through 248 removed outlier: 4.820A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 284 through 294 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.542A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 341 Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 392 removed outlier: 4.668A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 396 Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 462 through 474 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 179 removed outlier: 4.715A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 231 through 246 Processing helix chain 'F' and resid 258 through 270 removed outlier: 3.613A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 294 Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 326 Processing helix chain 'F' and resid 327 through 329 No H-bonds generated for 'chain 'F' and resid 327 through 329' Processing helix chain 'F' and resid 336 through 342 removed outlier: 3.837A pdb=" N LEU F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 384 removed outlier: 7.382A pdb=" N GLN F 365 " --> pdb=" O ALA F 361 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N GLU F 366 " --> pdb=" O VAL F 362 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HIS F 367 " --> pdb=" O VAL F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 391 Processing helix chain 'F' and resid 392 through 396 removed outlier: 3.811A pdb=" N GLU F 395 " --> pdb=" O GLY F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 415 removed outlier: 3.739A pdb=" N SER F 415 " --> pdb=" O GLN F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 461 through 475 removed outlier: 4.128A pdb=" N ASP F 465 " --> pdb=" O GLY F 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 55 removed outlier: 3.712A pdb=" N SER G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 100 Processing helix chain 'G' and resid 111 through 121 Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.520A pdb=" N ASN G 125 " --> pdb=" O HIS G 122 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE G 126 " --> pdb=" O PRO G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 139 through 153 Processing helix chain 'G' and resid 155 through 159 removed outlier: 3.673A pdb=" N TYR G 159 " --> pdb=" O ALA G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 Processing helix chain 'G' and resid 205 through 275 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 removed outlier: 5.466A pdb=" N VAL A 33 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE A 44 " --> pdb=" O VAL A 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 40 through 45 current: chain 'A' and resid 62 through 68 removed outlier: 5.797A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 73 through 77 current: chain 'D' and resid 20 through 24 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 20 through 24 current: chain 'D' and resid 44 through 55 removed outlier: 5.631A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 58 through 63 current: chain 'E' and resid 20 through 24 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 20 through 24 current: chain 'E' and resid 46 through 55 removed outlier: 6.559A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.291A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148 removed outlier: 4.562A pdb=" N ILE A 161 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.653A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU A 354 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 170 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 37 removed outlier: 6.506A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 40 through 45 current: chain 'B' and resid 62 through 69 removed outlier: 6.480A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU B 68 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 72 through 77 current: chain 'C' and resid 40 through 45 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 40 through 45 current: chain 'C' and resid 62 through 68 removed outlier: 5.618A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 73 through 77 current: chain 'F' and resid 20 through 24 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 20 through 24 current: chain 'F' and resid 44 through 55 removed outlier: 6.601A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.633A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB1, first strand: chain 'C' and resid 109 through 110 removed outlier: 8.724A pdb=" N ILE C 232 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.124A pdb=" N ILE D 96 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLN D 221 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER D 182 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL D 218 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHE D 184 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY D 220 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY D 186 