Starting phenix.real_space_refine on Fri Jun 20 00:06:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjt_25931/06_2025/7tjt_25931.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjt_25931/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tjt_25931/06_2025/7tjt_25931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjt_25931/06_2025/7tjt_25931.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjt_25931/06_2025/7tjt_25931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjt_25931/06_2025/7tjt_25931.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 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: {'PHE:plan': 1, 'GLU:plan': 4, '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: {'PHE:plan': 1, 'GLU:plan': 3, '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, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} 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: 14.05, per 1000 atoms: 0.61 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: 5.62 Conformation dependent library (CDL) restraints added in 2.9 seconds 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5630 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 20 sheets defined 51.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 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: 7.65 Time building geometry restraints manager: 6.64 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 509 or resid 600 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 509 or resid 600 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 509 or resid 6 \ 00 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 51.300 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (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 TRP 0.016 0.003 TRP C 191 HIS 0.004 0.001 HIS F 367 PHE 0.016 0.001 PHE E 243 TYR 0.014 0.002 TYR C 360 ARG 0.009 0.001 ARG E 433 Details of bonding type rmsd hydrogen bonds : bond 0.14232 ( 1138) hydrogen bonds : angle 7.09958 ( 3180) covalent geometry : bond 0.00290 (23483) covalent geometry : angle 0.62938 (31892) *********************** 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 : 2.511 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: 0.3997 time to fit residues: 184.5627 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 : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 145 optimal weight: 0.6980 chunk 178 optimal weight: 8.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 F 328 HIS G 49 GLN G 117 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102584 restraints weight = 28686.442| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.61 r_work: 0.2950 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1241 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= 0.178 Angle : 0.591 7.459 31892 Z= 0.312 Chirality : 0.047 0.247 3787 Planarity : 0.004 0.046 4135 Dihedral : 6.632 84.980 3426 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.93 % Allowed : 4.68 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.15), residues: 3079 helix: 1.26 (0.15), residues: 1269 sheet: 0.04 (0.23), residues: 524 loop : 0.46 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 191 HIS 0.005 0.001 HIS A 478 PHE 0.019 0.002 PHE C 395 TYR 0.025 0.002 TYR F 449 ARG 0.006 0.001 ARG E 433 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 1138) hydrogen bonds : angle 5.40836 ( 3180) covalent geometry : bond 0.00429 (23483) covalent geometry : angle 0.59108 (31892) *********************** 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 257 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 2.692 Fit side-chains REVERT: A 451 VAL cc_start: 0.8400 (p) cc_final: 0.8147 (p) REVERT: B 418 GLN cc_start: 0.7363 (tt0) cc_final: 0.6638 (tp40) REVERT: B 422 ARG cc_start: 0.7375 (ttm170) cc_final: 0.6669 (ttm170) REVERT: B 506 PHE cc_start: 0.7866 (t80) cc_final: 0.6942 (t80) REVERT: C 129 SER cc_start: 0.8948 (m) cc_final: 0.8452 (p) REVERT: C 399 TYR cc_start: 0.8956 (t80) cc_final: 0.8618 (t80) REVERT: D 256 ASP cc_start: 0.8312 (t0) cc_final: 0.8104 (t0) REVERT: D 260 ARG cc_start: 0.8775 (mmt180) cc_final: 0.8514 (mmt90) REVERT: D 472 LYS cc_start: 0.7698 (mttm) cc_final: 0.7130 (tptt) REVERT: E 241 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7403 (mt-10) REVERT: F 172 ASN cc_start: 0.8524 (t0) cc_final: 0.8262 (t0) REVERT: F 256 ASP cc_start: 0.7981 (t0) cc_final: 0.7719 (t0) REVERT: G 5 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7757 (mt-10) REVERT: G 17 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6877 (tm-30) REVERT: G 21 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7971 (mtpp) REVERT: G 222 MET cc_start: 0.7571 (ttp) cc_final: 0.7263 (ttm) outliers start: 22 outliers final: 17 residues processed: 247 average time/residue: 0.5065 time to fit residues: 195.9053 Evaluate side-chains 222 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 4.