Starting phenix.real_space_refine on Sat Jul 4 17:36:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f2k_28818/07_2026/8f2k_28818.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f2k_28818/07_2026/8f2k_28818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f2k_28818/07_2026/8f2k_28818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f2k_28818/07_2026/8f2k_28818.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8f2k_28818/07_2026/8f2k_28818.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f2k_28818/07_2026/8f2k_28818.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f2k_28818/07_2026/8f2k_28818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f2k_28818/07_2026/8f2k_28818.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.184 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 15 5.49 5 Mg 5 5.21 5 S 32 5.16 5 C 14164 2.51 5 N 3908 2.21 5 O 4278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22402 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3657 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3641 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3666 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3472 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3485 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3490 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "G" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 747 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 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: "E" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'XBC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'XBC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.99, per 1000 atoms: 0.22 Number of scatterers: 22402 At special positions: 0 Unit cell: (133.916, 124.5, 126.593, 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 32 16.00 P 15 15.00 Mg 5 11.99 O 4278 8.00 N 3908 7.00 C 14164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5366 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 19 sheets defined 49.9% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.820A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.939A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.702A 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 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 241 through 262 Proline residue: A 249 - end of helix removed outlier: 3.632A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.670A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 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 Processing helix chain 'A' and resid 382 through 403 removed outlier: 3.821A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.052A pdb=" N GLY A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.558A pdb=" N LYS A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 453 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.505A pdb=" N GLU A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 489 Processing helix chain 'A' and resid 492 through 510 Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.730A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 removed outlier: 3.645A 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: 3.952A 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: 3.521A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.590A 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: 3.508A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 332 through 335 Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.585A pdb=" N ALA B 379 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 Processing helix chain 'B' and resid 391 through 407 removed outlier: 3.592A pdb=" N PHE B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 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: 4.198A 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 Processing helix chain 'B' and resid 478 through 489 removed outlier: 3.586A pdb=" N LEU B 482 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 510 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.928A pdb=" N LEU C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.751A 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: 3.748A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' 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 263 Proline residue: C 249 - end of helix removed outlier: 3.653A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.757A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 297 through 298 No H-bonds generated for 'chain 'C' and resid 297 through 298' 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 346 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 380 Processing helix chain 'C' and resid 382 through 390 Processing helix chain 'C' and resid 391 through 407 removed outlier: 3.692A pdb=" N ALA C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.695A pdb=" N GLY C 457 " --> pdb=" O HIS C 454 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 492 through 510 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 179 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 248 removed outlier: 4.776A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 273 removed outlier: 3.705A pdb=" N PHE D 261 " --> pdb=" O ASN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.542A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.589A pdb=" N SER D 340 " --> pdb=" O SER D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 392 removed outlier: 4.459A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 414 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 476 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.799A pdb=" N GLN E 127 " --> pdb=" O PHE E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 175 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 225 through 246 removed outlier: 4.892A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 273 Processing helix chain 'E' and resid 284 through 294 Processing helix chain 'E' and resid 313 through 316 Processing helix chain 'E' and resid 319 through 327 removed outlier: 4.088A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 392 removed outlier: 4.737A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.135A 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 418 through 420 No H-bonds generated for 'chain 'E' and resid 418 through 420' 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 removed outlier: 3.885A pdb=" N PHE E 457 " --> pdb=" O PRO E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 476 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 174 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 273 removed outlier: 3.733A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 294 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 Processing helix chain 'F' and resid 364 through 391 removed outlier: 3.543A pdb=" N GLN