Starting phenix.real_space_refine on Sun Aug 24 21:26:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjt_25931/08_2025/7tjt_25931.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjt_25931/08_2025/7tjt_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tjt_25931/08_2025/7tjt_25931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjt_25931/08_2025/7tjt_25931.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tjt_25931/08_2025/7tjt_25931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjt_25931/08_2025/7tjt_25931.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.39, per 1000 atoms: 0.23 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: 2.18 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.86 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: 4.51 Time building geometry restraints manager: 2.82 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: 13291 18.00 - 36.00: 745 36.00 - 53.99: 157 53.99 - 71.99: 45 71.99 - 89.99: 20 Dihedral angle restraints: 14258 sinusoidal: 5460 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 14255 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 21.570 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 13.045 89.991 8628 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 aren 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 covalent geometry : bond 0.00290 (23483) covalent geometry : angle 0.62938 (31892) hydrogen bonds : bond 0.14232 ( 1138) hydrogen bonds : angle 7.09958 ( 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 : 1.031 Fit side-chains REVERT: A 228 MET cc_start: 0.8913 (mmm) cc_final: 0.8672 (mmt) REVERT: A 271 ASP cc_start: 0.8267 (t0) cc_final: 0.7803 (t0) REVERT: B 418 GLN cc_start: 0.7056 (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: 0.6712 (mmtt) REVERT: G 117 GLN cc_start: 0.6598 (mm-40) cc_final: 0.6327 (mm-40) REVERT: G 222 MET cc_start: 0.7330 (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: 0.1800 time to fit residues: 82.8106 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 : 1.179 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3532 r_free = 0.3532 target = 0.133210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.102721 restraints weight = 28735.392| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.62 r_work: 0.2951 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23483 Z= 0.176 Angle : 0.594 7.454 31892 Z= 0.313 Chirality : 0.047 0.246 3787 Planarity : 0.004 0.045 4135 Dihedral : 6.612 84.856 3426 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.97 % Allowed : 4.80 % Favored : 94.23 % 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 aren not related in a simple way. whole: 0.95 (0.15), residues: 3079 helix: 1.25 (0.15), residues: 1269 sheet: 0.06 (0.23), residues: 520 loop : 0.44 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 433 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 covalent geometry : bond 0.00424 (23483) covalent geometry : angle 0.59423 (31892) hydrogen bonds : bond 0.04864 ( 1138) hydrogen bonds : angle 5.38166 ( 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: 23 poor density : 237 time to evaluate : 0.843 Fit side-chains REVERT: A 451 VAL cc_start: 0.8399 (p) cc_final: 0.8140 (p) REVERT: B 161 ILE cc_start: 0.9031 (mt) cc_final: 0.8811 (mt) REVERT: B 418 GLN cc_start: 0.7360 (tt0) cc_final: 0.6636 (tp40) REVERT: B 422 ARG cc_start: 0.7369 (ttm170) cc_final: 0.6702 (ttm170) REVERT: B 506 PHE cc_start: 0.7864 (t80) cc_final: 0.6952 (t80) REVERT: C 129 SER cc_start: 0.8945 (m) cc_final: 0.8448 (p) REVERT: C 399 TYR cc_start: 0.8955 (t80) cc_final: 0.8617 (t80) REVERT: D 256 ASP cc_start: 0.8302 (t0) cc_final: 0.8081 (t0) REVERT: D 260 ARG cc_start: 0.8777 (mmt180) cc_final: 0.8511 (mmt90) REVERT: D 472 LYS cc_start: 0.7695 (mttm) cc_final: 0.7127 (tptt) REVERT: F 172 ASN cc_start: 0.8519 (t0) cc_final: 0.8259 (t0) REVERT: F 256 ASP cc_start: 0.7980 (t0) cc_final: 0.7719 (t0) REVERT: G 5 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7761 (mt-10) REVERT: G 17 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6605 (tm-30) REVERT: G 21 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7895 (mtpp) REVERT: G 222 MET cc_start: 0.7570 (ttp) cc_final: 0.7263 (ttm) outliers start: 23 outliers final: 17 residues processed: 250 average time/residue: 0.1854 time to fit residues: 70.2801 Evaluate side-chains 221 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 F residue 292 LEU 