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 162 ILE 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 55 optimal weight: 3.9990 chunk 223 optimal weight: 0.0770 chunk 2 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 216 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 276 optimal weight: 0.7980 chunk 204 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS E 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.105985 restraints weight = 28385.064| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.61 r_work: 0.2974 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23483 Z= 0.109 Angle : 0.504 7.561 31892 Z= 0.265 Chirality : 0.044 0.270 3787 Planarity : 0.004 0.039 4135 Dihedral : 6.186 84.813 3426 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.88 % Allowed : 6.23 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 3079 helix: 1.67 (0.15), residues: 1286 sheet: 0.22 (0.24), residues: 492 loop : 0.55 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 PHE 0.017 0.001 PHE B 466 TYR 0.017 0.001 TYR F 449 ARG 0.004 0.000 ARG C 425 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 1138) hydrogen bonds : angle 4.97180 ( 3180) covalent geometry : bond 0.00237 (23483) covalent geometry : angle 0.50362 (31892) *********************** 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 274 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 2.592 Fit side-chains REVERT: A 149 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: A 228 MET cc_start: 0.9116 (mmt) cc_final: 0.8886 (tpp) REVERT: A 451 VAL cc_start: 0.8418 (p) cc_final: 0.8181 (p) REVERT: B 418 GLN cc_start: 0.7295 (tt0) cc_final: 0.6740 (tp40) REVERT: C 129 SER cc_start: 0.8996 (m) cc_final: 0.8492 (p) REVERT: D 249 GLN cc_start: 0.8568 (mt0) cc_final: 0.7789 (mm-40) REVERT: D 256 ASP cc_start: 0.8118 (t0) cc_final: 0.7849 (t0) REVERT: D 260 ARG cc_start: 0.8736 (mmt180) cc_final: 0.8352 (mmt180) REVERT: D 408 ARG cc_start: 0.6778 (mtp85) cc_final: 0.6545 (mtp85) REVERT: D 472 LYS cc_start: 0.7662 (mttm) cc_final: 0.7117 (tptt) REVERT: E 41 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7176 (p) REVERT: E 472 LYS cc_start: 0.7956 (mmmt) cc_final: 0.7747 (tttm) REVERT: F 172 ASN cc_start: 0.8411 (t0) cc_final: 0.8105 (t0) REVERT: G 5 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7711 (mt-10) REVERT: G 7 GLU cc_start: 0.7660 (tt0) cc_final: 0.7444 (tt0) REVERT: G 17 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6727 (tm-30) REVERT: G 21 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7815 (mtpp) REVERT: G 180 LYS cc_start: 0.7870 (mtpp) cc_final: 0.6879 (mmtp) outliers start: 21 outliers final: 12 residues processed: 263 average time/residue: 0.3665 time to fit residues: 148.6383 Evaluate side-chains 226 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 149 GLN 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 113 LEU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 41 THR 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 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 172 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 297 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 136 optimal weight: 0.0060 chunk 195 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- 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 D 293 GLN D 308 GLN E 24 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105616 restraints weight = 28823.365| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.76 r_work: 0.2974 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23483 Z= 0.123 Angle : 0.501 7.979 31892 Z= 0.262 Chirality : 0.044 0.283 3787 Planarity : 0.004 0.041 4135 Dihedral : 6.006 86.305 3426 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.14 % Allowed : 7.83 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.16), residues: 3079 helix: 1.84 (0.15), residues: 1286 sheet: 0.27 (0.24), residues: 489 loop : 0.57 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 PHE 0.018 0.001 PHE B 466 TYR 0.017 0.001 TYR B 473 ARG 0.004 0.000 ARG C 425 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 1138) hydrogen bonds : angle 4.84810 ( 3180) covalent geometry : bond 0.00287 (23483) covalent geometry : angle 0.50107 (31892) *********************** 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 258 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 5.048 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: B 418 GLN cc_start: 