F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 396 Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 420 through 426 removed outlier: 4.219A pdb=" N PHE F 424 " --> pdb=" O VAL F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 476 Processing helix chain 'G' and resid 2 through 42 Processing helix chain 'G' and resid 219 through 275 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68 removed outlier: 4.325A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (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: 6.260A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 68 removed outlier: 4.138A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU B 68 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA E 36 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASN E 35 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA6, first strand: chain 'B' and resid 109 through 111 removed outlier: 6.346A pdb=" N VAL B 110 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 69 removed outlier: 4.221A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS F 75 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS F 40 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS F 24 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL F 13 " --> pdb=" O HIS F 24 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AA9, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.319A pdb=" N VAL C 110 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ILE C 232 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.319A pdb=" N VAL C 110 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ILE C 232 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (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: 6.211A pdb=" N ILE D 96 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLN D 221 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE D 153 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS D 152 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR D 333 " --> pdb=" O LYS D 152 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY D 154 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.207A 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 87 removed outlier: 4.830A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.166A pdb=" N ILE E 96 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE E 153 " --> pdb=" O GLN E 308 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL E 310 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU E 155 " --> pdb=" O VAL E 310 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 133 through 134 removed outlier: 4.159A 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 87 removed outlier: 4.555A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.291A pdb=" N ILE F 96 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS F 152 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N THR F 333 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY F 154 " --> pdb=" O THR F 333 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.223A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) 1181 hydrogen bonds defined for protein. 3342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3782 1.31 - 1.44: 5433 1.44 - 1.56: 13446 1.56 - 1.69: 26 1.69 - 1.81: 61 Bond restraints: 22748 Sorted by residual: bond pdb=" C31 XBC F 503 " pdb=" C32 XBC F 503 " ideal model delta sigma weight residual 1.455 1.559 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C31 XBC E 503 " pdb=" C32 XBC E 503 " ideal model delta sigma weight residual 1.455 1.556 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C19 XBC E 503 " pdb=" N18 XBC E 503 " ideal model delta sigma weight residual 1.379 1.477 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C19 XBC F 503 " pdb=" N18 XBC F 503 " ideal model delta sigma weight residual 1.379 1.475 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C09 XBC E 503 " pdb=" O30 XBC E 503 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 22743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 30587 2.97 - 5.93: 253 5.93 - 8.90: 37 8.90 - 11.86: 1 11.86 - 14.83: 2 Bond angle restraints: 30880 Sorted by residual: angle pdb=" CA PRO E 42 " pdb=" N PRO E 42 " pdb=" CD PRO E 42 " ideal model delta sigma weight residual 112.00 97.17 14.83 1.40e+00 5.10e-01 1.12e+02 angle pdb=" N PRO E 42 " pdb=" CD PRO E 42 " pdb=" CG PRO E 42 " ideal model delta sigma weight residual 103.20 96.59 6.61 1.50e+00 4.44e-01 1.94e+01 angle pdb=" C15 XBC F 503 " pdb=" C16 XBC F 503 " pdb=" C17 XBC F 503 " ideal model delta sigma weight residual 124.46 137.24 -12.78 3.00e+00 1.11e-01 1.82e+01 angle pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 121.54 128.57 -7.03 1.91e+00 2.74e-01 1.35e+01 angle pdb=" N PRO E 42 " pdb=" CA PRO E 42 " pdb=" CB PRO E 42 " ideal model delta sigma weight residual 103.30 99.36 3.94 1.12e+00 7.97e-01 1.23e+01 ... (remaining 30875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 12611 17.97 - 35.94: 825 35.94 - 53.91: 214 53.91 - 71.88: 67 71.88 - 89.85: 30 Dihedral angle restraints: 13747 sinusoidal: 5352 harmonic: 8395 Sorted by residual: dihedral pdb=" CA ASP A 271 " pdb=" C ASP A 271 " pdb=" N ASP A 272 " pdb=" CA ASP A 272 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA GLN E 282 " pdb=" C GLN E 282 " pdb=" N PRO E 283 " pdb=" CA PRO E 283 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL F 312 " pdb=" C VAL F 312 " pdb=" N PRO F 313 " pdb=" CA PRO F 313 " ideal model delta harmonic sigma weight residual -180.00 -151.87 -28.13 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 13744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3047 0.062 - 0.124: 511 0.124 - 0.186: 76 0.186 - 0.247: 4 0.247 - 0.309: 16 Chirality restraints: 3654 Sorted by residual: chirality pdb=" C2' ATP E 501 " pdb=" C1' ATP E 501 " pdb=" C3' ATP E 501 " pdb=" O2' ATP E 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3' ATP B 600 " pdb=" C2' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O3' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.13e+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 2.13e+00 ... (remaining 3651 not shown) Planarity restraints: 3978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 41 " -0.124 5.00e-02 4.00e+02 1.73e-01 4.80e+01 pdb=" N PRO E 42 " 0.299 5.00e-02 4.00e+02 pdb=" CA PRO E 42 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO E 42 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 166 " -0.417 9.50e-02 1.11e+02 1.88e-01 2.59e+01 pdb=" NE ARG C 166 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG C 166 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG C 166 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG C 166 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 191 " -0.043 2.00e-02 2.50e+03 3.05e-02 2.32e+01 pdb=" CG TRP C 191 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP C 191 