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: 6.9990 chunk 246 optimal weight: 0.0020 chunk 285 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 282 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN E 24 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.102962 restraints weight = 28834.021| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.62 r_work: 0.2878 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1567 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= 0.165 Angle : 0.547 7.624 31892 Z= 0.287 Chirality : 0.045 0.271 3787 Planarity : 0.004 0.042 4135 Dihedral : 6.440 86.157 3426 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.93 % Allowed : 6.49 % Favored : 92.59 % 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 aren not related in a simple way. whole: 1.09 (0.16), residues: 3079 helix: 1.49 (0.15), residues: 1274 sheet: -0.03 (0.23), residues: 506 loop : 0.42 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 425 TYR 0.019 0.001 TYR F 449 PHE 0.016 0.001 PHE C 395 TRP 0.011 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00394 (23483) covalent geometry : angle 0.54707 (31892) hydrogen bonds : bond 0.04450 ( 1138) hydrogen bonds : angle 5.14865 ( 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 248 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.990 Fit side-chains REVERT: A 149 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: B 161 ILE cc_start: 0.8939 (mt) cc_final: 0.8705 (mt) REVERT: B 418 GLN cc_start: 0.7279 (tt0) cc_final: 0.6550 (tp40) REVERT: B 422 ARG cc_start: 0.7126 (ttm170) cc_final: 0.6434 (ttm170) REVERT: C 56 GLU cc_start: 0.8277 (tt0) cc_final: 0.8023 (tt0) REVERT: C 129 SER cc_start: 0.8971 (m) cc_final: 0.8406 (p) REVERT: D 256 ASP cc_start: 0.8172 (t0) cc_final: 0.7935 (t0) REVERT: D 260 ARG cc_start: 0.8705 (mmt180) cc_final: 0.8291 (mmt180) REVERT: F 172 ASN cc_start: 0.8444 (t0) cc_final: 0.8125 (t0) REVERT: G 5 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7729 (mt-10) REVERT: G 7 GLU cc_start: 0.7692 (tt0) cc_final: 0.7486 (tt0) REVERT: G 17 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6562 (tm-30) REVERT: G 21 LYS cc_start: 0.8082 (mtpp) cc_final: 0.7766 (mtpp) REVERT: G 180 LYS cc_start: 0.7942 (mtpp) cc_final: 0.6960 (mmmt) outliers start: 22 outliers final: 16 residues processed: 239 average time/residue: 0.1719 time to fit residues: 62.8203 Evaluate side-chains 219 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 420 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 113 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 72 optimal weight: 0.9980 chunk 19 optimal weight: 0.0060 chunk 190 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A 304 HIS C 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.101860 restraints weight = 28788.229| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.76 r_work: 0.2938 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23483 Z= 0.121 Angle : 0.502 7.671 31892 Z= 0.263 Chirality : 0.044 0.283 3787 Planarity : 0.004 0.042 4135 Dihedral : 6.111 86.828 3426 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.01 % Allowed : 7.37 % Favored : 91.62 % 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 aren not related in a simple way. whole: 1.35 (0.16), residues: 3079 helix: 1.75 (0.15), residues: 1283 sheet: 0.13 (0.24), residues: 494 loop : 0.50 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 425 TYR 0.018 0.001 TYR B 473 PHE 0.014 0.001 PHE B 466 TRP 0.010 0.001 TRP C 191 HIS 0.004 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00279 (23483) covalent geometry : angle 0.50152 (31892) hydrogen bonds : bond 0.03853 ( 1138) hydrogen bonds : angle 4.89087 ( 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 256 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: B 418 GLN cc_start: 0.7279 (tt0) cc_final: 0.6787 (tp40) REVERT: C 56 GLU cc_start: 0.8373 (tt0) cc_final: 0.7919 (tp30) REVERT: C 129 SER cc_start: 0.9009 (m) cc_final: 0.8551 (p) REVERT: D 249 GLN cc_start: 0.8657 (mt0) cc_final: 0.7889 (mm-40) REVERT: D 256 ASP cc_start: 0.8165 (t0) cc_final: 0.7932 (t0) REVERT: D 260 ARG cc_start: 0.8838 (mmt180) cc_final: 0.8525 (mmt180) REVERT: E 41 THR cc_start: 0.7546 (OUTLIER) cc_final: 0.7113 (p) REVERT: E 472 LYS cc_start: 0.8023 (mmmt) cc_final: 0.7820 (tttm) REVERT: F 172 ASN cc_start: 0.8500 (t0) cc_final: 0.8179 (t0) REVERT: F 222 MET cc_start: 0.9516 (ptp) cc_final: 0.9259 (ptp) REVERT: G 72 GLU cc_start: 