0.7239 (tt0) cc_final: 0.6728 (tp40) REVERT: B 486 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7588 (ttm110) REVERT: C 56 GLU cc_start: 0.8326 (tt0) cc_final: 0.7875 (tp30) REVERT: C 129 SER cc_start: 0.9011 (m) cc_final: 0.8539 (p) REVERT: C 496 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8327 (mt) REVERT: D 249 GLN cc_start: 0.8630 (mt0) cc_final: 0.7872 (mm-40) REVERT: D 260 ARG cc_start: 0.8803 (mmt180) cc_final: 0.8494 (mmt180) REVERT: D 356 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7676 (ttm-80) REVERT: D 408 ARG cc_start: 0.6925 (mtp85) cc_final: 0.6613 (mtp85) REVERT: E 241 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7527 (mt-10) REVERT: E 294 GLU cc_start: 0.8123 (pt0) cc_final: 0.7552 (tp30) REVERT: E 354 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8007 (mttp) REVERT: F 172 ASN cc_start: 0.8458 (t0) cc_final: 0.8134 (t0) REVERT: F 222 MET cc_start: 0.9480 (ptp) cc_final: 0.9161 (ptp) REVERT: G 17 GLU cc_start: 0.7232 (tm-30) cc_final: 0.7029 (tm-30) REVERT: G 30 ARG cc_start: 0.6119 (OUTLIER) cc_final: 0.5453 (mpp80) REVERT: G 180 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7128 (mmmt) outliers start: 27 outliers final: 15 residues processed: 248 average time/residue: 0.4465 time to fit residues: 169.5302 Evaluate side-chains 227 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 2.711 ------------------------------------------------------------------------------- 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 C residue 496 LEU 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 30 ARG Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 222 optimal weight: 0.3980 chunk 229 optimal weight: 4.9990 chunk 34 optimal weight: 0.0980 chunk 177 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 299 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107098 restraints weight = 28595.870| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.61 r_work: 0.3015 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23483 Z= 0.097 Angle : 0.474 7.653 31892 Z= 0.247 Chirality : 0.043 0.288 3787 Planarity : 0.004 0.040 4135 Dihedral : 5.788 87.588 3426 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.05 % Allowed : 8.55 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.16), residues: 3079 helix: 2.06 (0.15), residues: 1281 sheet: 0.30 (0.24), residues: 486 loop : 0.66 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 191 HIS 0.005 0.000 HIS A 478 PHE 0.012 0.001 PHE B 466 TYR 0.021 0.001 TYR D 381 ARG 0.004 0.000 ARG E 337 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 1138) hydrogen bonds : angle 4.68220 ( 3180) covalent geometry : bond 0.00214 (23483) covalent geometry : angle 0.47357 (31892) *********************** 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 263 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 5.292 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8349 (mt0) REVERT: B 418 GLN cc_start: 0.6875 (tt0) cc_final: 0.6484 (tp40) REVERT: C 56 GLU cc_start: 0.8341 (tt0) cc_final: 0.7895 (tp30) REVERT: C 129 SER cc_start: 0.9019 (m) cc_final: 0.8522 (p) REVERT: D 249 GLN cc_start: 0.8622 (mt0) cc_final: 0.7798 (mm-40) REVERT: D 260 ARG cc_start: 0.8750 (mmt180) cc_final: 0.8456 (mmt180) REVERT: E 222 MET cc_start: 0.8465 (ttm) cc_final: 0.8224 (ttp) REVERT: E 247 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8315 (mt-10) REVERT: E 294 GLU cc_start: 0.8084 (pt0) cc_final: 0.7489 (tp30) REVERT: E 354 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8162 (mttp) REVERT: F 172 ASN cc_start: 0.8412 (t0) cc_final: 0.8071 (t0) REVERT: F 222 MET cc_start: 0.9421 (ptp) cc_final: 0.9066 (ptp) REVERT: F 405 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8119 (pt0) REVERT: F 449 TYR cc_start: 0.8834 (m-80) cc_final: 0.8631 (m-80) REVERT: G 180 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7108 (mmmt) outliers start: 25 outliers final: 17 residues processed: 253 average time/residue: 0.4429 time to fit residues: 172.5616 Evaluate side-chains 232 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 2.484 ------------------------------------------------------------------------------- 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 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 D residue 113 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 336 SER 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 246 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 99 optimal weight: 0.0010 chunk 89 optimal weight: 6.9990 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106789 restraints weight = 28511.428| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.69 r_work: 