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE D 153 " --> pdb=" O GLN D 308 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.454A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.639A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE E 153 " --> pdb=" O GLN E 308 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 133 through 134 removed outlier: 4.351A pdb=" N TYR E 147 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.300A pdb=" N ILE F 96 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.195A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 106 through 110 removed outlier: 6.434A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASN G 167 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) 1138 hydrogen bonds defined for protein. 3180 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: 4.61 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7814 1.34 - 1.46: 3733 1.46 - 1.58: 11859 1.58 - 1.69: 15 1.69 - 1.81: 62 Bond restraints: 23483 Sorted by residual: bond pdb=" O3 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" O4 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.568 1.507 0.061 2.00e-02 2.50e+03 9.22e+00 bond pdb=" O2 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.567 1.507 0.060 2.00e-02 2.50e+03 9.13e+00 bond pdb=" O1 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.565 1.507 0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" N ALA G 1 " pdb=" CA ALA G 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 23478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 30600 1.35 - 2.70: 1018 2.70 - 4.06: 208 4.06 - 5.41: 52 5.41 - 6.76: 14 Bond angle restraints: 31892 Sorted by residual: angle pdb=" C TYR B 339 " pdb=" N ILE B 340 " pdb=" CA ILE B 340 " ideal model delta sigma weight residual 120.24 122.61 -2.37 6.30e-01 2.52e+00 1.41e+01 angle pdb=" N GLY E 220 " pdb=" CA GLY E 220 " pdb=" C GLY E 220 " ideal model delta sigma weight residual 112.82 108.04 4.78 1.38e+00 5.25e-01 1.20e+01 angle pdb=" C ASP B 271 " pdb=" N ASP B 272 " pdb=" CA ASP B 272 " ideal model delta sigma weight residual 121.70 127.75 -6.05 1.80e+00 3.09e-01 1.13e+01 angle pdb=" C ILE B 340 " pdb=" CA ILE B 340 " pdb=" CB ILE B 340 " ideal model delta sigma weight residual 114.35 110.85 3.50 1.06e+00 8.90e-01 1.09e+01 angle pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 121.70 127.31 -5.61 1.80e+00 3.09e-01 9.71e+00 ... (remaining 31887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13251 18.00 - 36.00: 720 36.00 - 53.99: 137 53.99 - 71.99: 39 71.99 - 89.99: 18 Dihedral angle restraints: 14165 sinusoidal: 5367 harmonic: 8798 Sorted by residual: dihedral pdb=" CA PHE E 219 " pdb=" C PHE E 219 " pdb=" N GLY E 220 " pdb=" CA GLY E 220 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA GLU E 294 " pdb=" C GLU E 294 " pdb=" N ARG E 295 " pdb=" CA ARG E 295 " ideal model delta harmonic sigma weight residual 180.00 155.43 24.57 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA GLY F 220 " pdb=" C GLY F 220 " pdb=" N GLN F 221 " pdb=" CA GLN F 221 " ideal model delta harmonic sigma weight residual 180.00 -157.48 -22.52 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 14162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3218 0.059 - 0.119: 484 0.119 - 0.178: 76 0.178 - 0.238: 3 0.238 - 0.297: 6 Chirality restraints: 3787 Sorted by residual: chirality pdb=" C3' ATP C 600 " pdb=" C2' ATP C 600 " pdb=" C4' ATP C 600 " pdb=" O3' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 3784 not shown) Planarity restraints: 4135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN G 102 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO G 103 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO G 103 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 103 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 173 " -0.139 9.50e-02 1.11e+02 6.24e-02 2.47e+00 pdb=" NE ARG A 173 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 173 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 173 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 173 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 470 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C PHE B 470 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE B 470 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU B 471 " 0.008 2.00e-02 2.50e+03 ... (remaining 4132 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 107 2.57 - 3.15: 20350 3.15 - 3.74: 34925 3.74 - 4.32: 52313 4.32 - 4.90: 86698 Nonbonded interactions: 194393 Sorted by model distance: nonbonded pdb=" OG SER B 239 " pdb=" OE2 GLU E 294 " model vdw 1.991 3.040 nonbonded pdb=" O GLY D 188 " pdb=" NH1 ARG D 260 " model vdw 1.999 3.120 nonbonded pdb=" OD1 ASP C 335 " pdb=" OG SER C 337 " model vdw 2.051 3.040 nonbonded pdb=" O3G ATP A 600 " pdb="MG MG A 601 " model vdw 2.052 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 2.064 2.170 ... (remaining 194388 