0.4467 (tm-30) cc_final: 0.4181 (tm-30) REVERT: G 180 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7125 (mmmt) outliers start: 24 outliers final: 13 residues processed: 248 average time/residue: 0.1704 time to fit residues: 64.6712 Evaluate side-chains 225 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 E residue 41 THR Chi-restraints excluded: chain E residue 460 VAL 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: 3.9990 chunk 304 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 8 optimal weight: 0.0060 chunk 141 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 199 optimal weight: 0.9980 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS D 24 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.102368 restraints weight = 28740.136| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.61 r_work: 0.2891 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23483 Z= 0.179 Angle : 0.534 7.839 31892 Z= 0.278 Chirality : 0.046 0.298 3787 Planarity : 0.004 0.043 4135 Dihedral : 6.144 89.131 3426 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.47 % Allowed : 8.21 % Favored : 90.31 % 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 aren not related in a simple way. whole: 1.28 (0.16), residues: 3079 helix: 1.72 (0.15), residues: 1287 sheet: 0.06 (0.24), residues: 488 loop : 0.43 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 425 TYR 0.021 0.002 TYR D 381 PHE 0.012 0.002 PHE F 261 TRP 0.009 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00433 (23483) covalent geometry : angle 0.53423 (31892) hydrogen bonds : bond 0.04172 ( 1138) hydrogen bonds : angle 4.88073 ( 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 258 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: B 418 GLN cc_start: 0.7145 (tt0) cc_final: 0.6528 (tp40) REVERT: C 56 GLU cc_start: 0.8362 (tt0) cc_final: 0.7801 (tp30) REVERT: C 129 SER cc_start: 0.9016 (m) cc_final: 0.8463 (p) REVERT: C 496 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8352 (mt) REVERT: D 249 GLN cc_start: 0.8826 (mt0) cc_final: 0.7941 (mm-40) REVERT: D 260 ARG cc_start: 0.8724 (mmt180) cc_final: 0.8383 (mmt180) REVERT: E 41 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7109 (p) REVERT: E 241 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7585 (mt-10) REVERT: E 294 GLU cc_start: 0.8339 (pt0) cc_final: 0.7586 (tp30) REVERT: F 172 ASN cc_start: 0.8469 (t0) cc_final: 0.8098 (t0) REVERT: F 222 MET cc_start: 0.9497 (ptp) cc_final: 0.9162 (ptp) REVERT: G 180 LYS cc_start: 0.7835 (mtpp) cc_final: 0.7110 (mmmt) outliers start: 35 outliers final: 23 residues processed: 244 average time/residue: 0.1854 time to fit residues: 69.0852 Evaluate side-chains 234 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 388 VAL 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 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 62 ILE 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 460 VAL 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: 3.9990 chunk 244 optimal weight: 0.0010 chunk 278 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 203 optimal weight: 0.0670 chunk 98 optimal weight: 0.0980 chunk 171 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A 210 GLN C 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104484 restraints weight = 28840.618| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.61 r_work: 0.2977 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2235 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= 0.121 Angle : 0.487 7.720 31892 Z= 0.254 Chirality : 0.043 0.300 3787 Planarity : 0.004 0.042 4135 Dihedral : 5.929 89.611 3426 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.26 % Allowed : 9.14 % Favored : 89.60 % 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 aren not related in a simple way. whole: 1.42 (0.16), residues: 3079 helix: 1.92 (0.15), residues: 1286 sheet: 0.12 (0.24), residues: 483 loop : 0.41 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 425 TYR 0.019 0.001 TYR C 473 PHE 0.010 0.001 PHE B 506 TRP 0.007 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00283 (23483) covalent geometry : angle 0.48749 (31892) hydrogen bonds : bond 0.03684 ( 1138) hydrogen bonds : angle 4.73376 ( 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 263 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.803 Fit side-chains REVERT: A 149 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: B 67 ASN cc_start: 0.8754 (m-40) cc_final: 0.8543 (m110) REVERT: B 418 GLN cc_start: 0.6915 (tt0) cc_final: 0.6531 (tp40) REVERT: C 56 GLU cc_start: 0.8341 (tt0) cc_final: 0.7932 (tp30) REVERT: C 129 SER cc_start: 0.9021 (m) cc_final: 0.8511 (p) REVERT: C 496 LEU cc_start: 0.8799 (mt) cc_final: 0.8393 (mt) REVERT: D 260 ARG cc_start: 0.8788 (mmt180) cc_final: 0.8484 (mmt180) REVERT: D 349 ASP cc_start: 0.8640 (t0) cc_final: 0.7924 (t0) REVERT: E 294 GLU cc_start: 0.8264 (pt0) cc_final: 0.7807 (tp30) REVERT: F 172 ASN cc_start: 0.8409 (t0) cc_final: 0.8068 (t0) REVERT: F 222 MET cc_start: 0.9424 (ptp) cc_final: 0.9001 (ptp) REVERT: G 180 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7093 (mmmt) REVERT: G 189 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6974 (mm-30) outliers start: 30 outliers final: 22 residues processed: 254 average time/residue: 0.1676 time to fit residues: 64.7920 Evaluate side-chains 229 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 382 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 392 LEU 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 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 136 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 460 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 200 optimal weight: 0.0970 chunk 159 optimal weight: 0.5980 chunk 240 optimal weight: 0.9990 chunk 294 optimal weight: 30.0000 chunk 105 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 208 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 118 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A 210 GLN C 95 ASN D 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.137290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.107446 restraints weight = 28605.461| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.61 r_work: 0.2989 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23483 Z= 0.109 Angle : 0.484 10.085 31892 Z= 0.251 Chirality : 0.043 0.321 3787 Planarity : 0.004 0.041 4135 Dihedral : 5.804 88.499 3426 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.26 % Allowed : 9.98 % Favored : 88.75 % 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 aren not related in a simple way. whole: 1.54 (0.16), residues: 3079 helix: 2.00 (0.15), residues: 1289 sheet: 0.17 (0.25), residues: 478 loop : 0.49 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 422 TYR 0.015 0.001 TYR C 473 PHE 0.014 0.001 PHE B 395 TRP 0.007 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00248 (23483) covalent geometry : angle 0.48415 (31892) hydrogen bonds : bond 0.03539 ( 1138) hydrogen bonds : angle 4.66652 ( 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 258 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.552 Fit side-chains REVERT: A 149 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8254 (mt0) REVERT: B 67 ASN cc_start: 0.8726 (m-40) cc_final: 0.8505 (m110) REVERT: B 418 GLN cc_start: 0.6974 (tt0) cc_final: 0.6561 (tp40) REVERT: C 56 GLU cc_start: 0.8364 (tt0) cc_final: 0.7985 (tp30) REVERT: C 129 SER cc_start: 0.9019 (m) cc_final: 0.8514 (p) REVERT: C 271 ASP cc_start: 0.7865 (t0) cc_final: 0.7603 (t70) REVERT: C 496 LEU cc_start: 0.8815 (mt) cc_final: 0.8432 (mt) REVERT: D 260 ARG cc_start: 0.8794 (mmt180) cc_final: 0.8509 (mmt180) REVERT: D 349 ASP cc_start: 0.8659 (t0) cc_final: 0.7952 (t0) REVERT: E 294 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7753 (tp30) REVERT: F 172 ASN cc_start: 0.8383 (t0) cc_final: 0.8031 (t0) REVERT: F 222 MET cc_start: 0.9189 (ptp) cc_final: 0.8777 (ptp) REVERT: G 180 LYS cc_start: 0.7857 (mtpp) cc_final: 0.7115 (mmmt) outliers start: 30 outliers final: 21 residues processed: 247 average time/residue: 0.1624 time to fit residues: 60.9599 Evaluate side-chains 238 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 382 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 392 LEU 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 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 136 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 460 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 0.0970 chunk 172 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 286 optimal weight: 4.9990 chunk 294 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS D 293 GLN D 308 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.135097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.106735 restraints weight = 28692.535| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.67 r_work: 0.2981 