0.3028 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23483 Z= 0.136 Angle : 0.495 7.704 31892 Z= 0.257 Chirality : 0.044 0.314 3787 Planarity : 0.004 0.041 4135 Dihedral : 5.811 89.344 3426 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.52 % Allowed : 8.80 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.16), residues: 3079 helix: 2.01 (0.15), residues: 1289 sheet: 0.31 (0.24), residues: 498 loop : 0.57 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 PHE 0.014 0.001 PHE B 395 TYR 0.021 0.001 TYR A 448 ARG 0.004 0.000 ARG C 425 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 1138) hydrogen bonds : angle 4.67239 ( 3180) covalent geometry : bond 0.00324 (23483) covalent geometry : angle 0.49526 (31892) *********************** 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 261 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 2.732 Fit side-chains REVERT: A 149 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: B 418 GLN cc_start: 0.7005 (tt0) cc_final: 0.6634 (tp40) REVERT: C 56 GLU cc_start: 0.8321 (tt0) cc_final: 0.8010 (tp30) REVERT: C 129 SER cc_start: 0.8955 (m) cc_final: 0.8547 (p) REVERT: D 260 ARG cc_start: 0.8835 (mmt180) cc_final: 0.8554 (mmt180) REVERT: E 241 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7526 (mt-10) REVERT: E 247 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8283 (mt-10) REVERT: E 294 GLU cc_start: 0.8081 (pt0) cc_final: 0.7880 (tp30) REVERT: E 354 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8318 (mttp) REVERT: F 172 ASN cc_start: 0.8489 (t0) cc_final: 0.8177 (t0) REVERT: F 222 MET cc_start: 0.9256 (ptp) cc_final: 0.8822 (ptp) REVERT: G 30 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5645 (mpp80) REVERT: G 180 LYS cc_start: 0.7890 (mtpp) cc_final: 0.7207 (mmmt) REVERT: G 189 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6774 (mm-30) outliers start: 36 outliers final: 26 residues processed: 247 average time/residue: 0.4177 time to fit residues: 159.2590 Evaluate side-chains 243 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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 373 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain 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 238 THR Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 72 GLU 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 278 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN D 24 HIS D 308 GLN F 178 HIS F 293 GLN F 308 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.105118 restraints weight = 29005.136| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.59 r_work: 0.3003 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 23483 Z= 0.274 Angle : 0.601 7.789 31892 Z= 0.312 Chirality : 0.048 0.316 3787 Planarity : 0.004 0.044 4135 Dihedral : 6.298 88.953 3426 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.73 % Allowed : 9.27 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.16), residues: 3079 helix: 1.66 (0.15), residues: 1287 sheet: -0.05 (0.24), residues: 504 loop : 0.38 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 191 HIS 0.006 0.001 HIS E 367 PHE 0.017 0.002 PHE B 506 TYR 0.015 0.002 TYR B 270 ARG 0.007 0.001 ARG B 422 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 1138) hydrogen bonds : angle 4.92318 ( 3180) covalent geometry : bond 0.00669 (23483) covalent geometry : angle 0.60140 (31892) *********************** 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 255 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 2.604 Fit side-chains REVERT: A 149 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: B 418 GLN cc_start: 0.7222 (tt0) cc_final: 0.6694 (tp40) REVERT: C 129 SER cc_start: 0.8858 (m) cc_final: 0.8443 (p) REVERT: C 496 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8641 (mt) REVERT: D 260 ARG cc_start: 0.8835 (mmt180) cc_final: 0.8475 (mmt180) REVERT: D 349 ASP cc_start: 0.8696 (t0) cc_final: 0.8128 (t0) REVERT: E 241 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7575 (mt-10) REVERT: E 294 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: F 401 LYS cc_start: 0.8590 (tttm) cc_final: 0.8090 (ttmm) REVERT: G 30 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.5812 (mpp80) outliers start: 41 outliers final: 28 residues processed: 241 average time/residue: 0.3824 time to fit residues: 140.0870 Evaluate side-chains 231 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 2.394 ------------------------------------------------------------------------------- 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 373 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 161 ILE 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 