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 30 through 222 or (resid 223 and (name N or name CA or nam \ e C or name O or name CB )) or resid 224 through 315 or (resid 316 and (name N o \ r name CA or name C or name O or name CB )) or resid 317 through 382 or (resid 3 \ 83 through 384 and (name N or name CA or name C or name O or name CB )) or resid \ 385 through 393 or (resid 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 404 or (resid 405 through 407 and (name N or name C \ A or name C or name O or name CB )) or resid 412 through 474 or (resid 475 and ( \ name N or name CA or name C or name O or name CB )) or resid 476 through 479 or \ (resid 480 and (name N or name CA or name C or name O or name CB )) or resid 481 \ through 493 or (resid 494 and (name N or name CA or name C or name O or name CB \ )) or resid 495 through 601)) selection = (chain 'B' and (resid 30 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 222 or (resid 223 and (name N or n \ ame CA or name C or name O or name CB )) or resid 224 through 354 or (resid 355 \ through 357 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 8 through 423 or (resid 424 and (name N or name CA or name C or name O or name C \ B )) or resid 425 through 464 or (resid 465 and (name N or name CA or name C or \ name O or name CB )) or resid 466 or (resid 467 and (name N or name CA or name C \ or name O or name CB )) or resid 468 through 474 or (resid 475 and (name N or n \ ame CA or name C or name O or name CB )) or resid 476 through 492 or (resid 493 \ through 494 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 5 through 601)) selection = (chain 'C' and (resid 30 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 315 or (resid 316 and (name N or n \ ame CA or name C or name O or name CB )) or resid 317 through 354 or (resid 355 \ through 357 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 8 through 382 or (resid 383 through 384 and (name N or name CA or name C or name \ O or name CB )) or resid 385 through 393 or (resid 394 and (name N or name CA o \ r name C or name O or name CB )) or resid 395 through 404 or (resid 405 through \ 407 and (name N or name CA or name C or name O or name CB )) or resid 412 throug \ h 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) or \ resid 425 through 464 or (resid 465 and (name N or name CA or name C or name O o \ r name CB )) or resid 466 or (resid 467 and (name N or name CA or name C or name \ O or name CB )) or resid 468 through 492 or (resid 493 through 494 and (name N \ or name CA or name C or name O or name CB )) or resid 495 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 27 or (resid 28 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 through 111 or (resid 112 and (n \ ame N or name CA or name C or name O or name CB )) or resid 113 through 168 or ( \ resid 169 and (name N or name CA or name C or name O or name CB )) or resid 170 \ through 175 or (resid 176 through 177 and (name N or name CA or name C or name O \ or name CB )) or resid 178 through 199 or (resid 200 and (name N or name CA or \ name C or name O or name CB )) or resid 201 through 299 or (resid 300 and (name \ N or name CA or name C or name O or name CB )) or resid 301 through 375 or (resi \ d 376 and (name N or name CA or name C or name O or name CB )) or resid 377 thro \ ugh 475)) selection = (chain 'E' and (resid 8 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 67 or (resid 68 and (name N or name \ CA or name C or name O or name CB )) or resid 69 through 104 or (resid 105 and \ (name N or name CA or name C or name O or name CB )) or resid 106 through 111 or \ (resid 112 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 3 through 168 or (resid 169 and (name N or name CA or name C or name O or name C \ B )) or resid 170 through 175 or (resid 176 through 177 and (name N or name CA o \ r name C or name O or name CB )) or resid 178 through 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 209 or (re \ sid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 th \ rough 383 or (resid 384 through 391 and (name N or name CA or name C or name O o \ r name CB )) or (resid 392 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 403 through 411 or (resid 412 and (name N or name CA or \ name C or name O or name CB )) or resid 413 through 434 or (resid 435 and (name \ N or name CA or name C or name O or name CB )) or resid 436 through 475)) selection = (chain 'F' and (resid 8 through 27 or (resid 28 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 through 42 or (resid 43 and (nam \ e N or name CA or name C or name O or name CB )) or resid 44 through 67 or (resi \ d 68 and (name N or name CA or name C or name O or name CB )) or resid 69 throug \ h 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) or \ resid 106 through 299 or (resid 300 and (name N or name CA or name C or name O o \ r name CB )) or resid 301 through 314 or (resid 315 and (name N or name CA