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP C 191 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 191 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TRP C 191 " -0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP C 191 " 0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 191 " -0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 191 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 191 " -0.026 2.00e-02 2.50e+03 ... (remaining 3975 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 124 2.55 - 3.14: 18615 3.14 - 3.72: 34670 3.72 - 4.31: 51912 4.31 - 4.90: 87139 Nonbonded interactions: 192460 Sorted by model distance: nonbonded pdb=" O3G ATP C 600 " pdb="MG MG C 601 " model vdw 1.959 2.170 nonbonded pdb=" O1G ATP E 501 " pdb="MG MG E 502 " model vdw 1.961 2.170 nonbonded pdb=" O2B ATP F 501 " pdb="MG MG F 502 " model vdw 1.992 2.170 nonbonded pdb=" OG1 THR C 178 " pdb="MG MG C 601 " model vdw 2.034 2.170 nonbonded pdb=" OG1 THR E 164 " pdb="MG MG E 502 " model vdw 2.037 2.170 ... (remaining 192455 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 26 through 194 or (resid 195 and (name N or name CA or nam \ e C or name O or name CB )) or resid 196 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 356 or (resid 3 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 358 through \ 406 or (resid 407 through 408 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 409 through 411 and (name N or name CA or name C or name O or \ name CB )) or resid 412 or (resid 413 through 414 and (name N or name CA or name \ C or name O or name CB )) or resid 415 through 458 or (resid 459 and (name N or \ name CA or name C or name O or name CB )) or resid 460 through 476 or (resid 47 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 478 through \ 486 or (resid 487 and (name N or name CA or name C or name O or name CB )) or re \ sid 488 through 489 or (resid 490 and (name N or name CA or name C or name O or \ name CB )) or resid 491 through 492 or (resid 493 through 494 and (name N or nam \ e CA or name C or name O or name CB )) or resid 495 through 601)) selection = (chain 'B' and (resid 26 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 68 or (resid 69 and (name N or nam \ e CA or name C or name O or name CB )) or resid 70 through 171 or (resid 172 and \ (name N or name CA or name C or name O or name CB )) or resid 173 through 182 o \ r (resid 183 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 84 through 293 or (resid 294 through 295 and (name N or name CA or name C or nam \ e O or name CB )) or resid 296 through 392 or (resid 393 and (name N or name CA \ or name C or name O or name CB )) or resid 394 through 407 or (resid 408 and (na \ me N or name CA or name C or name O or name CB )) or resid 409 through 423 or (r \ esid 424 and (name N or name CA or name C or name O or name CB )) or resid 425 t \ hrough 601)) selection = (chain 'C' and (resid 26 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 37 or (resid 38 and (name N or nam \ e CA or name C or name O or name CB )) or resid 39 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 through 171 or ( \ resid 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ through 182 or (resid 183 and (name N or name CA or name C or name O or name CB \ )) or resid 184 through 194 or (resid 195 and (name N or name CA or name C or na \ me O or name CB )) or resid 196 through 293 or (resid 294 through 295 and (name \ N or name CA or name C or name O or name CB )) or resid 296 through 356 or (resi \ d 357 and (name N or name CA or name C or name O or name CB )) or resid 358 thro \ ugh 392 or (resid 393 and (name N or name CA or name C or name O or name CB )) o \ r resid 394 through 406 or (resid 407 through 408 and (name N or name CA or name \ C or name O or name CB )) or resid 409 through 423 or (resid 424 and (name N or \ name CA or name C or name O or name CB )) or resid 425 through 458 or (resid 45 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 460 through \ 476 or (resid 477 and (name N or name CA or name C or name O or name CB )) or re \ sid 478 through 479 or (resid 480 and (name N or name CA or name C or name O or \ name CB )) or resid 481 through 486 or (resid 487 and (name N or name CA or name \ C or name O or name CB )) or resid 488 through 489 or (resid 490 and (name N or \ name CA or name C or name O or name CB )) or resid 491 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 42 or (resid 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 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 188 or (resid 189 and (name N or name CA or name C or name O or name C \ B )) or resid 190 through 199 or (resid 200 and (name N or name CA or name C or \ name O or name CB )) or resid 201 through 209 or (resid 210 and (name N or name \ CA or name C or name O or name CB )) or resid 211 through 245 or (resid 246 and \ (name N or name CA or name C or name O or name CB )) or resid 247 through 372 or \ (resid 373 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 4 through 375 or (resid 376 and (name N or name CA or name C or name O or name C \ B )) or resid 377 through 398 or (resid 399 and (name N or name CA or name C or \ name O or name CB )) or resid 400 through 470 or (resid 471 through 472 and (nam \ e N or name CA or name C or name O or name CB )) or resid 473 through 476)) selection = (chain 'E' and (resid 8 through 25 or (resid 26 through 27 and (name N or name C \ A or name C or name O or name CB )) or resid 28 through 175 or (resid 176 throug \ h 177 and (name N or name CA or name C or name O or name CB )) or resid 178 thro \ ugh 188 or (resid 189 and (name N or name CA or name C or name O or name CB )) o \ r resid 190 through 358 or (resid 359 through 361 and (name N or name CA or name \ C or name O or name CB )) or resid 362 through 384 or (resid 385 through 386 an \ d (name N or name CA or name C or name O or name CB )) or resid 387 through 389 \ or (resid 390 through 391 and (name N or name CA or name C or name O or name CB \ )) or resid 392 or (resid 393 through 396 and (name N or name CA or name C or na \ me O or name CB )) or resid 397 through 398 or (resid 399 and (name N or name CA \ or name C or name O or name CB )) or resid 400 or (resid 401 and (name N or nam \ e CA or name C or name O or name CB )) or resid 402 through 434 or (resid 435 an \ d (name N or name CA or name C or name O or name CB )) or resid 436 through 463 \ or (resid 464 and (name N or name CA or name C or name O or name CB )) or resid \ 465 through 471 or (resid 472 and (name N or name CA or name C or name O or name \ CB )) or resid 473 through 476)) selection = (chain 'F' and (resid 8 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 175 or (resid 176 t \ hrough 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 358 or (resid 359 through 361 and (name N or name CA or \ name C or name O or