148 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 72 GLU 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 75 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 244 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 169 optimal weight: 0.7980 chunk 253 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 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 F 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104735 restraints weight = 28587.437| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.63 r_work: 0.2959 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2433 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= 0.111 Angle : 0.487 7.535 31892 Z= 0.253 Chirality : 0.043 0.327 3787 Planarity : 0.004 0.043 4135 Dihedral : 5.889 87.980 3426 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.18 % Allowed : 9.90 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.16), residues: 3079 helix: 1.93 (0.15), residues: 1290 sheet: 0.13 (0.24), residues: 497 loop : 0.45 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 191 HIS 0.005 0.001 HIS A 478 PHE 0.013 0.001 PHE B 395 TYR 0.025 0.001 TYR A 448 ARG 0.005 0.000 ARG B 422 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 1138) hydrogen bonds : angle 4.70581 ( 3180) covalent geometry : bond 0.00253 (23483) covalent geometry : angle 0.48682 (31892) *********************** 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 253 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 2.664 Fit side-chains REVERT: A 149 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: A 293 ARG cc_start: 0.8381 (ttt180) cc_final: 0.8110 (ttt180) REVERT: B 67 ASN cc_start: 0.8688 (m-40) cc_final: 0.8458 (m110) REVERT: B 395 PHE cc_start: 0.7241 (t80) cc_final: 0.6594 (t80) REVERT: B 418 GLN cc_start: 0.7178 (tt0) cc_final: 0.6586 (tp40) REVERT: B 422 ARG cc_start: 0.6992 (ttm170) cc_final: 0.6488 (ttm-80) REVERT: C 56 GLU cc_start: 0.8366 (tt0) cc_final: 0.7894 (tp30) REVERT: C 129 SER cc_start: 0.9038 (m) cc_final: 0.8516 (p) REVERT: D 260 ARG cc_start: 0.8831 (mmt180) cc_final: 0.8518 (mmt180) REVERT: D 349 ASP cc_start: 0.8620 (t0) cc_final: 0.7927 (t0) REVERT: D 465 ASP cc_start: 0.7913 (m-30) cc_final: 0.7690 (m-30) REVERT: E 294 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7672 (tp30) REVERT: G 180 LYS cc_start: 0.7925 (mtpp) cc_final: 0.6896 (mmtp) outliers start: 28 outliers final: 22 residues processed: 241 average time/residue: 0.3801 time to fit residues: 140.6128 Evaluate side-chains 235 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 483 THR 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 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 140 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 336 SER 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 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 75 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 182 optimal weight: 30.0000 chunk 117 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 233 optimal weight: 0.1980 chunk 269 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 290 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 F 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103168 restraints weight = 28670.740| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.74 r_work: 0.2971 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23483 Z= 0.135 Angle : 0.498 7.598 31892 Z= 0.258 Chirality : 0.044 0.335 3787 Planarity : 0.004 0.043 4135 Dihedral : 5.840 87.888 3426 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.26 % Allowed : 10.07 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.16), residues: 3079 helix: 1.94 (0.15), residues: 1292 sheet: 0.10 (0.24), residues: 496 loop : 0.44 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 PHE 0.013 0.001 PHE B 395 TYR 0.014 0.001 TYR C 473 ARG 0.004 0.000 ARG B 422 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 1138) hydrogen bonds : angle 4.67428 ( 3180) covalent geometry : bond 0.00320 (23483) covalent geometry : angle 0.49768 (31892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 2.596 Fit side-chains REVERT: A 149 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: A 293 ARG cc_start: 0.8453 (ttt180) cc_final: 0.8191 (ttt180) REVERT: B 67 ASN cc_start: 0.8682 (m-40) cc_final: 0.8457 (m110) REVERT: B 395 PHE cc_start: 0.7358 (t80) cc_final: 0.6710 (t80) REVERT: B 418 GLN cc_start: 0.7209 (tt0) cc_final: 0.6796 (tp40) REVERT: B 422 ARG cc_start: 0.7031 (ttm170) cc_final: 0.6635 (ttm-80) REVERT: C 129 SER cc_start: 0.9030 (m) cc_final: 0.8530 (p) REVERT: D 260 ARG cc_start: 0.8847 (mmt180) cc_final: 0.8548 (mmt180) REVERT: D 349 ASP cc_start: 