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23483 Z= 0.162 Angle : 0.514 7.978 31892 Z= 0.266 Chirality : 0.045 0.331 3787 Planarity : 0.004 0.042 4135 Dihedral : 5.892 87.882 3426 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.39 % Allowed : 10.07 % 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 aren not related in a simple way. whole: 1.43 (0.16), residues: 3079 helix: 1.94 (0.15), residues: 1287 sheet: 0.12 (0.24), residues: 490 loop : 0.41 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 422 TYR 0.023 0.001 TYR A 448 PHE 0.014 0.001 PHE B 395 TRP 0.007 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00392 (23483) covalent geometry : angle 0.51402 (31892) hydrogen bonds : bond 0.03856 ( 1138) hydrogen bonds : angle 4.70014 ( 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 249 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.921 Fit side-chains REVERT: A 149 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8258 (mt0) REVERT: B 418 GLN cc_start: 0.7173 (tt0) cc_final: 0.6769 (tp40) REVERT: C 56 GLU cc_start: 0.8300 (tt0) cc_final: 0.7983 (tp30) REVERT: C 129 SER cc_start: 0.8996 (m) cc_final: 0.8543 (p) REVERT: C 271 ASP cc_start: 0.8162 (t0) cc_final: 0.7922 (t70) REVERT: C 496 LEU cc_start: 0.8988 (mt) cc_final: 0.8621 (mt) REVERT: D 260 ARG cc_start: 0.8852 (mmt180) cc_final: 0.8556 (mmt180) REVERT: D 289 MET cc_start: 0.8934 (mmm) cc_final: 0.8712 (tpt) REVERT: D 349 ASP cc_start: 0.8676 (t0) cc_final: 0.8053 (t0) REVERT: E 294 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7691 (tp30) REVERT: F 172 ASN cc_start: 0.8501 (t0) cc_final: 0.8150 (t0) REVERT: G 180 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7191 (mmmt) outliers start: 33 outliers final: 24 residues processed: 238 average time/residue: 0.1773 time to fit residues: 64.0431 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 : 0.896 ------------------------------------------------------------------------------- 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 B residue 272 ASP Chi-restraints excluded: chain B residue 392 LEU 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 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 136 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 72 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.4366 > 50: distance: 50 - 54: 11.309 distance: 51 - 77: 9.037 distance: 54 - 55: 3.084 distance: 55 - 56: 4.961 distance: 55 - 58: 8.176 distance: 56 - 57: 7.964 distance: 56 - 65: 7.882 distance: 57 - 83: 22.923 distance: 58 - 59: 14.646 distance: 59 - 60: 12.085 distance: 60 - 61: 8.835 distance: 61 - 62: 4.737 distance: 62 - 63: 13.960 distance: 62 - 64: 5.764 distance: 65 - 66: 3.119 distance: 66 - 67: 7.002 distance: 67 - 68: 10.683 distance: 67 - 69: 4.264 distance: 69 - 70: 15.341 distance: 70 - 71: 17.074 distance: 70 - 73: 8.799 distance: 71 - 72: 13.601 distance: 71 - 77: 24.197 distance: 73 - 74: 13.856 distance: 73 - 75: 10.046 distance: 74 - 76: 14.931 distance: 77 - 78: 11.714 distance: 78 - 79: 10.828 distance: 78 - 81: 14.074 distance: 79 - 80: 17.075 distance: 79 - 83: 10.814 distance: 81 - 82: 5.684 distance: 83 - 84: 6.303 distance: 84 - 85: 5.243 distance: 84 - 87: 7.160 distance: 85 - 86: 26.017 distance: 85 - 92: 17.367 distance: 87 - 88: 11.749 distance: 88 - 89: 9.847 distance: 89 - 90: 11.694 distance: 89 - 91: 8.662 distance: 92 - 93: 17.549 distance: 93 - 94: 24.184 distance: 93 - 96: 18.376 distance: 94 - 95: 9.769 distance: 94 - 100: 13.428 distance: 96 - 97: 17.131 distance: 97 - 98: 15.660 distance: 97 - 99: 5.489 distance: 100 - 101: 8.068 distance: 101 - 102: 22.450 distance: 102 - 103: 23.149 distance: 102 - 104: 3.436 distance: 104 - 105: 23.345 distance: 105 - 106: 8.867 distance: 105 - 108: 22.554 distance: 106 - 107: 17.803 distance: 106 - 112: 19.853 distance: 108 - 109: 13.161 distance: 108 - 110: 17.139 distance: 109 - 111: 28.388 distance: 112 - 113: 5.121 distance: 113 - 114: 12.423 distance: 113 - 116: 16.870 distance: 114 - 115: 10.283 distance: 114 - 124: 26.278 distance: 116 - 117: 3.407 distance: 117 - 118: 20.188 distance: 117 - 119: 21.620 distance: 118 - 120: 9.328 distance: 119 - 121: 5.309 distance: 120 - 122: 29.195 distance: 121 - 122: 20.104 distance: 122 - 123: 12.680 distance: 124 - 125: 8.705 distance: 124 - 130: 29.166 distance: 125 - 126: 11.709 distance: 125 - 128: 19.404 distance: 126 - 127: 8.106 distance: 126 - 131: 13.351 distance: 128 - 129: 13.316