name CB )) or resid 362 through 375 or (resid 376 and (name \ N or name CA or name C or name O or name CB )) or resid 377 through 384 or (res \ id 385 through 386 and (name N or name CA or name C or name O or name CB )) or r \ esid 387 through 389 or (resid 390 through 391 and (name N or name CA or name C \ or name O or name CB )) or resid 392 or (resid 393 through 396 and (name N or na \ me CA or name C or name O or name CB )) or resid 397 through 400 or (resid 401 a \ nd (name N or name CA or name C or name O or name CB )) or resid 402 through 434 \ or (resid 435 and (name N or name CA or name C or name O or name CB )) or resid \ 436 through 463 or (resid 464 and (name N or name CA or name C or name O or nam \ e CB )) or resid 465 through 470 or (resid 471 through 472 and (name N or name C \ A or name C or name O or name CB )) or resid 473 through 475 or (resid 476 and ( \ name N or name CA or name C or name O or name CB )))) } 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.050 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 22748 Z= 0.205 Angle : 0.774 14.830 30880 Z= 0.436 Chirality : 0.050 0.309 3654 Planarity : 0.011 0.188 3978 Dihedral : 14.547 89.854 8381 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Rotamer: Outliers : 0.74 % Allowed : 9.07 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.15), residues: 2946 helix: -0.20 (0.13), residues: 1240 sheet: 0.22 (0.23), residues: 496 loop : 0.25 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.004 ARG C 166 TYR 0.028 0.005 TYR E 368 PHE 0.027 0.005 PHE B 395 TRP 0.054 0.016 TRP C 191 HIS 0.010 0.002 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (22748) covalent geometry : angle 0.77433 / 0.44 (30880) hydrogen bonds : bond 0.13083 / 8.73 ( 1170) hydrogen bonds : angle 7.18931 / 5.00 ( 3342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 247 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7996 (tt0) cc_final: 0.7784 (tt0) REVERT: B 448 TYR cc_start: 0.8405 (t80) cc_final: 0.7969 (t80) REVERT: C 64 MET cc_start: 0.8816 (ttt) cc_final: 0.8465 (ttm) REVERT: C 257 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7828 (mt-10) REVERT: D 172 ASN cc_start: 0.8595 (t0) cc_final: 0.8189 (t0) REVERT: E 386 ASP cc_start: 0.8286 (p0) cc_final: 0.8040 (p0) REVERT: F 212 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7576 (tp30) outliers start: 17 outliers final: 11 residues processed: 259 average time/residue: 0.6112 time to fit residues: 182.0082 Evaluate side-chains 201 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 32 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS A 452 ASN B 26 ASN D 208 ASN E 308 GLN E 455 HIS F 27 GLN F 195 ASN F 223 ASN F 385 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.093542 restraints weight = 30381.362| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.87 r_work: 0.2922 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22748 Z= 0.122 Angle : 0.564 7.431 30880 Z= 0.295 Chirality : 0.044 0.191 3654 Planarity : 0.004 0.073 3978 Dihedral : 6.602 82.187 3320 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.26 % Allowed : 10.67 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.16), residues: 2946 helix: 1.56 (0.15), residues: 1224 sheet: 0.43 (0.23), residues: 475 loop : 0.68 (0.19), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 337 TYR 0.019 0.001 TYR D 381 PHE 0.033 0.002 PHE B 405 TRP 0.015 0.002 TRP A 191 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (22748) covalent geometry : angle 0.56416 / 0.29 (30880) hydrogen bonds : bond 0.04325 / 2.97 ( 1170) hydrogen bonds : angle 5.11320 / 3.56 ( 3342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 133 VAL cc_start: 0.8827 (p) cc_final: 0.8533 (m) REVERT: A 173 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8396 (ptt90) REVERT: A 237 THR cc_start: 0.8001 (p) cc_final: 0.7645 (p) REVERT: A 418 GLN cc_start: 0.7441 (tp40) cc_final: 0.7109 (tp40) REVERT: B 442 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7827 (mt-10) REVERT: C 257 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7541 (mt-10) REVERT: C 299 ASP cc_start: 0.8326 (p0) cc_final: 0.7993 (p0) REVERT: D 172 ASN cc_start: 0.8233 (t0) cc_final: 0.7832 (t0) REVERT: D 263 GLN cc_start: 0.7183 (tt0) cc_final: 0.6813 (tt0) REVERT: E 38 GLU cc_start: 0.7809 (tt0) cc_final: 0.7595 (tt0) REVERT: E 74 GLU cc_start: 0.8708 (tt0) cc_final: 0.8487 (tt0) REVERT: E 77 LEU cc_start: 0.7793 (tt) cc_final: 0.7407 (mp) REVERT: E 423 VAL cc_start: 0.9004 (t) cc_final: 0.8699 (p) REVERT: F 149 ARG cc_start: 0.8274 (ttt180) cc_final: 0.7985 (ttt-90) REVERT: F 212 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7530 (tp30) REVERT: F 281 TYR cc_start: 0.9151 (m-80) cc_final: 0.8695 (m-80) REVERT: F 349 ASP cc_start: 0.8356 (t0) cc_final: 0.8095 (t0) REVERT: G 8 MET cc_start: 0.8404 (mmp) cc_final: 0.7996 (mmm) REVERT: G 265 ASN cc_start: 0.8286 (m-40) cc_final: 0.7765 (m-40) outliers start: 29 outliers final: 8 residues processed: 263 average time/residue: 0.6749 time to fit residues: 201.9025 Evaluate side-chains 221 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 212 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 119 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 257 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 134 optimal weight: 0.0980 chunk 234 optimal weight: 0.0060 chunk 244 optimal weight: 0.7980 chunk 245 optimal weight: 0.0980 chunk 279 optimal weight: 0.8980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN B 26 ASN C 428 GLN C 433 ASN D 208 ASN E 308 GLN F 195 ASN F 223 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.095458 restraints weight = 30269.614| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.89 r_work: 0.2959 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22748 Z= 0.098 Angle : 0.497 8.728 30880 Z= 0.257 Chirality : 0.043 0.211 3654 Planarity : 0.004 0.057 3978 Dihedral : 5.722 70.013 3307 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.74 % Allowed : 11.67 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.16), residues: 2946 helix: 2.07 (0.15), residues: 1213 sheet: 0.54 (0.24), residues: 476 loop : 0.69 (0.19), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 462 TYR 0.019 0.001 TYR D 458 PHE 0.028 0.001 PHE B 405 TRP 0.010 0.001 TRP A 191 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (22748) covalent geometry : angle 0.49724 / 0.26 (30880) hydrogen bonds : bond 0.03673 / 2.51 ( 1170) hydrogen bonds : angle 4.68095 / 3.28 ( 3342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 95 ASN cc_start: 0.8266 (m-40) cc_final: 0.7967 (m-40) REVERT: A 133 VAL cc_start: 0.8766 (p) cc_final: 0.8533 (m) REVERT: A 173 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8417 (ptt90) REVERT: A 237 THR cc_start: 0.7849 (p) cc_final: 0.7571 (p) REVERT: A 467 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7087 (tt0) REVERT: A 493 LYS cc_start: 0.7563 (ptpp) cc_final: 0.7293 (mmtt) REVERT: B 349 ASP cc_start: 0.8665 (m-30) cc_final: 0.8444 (m-30) REVERT: B 442 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7865 (mt-10) REVERT: B 451 VAL cc_start: 0.8257 (t) cc_final: 0.7772 (m) REVERT: C 257 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7434 (mt-10) REVERT: C 299 ASP cc_start: 0.8325 (p0) cc_final: 0.7969 (p0) REVERT: C 500 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6896 (tttm) REVERT: D 172 ASN cc_start: 0.8184 (t0) cc_final: 0.7861 (t0) REVERT: D 263 GLN cc_start: 0.7243 (tt0) cc_final: 0.6954 (tt0) REVERT: D 289 MET cc_start: 0.8499 (tpp) cc_final: 0.8014 (tpp) REVERT: D 317 LEU cc_start: 0.8804 (mt) cc_final: 0.8581 (mm) REVERT: D 366 GLU cc_start: 0.8143 (tt0) cc_final: 0.7761 (pm20) REVERT: E 38 GLU cc_start: 0.7746 (tt0) cc_final: 0.7504 (tt0) REVERT: E 77 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7467 (mp) REVERT: E 110 LYS cc_start: 0.8554 (tttt) cc_final: 0.8326 (ttmm) REVERT: E 281 TYR cc_start: 0.8622 (m-80) cc_final: 0.8420 (m-80) REVERT: E 359 ASP cc_start: 0.7236 (m-30) cc_final: 0.6920 (p0) REVERT: E 423 VAL cc_start: 0.9007 (t) cc_final: 0.8793 (p) REVERT: F 212 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7506 (tp30) REVERT: F 294 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8255 (mm-30) REVERT: F 349 ASP cc_start: 0.8386 (t0) cc_final: 0.8063 (t0) REVERT: G 8 MET cc_start: 0.8377 (mmp) cc_final: 0.7933 (mmm) outliers start: 40 outliers final: 12 residues processed: 287 average time/residue: 0.6134 time to fit residues: 202.4094 Evaluate side-chains 229 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 155 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 69 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 234 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 418 GLN B 26 ASN C 428 GLN E 293 GLN F 195 ASN F 223 ASN F 328 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.091494 restraints weight = 30646.865| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.89 r_work: 0.2900 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22748 Z= 0.142 Angle : 0.525 7.395 30880 Z= 0.270 Chirality : 0.044 0.197 3654 Planarity : 0.004 0.055 3978 Dihedral : 5.455 56.797 3306 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.65 % Allowed : 12.36 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.16), residues: 2946 helix: 2.15 (0.15), residues: 1201 sheet: 0.46 (0.24), residues: 488 loop : 0.54 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 462 TYR 0.016 0.001 TYR D 458 PHE 0.029 0.001 PHE B 405 TRP 0.008 0.002 TRP A 191 HIS 0.004 0.001 HIS D 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (22748) covalent geometry : angle 0.52452 / 0.27 (30880) hydrogen bonds : bond 0.04034 / 2.77 ( 1170) hydrogen bonds : angle 4.65729 / 3.25 ( 3342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 95 ASN cc_start: 0.8168 (m-40) cc_final: 0.7878 (m-40) REVERT: A 133 VAL cc_start: 0.8731 (p) cc_final: 0.8504 (m) REVERT: A 173 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8343 (ptt90) REVERT: A 303 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7767 (tp) REVERT: A 418 GLN cc_start: 0.8015 (tp40) cc_final: 0.7554 (tp40) REVERT: A 467 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7098 (tt0) REVERT: A 493 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7360 (mmtt) REVERT: B 442 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7856 (mt-10) REVERT: B 451 VAL cc_start: 0.8265 (t) cc_final: 0.7720 (m) REVERT: B 484 GLU cc_start: 0.7305 (tt0) cc_final: 0.7005 (tt0) REVERT: C 257 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7475 (mt-10) REVERT: C 299 ASP cc_start: 0.8378 (p0) cc_final: 0.8023 (p0) REVERT: C 391 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.7930 (t) REVERT: D 172 ASN cc_start: 0.8308 (t0) cc_final: 0.8068 (t0) REVERT: D 263 GLN cc_start: 0.7287 (tt0) cc_final: 0.6996 (tt0) REVERT: D 345 TYR cc_start: 0.6817 (m-80) cc_final: 0.6562 (m-80) REVERT: D 366 GLU cc_start: 0.8132 (tt0) cc_final: 0.7756 (pm20) REVERT: E 38 GLU cc_start: 0.7796 (tt0) cc_final: 0.7567 (tt0) REVERT: E 77 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7446 (mp) REVERT: E 110 LYS cc_start: 0.8572 (tttt) cc_final: 0.8352 (ttmm) REVERT: E 359 ASP cc_start: 0.7303 (m-30) cc_final: 0.6911 (p0) REVERT: E 385 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6337 (mt0) REVERT: E 423 VAL cc_start: 0.8993 (t) cc_final: 0.8716 (p) REVERT: F 212 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7510 (tp30) REVERT: F 250 ASP cc_start: 0.7766 (m-30) cc_final: 0.7279 (m-30) REVERT: F 281 TYR cc_start: 0.9160 (m-80) cc_final: 0.8735 (m-80) REVERT: F 294 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8400 (mm-30) REVERT: F 381 TYR cc_start: 0.8647 (t80) cc_final: 0.8037 (t80) REVERT: F 385 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.5677 (mp10) outliers start: 61 outliers final: 17 residues processed: 255 average time/residue: 0.6364 time to fit residues: 184.6786 Evaluate side-chains 227 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 385 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN B 478 HIS C 428 GLN E 127 GLN F 53 HIS F 223 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.086829 restraints weight = 30788.401| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.88 r_work: 0.2814 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 22748 Z= 0.268 Angle : 0.611 7.559 30880 Z= 0.313 Chirality : 0.048 0.223 3654 Planarity : 0.005 0.056 3978 Dihedral : 5.818 60.646 3306 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.99 % Allowed : 12.75 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.16), residues: 2946 helix: 1.81 (0.15), residues: 1209 sheet: 0.17 (0.23), residues: 528 loop : 0.29 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 149 TYR 0.017 0.002 TYR F 147 PHE 0.025 0.002 PHE B 405 TRP 0.008 0.002 TRP C 191 HIS 0.007 0.001 HIS D 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.27 (22748) covalent geometry : angle 0.61071 / 0.31 (30880) hydrogen bonds : bond 0.05000 / 3.44 ( 1170) hydrogen bonds : angle 4.89979 / 3.42 ( 3342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 95 ASN cc_start: 0.8123 (m-40) cc_final: 0.7796 (m-40) REVERT: A 133 VAL cc_start: 0.8822 (p) cc_final: 0.8531 (m) REVERT: A 173 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8307 (mtm-85) REVERT: A 303 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8021 (tp) REVERT: A 355 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7701 (mm-30) REVERT: A 357 GLU cc_start: 0.7996 (tt0) cc_final: 0.7793 (tm-30) REVERT: A 373 VAL cc_start: 0.8261 (p) cc_final: 0.7914 (m) REVERT: A 375 ARG cc_start: 0.8510 (mtp85) cc_final: 0.8270 (mtm180) REVERT: A 418 GLN cc_start: 0.8119 (tp40) cc_final: 0.7702 (tp40) REVERT: A 493 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7730 (mmtt) REVERT: B 66 LEU cc_start: 0.9014 (tp) cc_final: 0.8786 (tt) REVERT: B 199 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7719 (mtpm) REVERT: B 303 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8677 (tp) REVERT: B 355 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: B 442 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7930 (mt-10) REVERT: B 484 GLU cc_start: 0.7417 (tt0) cc_final: 0.6884 (tp30) REVERT: B 495 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7825 (tt) REVERT: C 257 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7656 (mt-10) REVERT: C 299 ASP cc_start: 0.8438 (p0) cc_final: 0.8103 (p0) REVERT: C 391 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8038 (t) REVERT: D 263 GLN cc_start: 0.7486 (tt0) cc_final: 0.7182 (tt0) REVERT: D 345 TYR cc_start: 0.6927 (m-80) cc_final: 0.6674 (m-80) REVERT: D 366 GLU cc_start: 0.8209 (tt0) cc_final: 0.7769 (pm20) REVERT: E 385 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6445 (mt0) REVERT: F 56 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8118 (mm-30) REVERT: F 74 GLU cc_start: 0.8208 (tt0) cc_final: 0.7991 (tt0) REVERT: F 294 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8502 (mm-30) REVERT: F 381 TYR cc_start: 0.8737 (t80) cc_final: 0.8125 (t80) REVERT: F 385 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.5762 (mp10) outliers start: 69 outliers final: 23 residues processed: 252 average time/residue: 0.6537 time to fit residues: 187.4102 Evaluate side-chains 230 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 385 GLN Chi-restraints excluded: chain F residue 387 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 44 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 274 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 163 optimal weight: 0.0670 chunk 157 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 ASN C 428 GLN D 208 ASN D 455 HIS E 375 GLN F 195 ASN F 223 ASN G 265 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.090824 restraints weight = 30468.532| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.89 r_work: 0.2881 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22748 Z= 0.116 Angle : 0.502 7.230 30880 Z= 0.259 Chirality : 0.043 0.205 3654 Planarity : 0.004 0.057 3978 Dihedral : 5.453 59.337 3306 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.04 % Allowed : 14.27 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.16), residues: 2946 helix: 2.01 (0.15), residues: 1220 sheet: 0.23 (0.23), residues: 528 loop : 0.38 (0.19), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 337 TYR 0.013 0.001 TYR D 458 PHE 0.012 0.001 PHE E 25 TRP 0.009 0.002 TRP C 258 HIS 0.003 0.001 HIS D 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (22748) covalent geometry : angle 0.50168 / 0.26 (30880) hydrogen bonds : bond 0.03833 / 2.63 ( 1170) hydrogen bonds : angle 4.65693 / 3.26 ( 3342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 95 ASN cc_start: 0.8096 (m-40) cc_final: 0.7764 (m-40) REVERT: A 133 VAL cc_start: 0.8788 (p) cc_final: 0.8534 (m) REVERT: A 173 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8344 (ptt90) REVERT: A 303 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7800 (tp) REVERT: A 355 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7547 (mm-30) REVERT: A 357 GLU cc_start: 0.7942 (tt0) cc_final: 0.7660 (tm-30) REVERT: A 373 VAL cc_start: 0.8202 (p) cc_final: 0.7859 (m) REVERT: A 375 ARG cc_start: 0.8491 (mtp85) cc_final: 0.8258 (mtm180) REVERT: A 418 GLN cc_start: 0.8060 (tp40) cc_final: 0.7725 (tp40) REVERT: A 467 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7053 (tt0) REVERT: A 493 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7719 (mmtt) REVERT: B 199 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7658 (mtpm) REVERT: B 442 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7895 (mt-10) REVERT: B 451 VAL cc_start: 0.8298 (t) cc_final: 0.7804 (m) REVERT: B 484 GLU cc_start: 0.7334 (tt0) cc_final: 0.6728 (tp30) REVERT: B 495 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7639 (tt) REVERT: C 257 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7472 (mt-10) REVERT: C 299 ASP cc_start: 0.8449 (p0) cc_final: 0.8094 (p0) REVERT: C 391 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.7959 (t) REVERT: C 417 LYS cc_start: 0.8149 (mttp) cc_final: 0.7606 (mmmm) REVERT: D 263 GLN cc_start: 0.7308 (tt0) cc_final: 0.7054 (tt0) REVERT: D 345 TYR cc_start: 0.6760 (m-80) cc_final: 0.6471 (m-80) REVERT: D 366 GLU cc_start: 0.8175 (tt0) cc_final: 0.7804 (pm20) REVERT: D 379 GLN cc_start: 0.8199 (tt0) cc_final: 0.7888 (mm-40) REVERT: E 77 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7656 (mp) REVERT: F 74 GLU cc_start: 0.8238 (tt0) cc_final: 0.7600 (mt-10) REVERT: F 281 TYR cc_start: 0.9155 (m-80) cc_final: 0.8763 (m-80) REVERT: F 294 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8477 (mm-30) outliers start: 47 outliers final: 18 residues processed: 243 average time/residue: 0.6623 time to fit residues: 183.7072 Evaluate side-chains 226 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 387 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 23 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN C 428 GLN D 168 GLN G 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.090752 restraints weight = 30470.337| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.90 r_work: 0.2882 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22748 Z= 0.124 Angle : 0.502 8.724 30880 Z= 0.257 Chirality : 0.043 0.203 3654 Planarity : 0.004 0.058 3978 Dihedral : 5.305 60.967 3306 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.87 % Allowed : 14.27 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.16), residues: 2946 helix: 2.18 (0.15), residues: 1203 sheet: 0.27 (0.23), residues: 528 loop : 0.40 (0.19), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 337 TYR 0.013 0.001 TYR F 147 PHE 0.028 0.001 PHE B 405 TRP 0.007 0.001 TRP C 258 HIS 0.004 0.001 HIS D 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (22748) covalent geometry : angle 0.50197 / 0.26 (30880) hydrogen bonds : bond 0.03823 / 2.62 ( 1170) hydrogen bonds : angle 4.58697 / 3.21 ( 3342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 95 ASN cc_start: 0.8140 (m-40) cc_final: 0.7812 (m-40) REVERT: A 133 VAL cc_start: 0.8790 (p) cc_final: 0.8542 (m) REVERT: A 173 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8395 (ptt90) REVERT: A 303 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7799 (tp) REVERT: A 355 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7590 (mm-30) REVERT: A 357 GLU cc_start: 0.7967 (tt0) cc_final: 0.7668 (tm-30) REVERT: A 373 VAL cc_start: 0.8186 (p) cc_final: 0.7862 (m) REVERT: A 375 ARG cc_start: 0.8485 (mtp85) cc_final: 0.8238 (mtm180) REVERT: A 418 GLN cc_start: 0.8084 (tp40) cc_final: 0.7748 (tp40) REVERT: A 467 