0.8664 (t0) cc_final: 0.8013 (t0) REVERT: D 465 ASP cc_start: 0.7921 (m-30) cc_final: 0.7677 (m-30) REVERT: E 241 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7583 (mt-10) REVERT: E 294 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7934 (tp30) REVERT: G 180 LYS cc_start: 0.7836 (mtpp) cc_final: 0.6906 (mmtp) outliers start: 30 outliers final: 23 residues processed: 233 average time/residue: 0.4049 time to fit residues: 145.0574 Evaluate side-chains 236 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL 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 140 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 336 SER 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 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 40 optimal weight: 0.0470 chunk 298 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 25 optimal weight: 0.0020 chunk 296 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 206 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS F 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.138453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.108552 restraints weight = 28501.983| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.63 r_work: 0.3030 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23483 Z= 0.099 Angle : 0.470 7.549 31892 Z= 0.244 Chirality : 0.043 0.343 3787 Planarity : 0.003 0.042 4135 Dihedral : 5.586 86.394 3426 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.97 % Allowed : 10.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.16), residues: 3079 helix: 2.14 (0.15), residues: 1290 sheet: 0.19 (0.25), residues: 485 loop : 0.58 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 191 HIS 0.006 0.001 HIS A 478 PHE 0.012 0.001 PHE B 395 TYR 0.014 0.001 TYR B 448 ARG 0.003 0.000 ARG C 425 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 1138) hydrogen bonds : angle 4.54648 ( 3180) covalent geometry : bond 0.00224 (23483) covalent geometry : angle 0.46951 (31892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 2.540 Fit side-chains REVERT: A 149 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: A 293 ARG cc_start: 0.8405 (ttt180) cc_final: 0.8135 (ttt180) REVERT: B 67 ASN cc_start: 0.8596 (m-40) cc_final: 0.8369 (m110) REVERT: B 418 GLN cc_start: 0.6899 (tt0) cc_final: 0.6574 (tp40) REVERT: B 422 ARG cc_start: 0.7022 (ttm170) cc_final: 0.6660 (ttm-80) REVERT: C 56 GLU cc_start: 0.8345 (tt0) cc_final: 0.7900 (tp30) REVERT: C 129 SER cc_start: 0.9040 (m) cc_final: 0.8513 (p) REVERT: C 496 LEU cc_start: 0.8814 (mt) cc_final: 0.8427 (mt) REVERT: D 144 LEU cc_start: 0.8175 (mp) cc_final: 0.7079 (tt) REVERT: D 260 ARG cc_start: 0.8675 (mmt180) cc_final: 0.8412 (mmt180) REVERT: D 349 ASP cc_start: 0.8619 (t0) cc_final: 0.7942 (t0) REVERT: D 465 ASP cc_start: 0.7914 (m-30) cc_final: 0.7656 (m-30) REVERT: E 222 MET cc_start: 0.8657 (ttm) cc_final: 0.8343 (ttp) REVERT: E 294 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: G 180 LYS cc_start: 0.7859 (mtpp) cc_final: 0.6915 (mmtp) outliers start: 23 outliers final: 18 residues processed: 245 average time/residue: 0.3785 time to fit residues: 141.2170 Evaluate side-chains 234 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 2.383 ------------------------------------------------------------------------------- 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 C residue 36 VAL Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 336 SER 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 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 256 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 116 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112940 restraints weight = 28778.577| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.44 r_work: 0.3120 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2702 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= 0.118 Angle : 0.481 7.596 31892 Z= 0.249 Chirality : 0.044 0.338 3787 Planarity : 0.004 0.042 4135 Dihedral : 5.591 86.080 3426 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.10 % Allowed : 10.49 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 3079 helix: 2.13 (0.15), residues: 1291 sheet: 0.17 (0.24), residues: 495 loop : 0.54 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 191 HIS 0.006 0.001 HIS A 478 PHE 0.012 0.001 PHE B 395 TYR 0.023 0.001 TYR A 448 ARG 0.005 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 1138) hydrogen bonds : angle 4.54321 ( 3180) covalent geometry : bond 0.00276 (23483) covalent geometry : angle 0.48082 (31892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12723.86 seconds wall clock time: 224 minutes 46.39 seconds (13486.39 seconds total)