or na \ me C or name O or name CB )) or resid 316 through 375 or (resid 376 and (name N \ or name CA or name C or name O or name CB )) or resid 377 through 383 or (resid \ 384 through 391 and (name N or name CA or name C or name O or name CB )) or resi \ d 392 or (resid 393 through 402 and (name N or name CA or name C or name O or na \ me CB )) or resid 403 through 404 or (resid 405 and (name N or name CA or name C \ or name O or name CB )) or resid 406 through 411 or (resid 412 and (name N or n \ ame CA or name C or name O or name CB )) or resid 413 through 475)) } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.070 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 23483 Z= 0.140 Angle : 0.629 6.759 31892 Z= 0.346 Chirality : 0.046 0.297 3787 Planarity : 0.004 0.065 4135 Dihedral : 12.675 89.991 8535 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.60 (0.15), residues: 3079 helix: 0.68 (0.14), residues: 1276 sheet: 0.08 (0.23), residues: 516 loop : 0.47 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 433 TYR 0.014 0.002 TYR C 360 PHE 0.016 0.001 PHE E 243 TRP 0.016 0.003 TRP C 191 HIS 0.004 0.001 HIS F 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (23483) covalent geometry : angle 0.62938 / 0.35 (31892) hydrogen bonds : bond 0.14232 / 9.32 ( 1138) hydrogen bonds : angle 7.09958 / 4.97 ( 3180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.903 Fit side-chains REVERT: A 228 MET cc_start: 0.8913 (mmm) cc_final: 0.8672 (mmt) REVERT: A 271 ASP cc_start: 0.8268 (t0) cc_final: 0.7803 (t0) REVERT: B 418 GLN cc_start: 0.7057 (tt0) cc_final: 0.6731 (tp40) REVERT: C 64 MET cc_start: 0.8426 (ttt) cc_final: 0.8185 (ttp) REVERT: C 129 SER cc_start: 0.8710 (m) cc_final: 0.8279 (p) REVERT: D 472 LYS cc_start: 0.7972 (mttm) cc_final: 0.7382 (tptt) REVERT: F 164 THR cc_start: 0.8724 (t) cc_final: 0.8288 (p) REVERT: F 172 ASN cc_start: 0.8283 (t0) cc_final: 0.8015 (t0) REVERT: F 311 TYR cc_start: 0.8746 (t80) cc_final: 0.8224 (t80) REVERT: G 113 LYS cc_start: 0.6951 (mmtt) cc_final: 0.6711 (mmtt) REVERT: G 117 GLN cc_start: 0.6598 (mm-40) cc_final: 0.6327 (mm-40) REVERT: G 222 MET cc_start: 0.7329 (ttp) cc_final: 0.7015 (ttm) REVERT: G 229 GLU cc_start: 0.7543 (tt0) cc_final: 0.7156 (tt0) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1812 time to fit residues: 84.0444 Evaluate side-chains 209 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 434 GLN C 224 GLN C 304 HIS D 263 GLN E 221 GLN F 328 HIS G 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.102665 restraints weight = 28750.312| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.62 r_work: 0.2951 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23483 Z= 0.180 Angle : 0.592 7.521 31892 Z= 0.313 Chirality : 0.047 0.248 3787 Planarity : 0.004 0.045 4135 Dihedral : 5.275 88.253 3333 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.93 % Allowed : 4.72 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.97 (0.15), residues: 3079 helix: 1.27 (0.15), residues: 1269 sheet: 0.06 (0.23), residues: 520 loop : 0.45 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 166 TYR 0.025 0.002 TYR F 449 PHE 0.019 0.002 PHE C 395 TRP 0.014 0.002 TRP C 191 HIS 0.006 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (23483) covalent geometry : angle 0.59230 / 0.31 (31892) hydrogen bonds : bond 0.04809 / 3.27 ( 1138) hydrogen bonds : angle 5.36971 / 3.74 ( 3180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 0.866 Fit side-chains REVERT: A 451 VAL cc_start: 0.8403 (p) cc_final: 0.8146 (p) REVERT: B 418 GLN cc_start: 0.7364 (tt0) cc_final: 0.6640 (tp40) REVERT: B 422 ARG cc_start: 0.7351 (ttm170) cc_final: 0.6665 (ttm170) REVERT: B 506 PHE cc_start: 0.7870 (t80) cc_final: 0.6950 (t80) REVERT: C 129 SER cc_start: 0.8946 (m) cc_final: 0.8453 (p) REVERT: C 399 TYR cc_start: 0.8957 (t80) cc_final: 0.8615 (t80) REVERT: D 256 ASP cc_start: 0.8297 (t0) cc_final: 0.8090 (t0) REVERT: D 260 ARG cc_start: 0.8779 (mmt180) cc_final: 0.8518 (mmt90) REVERT: D 472 LYS cc_start: 0.7700 (mttm) cc_final: 0.7131 (tptt) REVERT: F 172 ASN cc_start: 0.8521 (t0) cc_final: 0.8261 (t0) REVERT: G 5 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7766 (mt-10) REVERT: G 17 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6796 (tm-30) REVERT: G 21 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7958 (mtpp) REVERT: G 222 MET cc_start: 0.7578 (ttp) cc_final: 0.7272 (ttm) outliers start: 22 outliers final: 16 residues processed: 250 average time/residue: 0.1812 time to fit residues: 68.9245 Evaluate side-chains 218 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 138 optimal weight: 5.9990 chunk 246 optimal weight: 0.0970 chunk 285 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 282 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.099993 restraints weight = 28984.922| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.75 r_work: 0.2909 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23483 