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7052 (tt0) REVERT: A 493 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7727 (mmtt) REVERT: B 199 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7664 (mtpm) REVERT: B 303 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8546 (tp) REVERT: B 442 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7897 (mt-10) REVERT: B 451 VAL cc_start: 0.8272 (t) cc_final: 0.7775 (m) REVERT: B 484 GLU cc_start: 0.7339 (tt0) cc_final: 0.6718 (tp30) REVERT: B 495 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7647 (tt) REVERT: C 257 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7528 (mt-10) REVERT: C 299 ASP cc_start: 0.8456 (p0) cc_final: 0.8093 (p0) REVERT: C 391 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.7981 (t) REVERT: C 417 LYS cc_start: 0.8181 (mttp) cc_final: 0.7646 (mmmm) REVERT: D 9 ILE cc_start: 0.8128 (mp) cc_final: 0.7581 (tp) REVERT: D 263 GLN cc_start: 0.7334 (tt0) cc_final: 0.7086 (tt0) REVERT: D 345 TYR cc_start: 0.6763 (m-80) cc_final: 0.6489 (m-80) REVERT: D 366 GLU cc_start: 0.8132 (tt0) cc_final: 0.7786 (pm20) REVERT: D 379 GLN cc_start: 0.8184 (tt0) cc_final: 0.7879 (mm-40) REVERT: E 77 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7625 (mt) REVERT: F 74 GLU cc_start: 0.8245 (tt0) cc_final: 0.7772 (tt0) REVERT: F 281 TYR cc_start: 0.9153 (m-80) cc_final: 0.8796 (m-80) REVERT: F 294 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8492 (mm-30) outliers start: 43 outliers final: 21 residues processed: 238 average time/residue: 0.6453 time to fit residues: 174.9020 Evaluate side-chains 229 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 270 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 228 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.2980 chunk 187 optimal weight: 0.5980 chunk 269 optimal weight: 2.9990 chunk 267 optimal weight: 0.0010 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 61 optimal weight: 0.0870 chunk 229 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN C 210 GLN C 428 GLN G 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.093781 restraints weight = 30164.446| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.89 r_work: 0.2933 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22748 Z= 0.093 Angle : 0.476 8.045 30880 Z= 0.244 Chirality : 0.042 0.198 3654 Planarity : 0.004 0.058 3978 Dihedral : 5.039 58.085 3306 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.56 % Allowed : 14.97 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.16), residues: 2946 helix: 2.41 (0.16), residues: 1181 sheet: 0.42 (0.24), residues: 505 loop : 0.47 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 412 TYR 0.011 0.001 TYR D 458 PHE 0.028 0.001 PHE B 405 TRP 0.009 0.001 TRP C 258 HIS 0.003 0.000 HIS D 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (22748) covalent geometry : angle 0.47556 / 0.24 (30880) hydrogen bonds : bond 0.03339 / 2.28 ( 1170) hydrogen bonds : angle 4.46618 / 3.13 ( 3342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6435 (tt0) REVERT: A 95 ASN cc_start: 0.8192 (m-40) cc_final: 0.7970 (m-40) REVERT: A 133 VAL cc_start: 0.8808 (p) cc_final: 0.8584 (m) REVERT: A 173 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8370 (ptt90) REVERT: A 237 THR cc_start: 0.8140 (p) cc_final: 0.7864 (p) REVERT: A 303 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7755 (tp) REVERT: A 355 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7575 (mm-30) REVERT: A 357 GLU cc_start: 0.8000 (tt0) cc_final: 0.7635 (tm-30) REVERT: A 373 VAL cc_start: 0.8191 (p) cc_final: 0.7868 (m) REVERT: A 418 GLN cc_start: 0.8117 (tp40) cc_final: 0.7791 (tp40) REVERT: A 467 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7052 (tt0) REVERT: A 493 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7796 (mmtt) REVERT: B 199 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7698 (mtpm) REVERT: B 303 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8545 (tp) REVERT: B 400 ARG cc_start: 0.8111 (mmm-85) cc_final: 0.7818 (tpt-90) REVERT: B 442 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7970 (mt-10) REVERT: B 451 VAL cc_start: 0.8278 (t) cc_final: 0.7819 (m) REVERT: B 484 GLU cc_start: 0.7301 (tt0) cc_final: 0.6638 (tp30) REVERT: B 495 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7643 (tt) REVERT: C 257 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7543 (mt-10) REVERT: C 299 ASP cc_start: 0.8409 (p0) cc_final: 0.8049 (p0) REVERT: C 391 SER cc_start: 0.8661 (m) cc_final: 0.8043 (t) REVERT: C 417 LYS cc_start: 0.8172 (mttp) cc_final: 0.7593 (mmmm) REVERT: D 9 ILE cc_start: 0.8161 (mp) cc_final: 0.7638 (tp) REVERT: D 263 GLN cc_start: 0.7278 (tt0) cc_final: 0.7070 (tt0) REVERT: D 289 MET cc_start: 0.8596 (tpp) cc_final: 0.8159 (tpp) REVERT: D 366 GLU cc_start: 0.8111 (tt0) cc_final: 0.7816 (pm20) REVERT: D 379 GLN cc_start: 0.8171 (tt0) cc_final: 0.7871 (mm-40) REVERT: D 382 LYS cc_start: 0.7802 (ttpp) cc_final: 0.7558 (ttpp) REVERT: E 77 LEU cc_start: 0.7850 (tt) cc_final: 0.7535 (mp) REVERT: F 74 GLU cc_start: 0.8266 (tt0) cc_final: 0.7783 (tt0) REVERT: F 281 TYR cc_start: 0.9121 (m-80) cc_final: 0.8778 (m-80) REVERT: F 294 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8526 (mm-30) REVERT: G 8 MET cc_start: 0.8393 (mmp) cc_final: 0.7951 (mmm) outliers start: 36 outliers final: 14 residues processed: 257 average time/residue: 0.6229 time to fit residues: 183.0182 Evaluate side-chains 236 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain F residue 155 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 285 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN C 428 GLN E 379 GLN F 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.091805 restraints weight = 30359.374| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.89 r_work: 0.2897 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22748 Z= 0.126 Angle : 0.499 8.599 30880 Z= 0.254 Chirality : 0.043 0.205 3654 Planarity : 0.004 0.057 3978 Dihedral : 5.091 60.412 3306 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.52 % Allowed : 15.53 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.16), residues: 2946 helix: 2.33 (0.15), residues: 1193 sheet: 0.34 (0.23), residues: 527 loop : 0.49 (0.19), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 412 TYR 0.015 0.001 TYR C 246 PHE 0.012 0.001 PHE C 506 TRP 0.006 0.001 TRP C 258 HIS 0.004 0.001 HIS D 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (22748) covalent geometry : angle 0.49857 / 0.25 (30880) hydrogen bonds : bond 0.03679 / 2.52 ( 1170) hydrogen bonds : angle 4.49122 / 3.14 ( 3342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASN cc_start: 0.8182 (m-40) cc_final: 0.7951 (m-40) REVERT: A 133 VAL cc_start: 0.8796 (p) cc_final: 0.8555 (m) REVERT: A 173 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8401 (ptt90) REVERT: A 303 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7745 (tp) REVERT: A 355 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7592 (mm-30) REVERT: A 357 GLU cc_start: 0.8028 (tt0) cc_final: 0.7694 (tm-30) REVERT: A 373 VAL cc_start: 0.8195 (p) cc_final: 0.7854 (m) REVERT: A 418 GLN cc_start: 0.8125 (tp40) cc_final: 0.7796 (tp40) REVERT: A 467 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7076 (tt0) REVERT: A 493 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7799 (mmtt) REVERT: B 199 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7728 (mtpm) REVERT: B 400 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7845 (tpt-90) REVERT: B 442 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7927 (mt-10) REVERT: B 451 VAL cc_start: 0.8270 (t) cc_final: 0.7779 (m) REVERT: B 484 GLU cc_start: 0.7308 (tt0) cc_final: 0.6582 (tp30) REVERT: B 495 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7656 (tt) REVERT: C 257 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7550 (mt-10) REVERT: C 299 ASP cc_start: 0.8409 (p0) cc_final: 0.8047 (p0) REVERT: C 391 SER cc_start: 0.8622 (m) cc_final: 0.7993 (t) REVERT: C 417 LYS cc_start: 0.8181 (mttp) cc_final: 0.7602 (mmmm) REVERT: C 467 GLU cc_start: 0.6887 (tt0) cc_final: 0.6517 (tt0) REVERT: D 263 GLN cc_start: 0.7297 (tt0) cc_final: 0.7084 (tt0) REVERT: D 366 GLU cc_start: 0.8050 (tt0) cc_final: 0.7763 (pm20) REVERT: D 379 GLN cc_start: 0.8172 (tt0) cc_final: 0.7881 (mm-40) REVERT: E 77 LEU cc_start: 0.7855 (tt) cc_final: 0.7523 (mp) REVERT: E 412 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6566 (mtm180) REVERT: F 74 GLU cc_start: 0.8241 (tt0) cc_final: 0.7781 (tt0) REVERT: F 281 TYR cc_start: 0.9151 (m-80) cc_final: 0.8870 (m-80) REVERT: F 294 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8514 (mm-30) REVERT: G 8 MET cc_start: 0.8398 (mmp) cc_final: 0.7954 (mmm) outliers start: 35 outliers final: 18 residues processed: 238 average time/residue: 0.6471 time to fit residues: 175.3171 Evaluate side-chains 235 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 412 ARG Chi-restraints excluded: chain F residue 155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 128 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 chunk 245 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN C 428 GLN D 249 GLN F 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.089226 restraints weight = 30617.512| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.90 r_work: 0.2857 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22748 Z= 0.184 Angle : 0.542 9.283 30880 Z= 0.276 Chirality : 0.045 0.206 3654 Planarity : 0.004 0.057 3978 Dihedral : 5.365 65.975 3306 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.52 % Allowed : 15.49 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.16), residues: 2946 helix: 2.17 (0.15), residues: 1200 sheet: 0.22 (0.23), residues: 533 loop : 0.39 (0.19), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 412 TYR 0.018 0.001 TYR F 147 PHE 0.030 0.002 PHE B 405 TRP 0.006 0.001 TRP A 258 HIS 0.005 0.001 HIS D 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (22748) covalent geometry : angle 0.54153 / 0.28 (30880) hydrogen bonds : bond 0.04233 / 2.91 ( 1170) hydrogen bonds : angle 4.63556 / 3.24 ( 3342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 95 ASN cc_start: 0.8087 (m-40) cc_final: 0.7800 (m-40) REVERT: A 133 VAL cc_start: 0.8797 (p) cc_final: 0.8528 (m) REVERT: A 173 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8318 (mtm-85) REVERT: A 303 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7800 (tp) REVERT: A 355 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7597 (mm-30) REVERT: A 357 GLU cc_start: 0.8030 (tt0) cc_final: 0.7714 (tm-30) REVERT: A 373 VAL cc_start: 0.8241 (p) cc_final: 0.7883 (m) REVERT: A 375 ARG cc_start: 0.8438 (mtp-110) cc_final: 0.8096 (mtm180) REVERT: A 418 GLN cc_start: 0.8111 (tp40) cc_final: 0.7786 (tp40) REVERT: A 467 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7070 (tt0) REVERT: A 493 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7808 (mmtt) REVERT: B 66 LEU cc_start: 0.9059 (tp) cc_final: 0.8856 (tt) REVERT: B 199 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7740 (mtpm) REVERT: B 400 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.7845 (tpt-90) REVERT: B 442 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7958 (mt-10) REVERT: B 451 VAL cc_start: 0.8281 (t) cc_final: 0.7752 (m) REVERT: B 484 GLU cc_start: 0.7336 (tt0) cc_final: 0.6671 (tp30) REVERT: B 495 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7674 (tt) REVERT: C 257 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7531 (mt-10) REVERT: C 299 ASP cc_start: 0.8440 (p0) cc_final: 0.8067 (p0) REVERT: C 391 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8031 (t) REVERT: C 417 LYS cc_start: 0.8185 (mttp) cc_final: 0.7605 (mmmm) REVERT: D 263 GLN cc_start: 0.7392 (tt0) cc_final: 0.7115 (tt0) REVERT: D 345 TYR cc_start: 0.6782 (m-80) cc_final: 0.6503 (m-80) REVERT: D 366 GLU cc_start: 0.8153 (tt0) cc_final: 0.7805 (pm20) REVERT: D 379 GLN cc_start: 0.8192 (tt0) cc_final: 0.7916 (mm-40) REVERT: E 77 LEU cc_start: 0.7899 (tt) cc_final: 0.7621 (mt) REVERT: E 412 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.6516 (mtm180) REVERT: F 74 GLU cc_start: 0.8235 (tt0) cc_final: 0.7811 (tt0) REVERT: F 294 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8570 (mm-30) outliers start: 35 outliers final: 20 residues processed: 231 average time/residue: 0.6837 time to fit residues: 179.5297 Evaluate side-chains 232 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 412 ARG Chi-restraints excluded: chain F residue 155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 231 optimal weight: 3.9990 chunk 269 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN C 428 GLN E 375 GLN F 223 ASN G 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.089471 restraints weight = 30550.248| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.88 r_work: 0.2858 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22748 Z= 0.168 Angle : 0.530 8.597 30880 Z= 0.271 Chirality : 0.045 0.206 3654 Planarity : 0.004 0.057 3978 Dihedral : 5.378 68.320 3306 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.26 % Allowed : 15.84 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.16), residues: 2946 helix: 2.11 (0.15), residues: 1201 sheet: 0.17 (0.23), residues: 533 loop : 0.32 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 412 TYR 0.016 0.001 TYR F 147 PHE 0.028 0.002 PHE B 405 TRP 0.006 0.002 TRP C 191 HIS 0.005 0.001 HIS D 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (22748) covalent geometry : angle 0.52962 / 0.27 (30880) hydrogen bonds : bond 0.04114 / 2.83 ( 1170) hydrogen bonds : angle 4.64656 / 3.25 ( 3342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6544.16 seconds wall clock time: 112 minutes 32.44 seconds (6752.44 seconds total)