Z= 0.166 Angle : 0.545 7.660 31892 Z= 0.286 Chirality : 0.045 0.259 3787 Planarity : 0.004 0.043 4135 Dihedral : 4.985 80.481 3333 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.88 % Allowed : 6.87 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.16), residues: 3079 helix: 1.54 (0.15), residues: 1275 sheet: -0.05 (0.23), residues: 506 loop : 0.40 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 433 TYR 0.018 0.001 TYR F 449 PHE 0.013 0.001 PHE A 470 TRP 0.012 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (23483) covalent geometry : angle 0.54510 / 0.29 (31892) hydrogen bonds : bond 0.04407 / 3.00 ( 1138) hydrogen bonds : angle 5.08661 / 3.54 ( 3180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 0.880 Fit side-chains REVERT: A 149 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: B 418 GLN cc_start: 0.7320 (tt0) cc_final: 0.6594 (tp40) REVERT: B 422 ARG cc_start: 0.7250 (ttm170) cc_final: 0.6938 (ttm170) REVERT: C 129 SER cc_start: 0.8981 (m) cc_final: 0.8526 (p) REVERT: C 210 GLN cc_start: 0.8442 (mt0) cc_final: 0.8122 (mt0) REVERT: D 256 ASP cc_start: 0.8230 (t0) cc_final: 0.8014 (t0) REVERT: D 260 ARG cc_start: 0.8827 (mmt180) cc_final: 0.8468 (mmt180) REVERT: D 408 ARG cc_start: 0.6957 (mtp85) cc_final: 0.6723 (mtp85) REVERT: E 41 THR cc_start: 0.7782 (OUTLIER) cc_final: 0.7188 (p) REVERT: E 241 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7617 (mt-10) REVERT: E 458 TYR cc_start: 0.8629 (t80) cc_final: 0.8370 (t80) REVERT: E 472 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7825 (tttm) REVERT: F 172 ASN cc_start: 0.8562 (t0) cc_final: 0.8261 (t0) REVERT: G 17 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6904 (tm-30) REVERT: G 21 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7918 (mtpp) REVERT: G 180 LYS cc_start: 0.7835 (mtpp) cc_final: 0.7456 (mtmt) outliers start: 21 outliers final: 13 residues processed: 248 average time/residue: 0.1720 time to fit residues: 65.9789 Evaluate side-chains 222 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 72 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 HIS A 304 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104886 restraints weight = 28650.163| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.69 r_work: 0.2896 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23483 Z= 0.125 Angle : 0.506 8.266 31892 Z= 0.264 Chirality : 0.044 0.283 3787 Planarity : 0.004 0.043 4135 Dihedral : 4.733 73.757 3333 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.18 % Allowed : 8.05 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.16), residues: 3079 helix: 1.71 (0.15), residues: 1294 sheet: -0.01 (0.23), residues: 508 loop : 0.52 (0.18), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 425 TYR 0.022 0.001 TYR F 449 PHE 0.011 0.001 PHE C 506 TRP 0.009 0.001 TRP C 191 HIS 0.004 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (23483) covalent geometry : angle 0.50630 / 0.26 (31892) hydrogen bonds : bond 0.03910 / 2.66 ( 1138) hydrogen bonds : angle 4.90291 / 3.41 ( 3180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: B 418 GLN cc_start: 0.7266 (tt0) cc_final: 0.6506 (tp40) REVERT: B 422 ARG cc_start: 0.7019 (ttm170) cc_final: 0.6776 (ttm170) REVERT: C 88 GLU cc_start: 0.8310 (tp30) cc_final: 0.8079 (tp30) REVERT: C 129 SER cc_start: 0.9002 (m) cc_final: 0.8443 (p) REVERT: D 249 GLN cc_start: 0.8762 (mt0) cc_final: 0.7842 (mm-40) REVERT: D 260 ARG cc_start: 0.8704 (mmt180) cc_final: 0.8362 (mmt180) REVERT: D 408 ARG cc_start: 0.6840 (mtp85) cc_final: 0.6526 (mtp85) REVERT: D 472 LYS cc_start: 0.7396 (mttm) cc_final: 0.7126 (mttm) REVERT: E 241 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7573 (mt-10) REVERT: E 472 LYS cc_start: 0.7914 (mmmt) cc_final: 0.7712 (tttm) REVERT: F 172 ASN cc_start: 0.8399 (t0) cc_final: 0.8050 (t0) REVERT: F 293 GLN cc_start: 0.8514 (mt0) cc_final: 0.8283 (mt0) REVERT: G 5 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7629 (mt-10) REVERT: G 30 ARG cc_start: 0.6015 (OUTLIER) cc_final: 0.5414 (mpp80) REVERT: G 180 LYS cc_start: 0.7834 (mtpp) cc_final: 0.7067 (mmmt) outliers start: 28 outliers final: 16 residues processed: 252 average time/residue: 0.1594 time to fit residues: 61.4030 Evaluate side-chains 231 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 237 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 200 optimal weight: 0.0970 chunk 102 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 HIS B 174 GLN D 24 HIS F 178 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.099270 restraints weight = 28993.097| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.61 r_work: 0.2883 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 23483 Z= 0.287 Angle : 0.623 8.006 31892 Z= 0.323 Chirality : 0.049 0.309 3787 Planarity : 0.005 0.047 4135 Dihedral : 5.006 65.959 3333 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.73 % Allowed : 9.18 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.92 (0.16), residues: 3079 helix: 1.45 (0.15), residues: 1277 sheet: -0.29 (0.23), residues: 503 loop : 0.29 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 166 TYR 0.022 0.002 TYR F 449 PHE 0.018 0.002 PHE B 506 TRP 0.009 0.001 TRP C 191 HIS 0.006 0.001 HIS E 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.29 (23483) covalent geometry : angle 0.62293 / 0.32 (31892) hydrogen bonds : bond 0.04872 / 3.32 ( 1138) hydrogen bonds : angle 5.07551 / 3.52 ( 3180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8319 (mt0) REVERT: B 418 GLN cc_start: 0.7340 (tt0) cc_final: 0.6728 (tp40) REVERT: B 422 ARG cc_start: 0.7200 (ttm170) cc_final: 0.6457 (ttm170) REVERT: C 496 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8385 (mt) REVERT: D 260 ARG cc_start: 0.8766 (mmt180) cc_final: 0.8349 (mmt180) REVERT: E 41 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7185 (p) REVERT: F 172 ASN cc_start: 0.8575 (t0) cc_final: 0.8356 (t0) REVERT: F 222 MET cc_start: 0.9444 (ptp) cc_final: 0.9113 (ptp) REVERT: F 293 GLN cc_start: 0.8765 (mt0) cc_final: 0.8500 (mt0) REVERT: G 30 ARG cc_start: 0.6035 (OUTLIER) cc_final: 0.5347 (mpp80) outliers start: 41 outliers final: 29 residues processed: 242 average time/residue: 0.1733 time to fit residues: 64.7776 Evaluate side-chains 233 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 267 optimal weight: 0.0980 chunk 244 optimal weight: 0.0970 chunk 278 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 203 optimal weight: 0.0870 chunk 98 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 HIS B 174 GLN D 293 GLN D 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.135389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.105471 restraints weight = 28754.738| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.61 r_work: 0.2971 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23483 Z= 0.097 Angle : 0.482 7.653 31892 Z= 0.251 Chirality : 0.043 0.292 3787 Planarity : 0.004 0.044 4135 Dihedral : 4.517 56.953 3333 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.05 % Allowed : 10.40 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.16), residues: 3079 helix: 1.91 (0.15), residues: 1278 sheet: 0.05 (0.24), residues: 485 loop : 0.39 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 425 TYR 0.018 0.001 TYR F 449 PHE 0.011 0.001 PHE C 466 TRP 0.008 0.001 TRP B 191 HIS 0.005 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (23483) covalent geometry : angle 0.48189 / 0.25 (31892) hydrogen bonds : bond 0.03498 / 2.38 ( 1138) hydrogen bonds : angle 4.74605 / 3.28 ( 3180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.889 Fit side-chains REVERT: A 149 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: B 67 ASN cc_start: 0.8749 (m-40) cc_final: 0.8537 (m110) REVERT: B 418 GLN cc_start: 0.7262 (tt0) cc_final: 0.6749 (tp40) REVERT: C 129 SER cc_start: 0.9017 (m) cc_final: 0.8485 (p) REVERT: C 496 LEU cc_start: 0.8825 (mt) cc_final: 0.8442 (mt) REVERT: D 260 ARG cc_start: 0.8703 (mmt180) cc_final: 0.8336 (mmt180) REVERT: D 349 ASP cc_start: 0.8603 (t0) cc_final: 0.7902 (t0) REVERT: E 247 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8357 (mt-10) REVERT: E 294 GLU cc_start: 0.8198 (pt0) cc_final: 0.7496 (tp30) REVERT: F 172 ASN cc_start: 0.8371 (t0) cc_final: 0.8037 (t0) REVERT: F 222 MET cc_start: 0.9366 (ptp) cc_final: 0.8961 (ptp) REVERT: F 293 GLN cc_start: 0.8588 (mt0) cc_final: 0.8362 (mt0) REVERT: G 180 LYS cc_start: 0.7814 (mtpp) cc_final: 0.6831 (mmtp) REVERT: G 189 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7079 (mm-30) outliers start: 25 outliers final: 19 residues processed: 253 average time/residue: 0.1767 time to fit residues: 68.7112 Evaluate side-chains 229 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 200 optimal weight: 5.9990 chunk 159 optimal weight: 0.4980 chunk 240 optimal weight: 2.9990 chunk 294 optimal weight: 30.0000 chunk 105 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 178 optimal weight: 0.0050 chunk 208 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 126 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 HIS D 249 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.105798 restraints weight = 28692.396| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.61 r_work: 0.2912 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23483 Z= 0.135 Angle : 0.499 7.688 31892 Z= 0.259 Chirality : 0.044 0.321 3787 Planarity : 0.004 0.043 4135 Dihedral : 4.457 55.484 3333 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.35 % Allowed : 10.53 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.16), residues: 3079 helix: 1.95 (0.15), residues: 1286 sheet: -0.02 (0.24), residues: 489 loop : 0.40 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.019 0.001 TYR C 473 PHE 0.012 0.001 PHE C 395 TRP 0.007 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (23483) covalent geometry : angle 0.49904 / 0.26 (31892) hydrogen bonds : bond 0.03747 / 2.55 ( 1138) hydrogen bonds : angle 4.72084 / 3.27 ( 3180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.890 Fit side-chains REVERT: A 149 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: B 67 ASN cc_start: 0.8790 (m-40) cc_final: 0.8570 (m110) REVERT: B 418 GLN cc_start: 0.7196 (tt0) cc_final: 0.6686 (tp40) REVERT: C 129 SER cc_start: 0.9019 (m) cc_final: 0.8447 (p) REVERT: C 496 LEU cc_start: 0.8722 (mt) cc_final: 0.8334 (mt) REVERT: D 260 ARG cc_start: 0.8730 (mmt180) cc_final: 0.8341 (mmt180) REVERT: D 289 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8169 (tpt) REVERT: D 349 ASP cc_start: 0.8588 (t0) cc_final: 0.7868 (t0) REVERT: E 247 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8490 (mt-10) REVERT: E 294 GLU cc_start: 0.8234 (pt0) cc_final: 0.7762 (tp30) REVERT: F 172 ASN cc_start: 0.8395 (t0) cc_final: 0.8008 (t0) REVERT: F 222 MET cc_start: 0.9163 (ptp) cc_final: 0.8739 (ptp) REVERT: F 293 GLN cc_start: 0.8766 (mt0) cc_final: 0.8448 (mt0) REVERT: G 17 GLU cc_start: 0.6889 (tm-30) cc_final: 0.6506 (tm-30) REVERT: G 180 LYS cc_start: 0.7885 (mtpp) cc_final: 0.6913 (mmtp) outliers start: 32 outliers final: 24 residues processed: 237 average time/residue: 0.1784 time to fit residues: 64.9844 Evaluate side-chains 232 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 34 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 286 optimal weight: 7.9990 chunk 294 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 95 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.101224 restraints weight = 29235.216| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.70 r_work: 0.2915 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.078 23483 Z= 0.418 Angle : 0.717 8.062 31892 Z= 0.372 Chirality : 0.054 0.331 3787 Planarity : 0.005 0.047 4135 Dihedral : 5.097 57.084 3333 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.73 % Allowed : 10.36 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.63 (0.15), residues: 3079 helix: 1.26 (0.15), residues: 1285 sheet: -0.48 (0.24), residues: 501 loop : 0.09 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 422 TYR 0.021 0.003 TYR B 270 PHE 0.022 0.003 PHE B 506 TRP 0.007 0.002 TRP C 191 HIS 0.007 0.002 HIS D 367 Details of bonding type rmsd/Z covalent geometry : bond 0.01030 / 0.42 (23483) covalent geometry : angle 0.71683 / 0.37 (31892) hydrogen bonds : bond 0.05294 / 3.61 ( 1138) hydrogen bonds : angle 5.13554 / 3.55 ( 3180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.920 Fit side-chains REVERT: A 149 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8360 (mt0) REVERT: B 355 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8407 (tp30) REVERT: B 418 GLN cc_start: 0.7400 (tt0) cc_final: 0.6780 (tp40) REVERT: B 422 ARG cc_start: 0.7317 (ttm170) cc_final: 0.6822 (ttm-80) REVERT: C 496 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8740 (mt) REVERT: D 289 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8585 (tpt) REVERT: D 349 ASP cc_start: 0.8756 (t0) cc_final: 0.8221 (t0) REVERT: F 172 ASN cc_start: 0.8752 (t0) cc_final: 0.8533 (t0) REVERT: F 257 ASN cc_start: 0.8753 (t0) cc_final: 0.8447 (t0) REVERT: F 401 LYS cc_start: 0.8543 (tttm) cc_final: 0.8124 (ttmm) REVERT: G 30 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.5856 (mpp80) REVERT: G 180 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7249 (mmmt) outliers start: 41 outliers final: 30 residues processed: 234 average time/residue: 0.1809 time to fit residues: 64.4535 Evaluate side-chains 236 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 248 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 210 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 199 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 268 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 HIS ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103187 restraints weight = 28920.623| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.64 r_work: 0.2928 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23483 Z= 0.131 Angle : 0.514 7.527 31892 Z= 0.267 Chirality : 0.044 0.323 3787 Planarity : 0.004 0.046 4135 Dihedral : 4.691 51.750 3333 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.22 % Allowed : 11.16 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 3079 helix: 1.65 (0.15), residues: 1291 sheet: -0.24 (0.24), residues: 479 loop : 0.18 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 173 TYR 0.026 0.001 TYR F 449 PHE 0.012 0.001 PHE B 395 TRP 0.008 0.001 TRP B 191 HIS 0.005 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (23483) covalent geometry : angle 0.51374 / 0.27 (31892) hydrogen bonds : bond 0.03922 / 2.67 ( 1138) hydrogen bonds : angle 4.84243 / 3.34 ( 3180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.908 Fit side-chains REVERT: A 149 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: B 67 ASN cc_start: 0.8772 (m-40) cc_final: 0.8565 (m110) REVERT: B 267 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8559 (tp) REVERT: B 418 GLN cc_start: 0.7283 (tt0) cc_final: 0.6624 (tp40) REVERT: B 422 ARG cc_start: 0.7076 (ttm170) cc_final: 0.6611 (ttm-80) REVERT: C 129 SER cc_start: 0.8952 (m) cc_final: 0.8408 (p) REVERT: C 496 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8448 (mt) REVERT: D 260 ARG cc_start: 0.8732 (mmt180) cc_final: 0.8487 (mmt180) REVERT: D 349 ASP cc_start: 0.8649 (t0) cc_final: 0.7991 (t0) REVERT: F 38 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8233 (mm-30) REVERT: F 172 ASN cc_start: 0.8489 (t0) cc_final: 0.8108 (t0) REVERT: F 293 GLN cc_start: 0.8795 (mt0) cc_final: 0.8449 (mt0) REVERT: G 7 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7357 (mm-30) REVERT: G 50 LEU cc_start: 0.7239 (mt) cc_final: 0.7030 (mt) REVERT: G 180 LYS cc_start: 0.7822 (mtpp) cc_final: 0.7223 (mmmt) outliers start: 29 outliers final: 22 residues processed: 230 average time/residue: 0.1822 time to fit residues: 64.0485 Evaluate side-chains 229 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 87 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 277 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 259 optimal weight: 4.9990 chunk 161 optimal weight: 0.0970 chunk 30 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 HIS A 434 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101342 restraints weight = 28711.661| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.75 r_work: 0.2951 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23483 Z= 0.112 Angle : 0.488 7.573 31892 Z= 0.253 Chirality : 0.043 0.340 3787 Planarity : 0.004 0.045 4135 Dihedral : 4.416 48.247 3333 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.14 % Allowed : 11.37 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.16), residues: 3079 helix: 1.88 (0.15), residues: 1290 sheet: -0.15 (0.24), residues: 489 loop : 0.30 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 422 TYR 0.020 0.001 TYR F 449 PHE 0.015 0.001 PHE B 395 TRP 0.008 0.001 TRP B 191 HIS 0.006 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (23483) covalent geometry : angle 0.48834 / 0.25 (31892) hydrogen bonds : bond 0.03599 / 2.45 ( 1138) hydrogen bonds : angle 4.70170 / 3.25 ( 3180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.960 Fit side-chains REVERT: A 149 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: B 67 ASN cc_start: 0.8749 (m-40) cc_final: 0.8544 (m110) REVERT: B 267 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8493 (tp) REVERT: B 395 PHE cc_start: 0.7303 (t80) cc_final: 0.6679 (t80) REVERT: B 418 GLN cc_start: 0.7273 (tt0) cc_final: 0.6624 (tp40) REVERT: B 422 ARG cc_start: 0.7067 (ttm170) cc_final: 0.6841 (ttm170) REVERT: C 129 SER cc_start: 0.9016 (m) cc_final: 0.8516 (p) REVERT: C 271 ASP cc_start: 0.8249 (t0) cc_final: 0.8004 (t0) REVERT: C 496 LEU cc_start: 0.8907 (mt) cc_final: 0.8523 (mt) REVERT: D 144 LEU cc_start: 0.8156 (mp) cc_final: 0.7042 (tt) REVERT: D 260 ARG cc_start: 0.8773 (mmt180) cc_final: 0.8490 (mmt180) REVERT: D 349 ASP cc_start: 0.8675 (t0) cc_final: 0.8043 (t0) REVERT: D 465 ASP cc_start: 0.7938 (m-30) cc_final: 0.7721 (m-30) REVERT: F 172 ASN cc_start: 0.8531 (t0) cc_final: 0.8193 (t0) REVERT: G 180 LYS cc_start: 0.7903 (mtpp) cc_final: 0.7135 (mmmt) outliers start: 27 outliers final: 19 residues processed: 228 average time/residue: 0.1783 time to fit residues: 62.7708 Evaluate side-chains 224 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 296 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 238 optimal weight: 0.0050 chunk 26 optimal weight: 0.1980 chunk 216 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 9 optimal weight: 0.0170 chunk 46 optimal weight: 5.9990 overall best weight: 1.0034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 HIS A 434 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.103720 restraints weight = 28800.342| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.62 r_work: 0.2892 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23483 Z= 0.122 Angle : 0.491 7.687 31892 Z= 0.254 Chirality : 0.044 0.337 3787 Planarity : 0.004 0.044 4135 Dihedral : 4.350 47.064 3333 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.97 % Allowed : 11.75 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.16), residues: 3079 helix: 1.94 (0.15), residues: 1290 sheet: -0.03 (0.25), residues: 475 loop : 0.32 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 422 TYR 0.021 0.001 TYR F 449 PHE 0.014 0.001 PHE B 395 TRP 0.007 0.001 TRP C 191 HIS 0.006 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (23483) covalent geometry : angle 0.49068 / 0.25 (31892) hydrogen bonds : bond 0.03626 / 2.46 ( 1138) hydrogen bonds : angle 4.66885 / 3.22 ( 3180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5566.70 seconds wall clock time: 96 minutes 19.76 seconds (5779.76 seconds total)