Starting phenix.real_space_refine on Sun Apr 5 20:25:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pbb_17583/04_2026/8pbb_17583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pbb_17583/04_2026/8pbb_17583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pbb_17583/04_2026/8pbb_17583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pbb_17583/04_2026/8pbb_17583.map" model { file = "/net/cci-nas-00/data/ceres_data/8pbb_17583/04_2026/8pbb_17583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pbb_17583/04_2026/8pbb_17583.cif" } resolution = 2.49 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= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 8 7.16 5 S 82 5.16 5 C 8522 2.51 5 N 2260 2.21 5 O 2462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13334 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3222 Classifications: {'peptide': 399} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 384} Chain breaks: 5 Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3437 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 418} Chain breaks: 2 Chain: "C" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3222 Classifications: {'peptide': 399} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 384} Chain breaks: 5 Chain: "D" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3437 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 418} Chain breaks: 2 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3913 SG CYS B 104 74.127 81.561 48.979 1.00 63.32 S ATOM 160 SG CYS A 75 73.206 78.168 51.875 1.00 35.82 S ATOM 3345 SG CYS B 20 70.359 76.400 46.744 1.00 25.80 S ATOM 3513 SG CYS B 45 76.826 76.293 46.828 1.00 44.32 S ATOM 6819 SG CYS C 75 33.917 20.571 51.857 1.00 35.40 S ATOM 10572 SG CYS D 104 32.989 17.200 48.953 1.00 62.56 S ATOM 10004 SG CYS D 20 36.766 22.473 46.864 1.00 26.07 S ATOM 10172 SG CYS D 45 30.164 22.484 46.872 1.00 43.60 S Time building chain proxies: 3.59, per 1000 atoms: 0.27 Number of scatterers: 13334 At special positions: 0 Unit cell: (107.973, 100.44, 101.277, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 8 26.01 S 82 16.00 O 2462 8.00 N 2260 7.00 C 8522 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 541.8 milliseconds 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 12 sheets defined 54.5% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 72 through 79 removed outlier: 3.911A pdb=" N THR A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR A 79 " --> pdb=" O CYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 182 through 191 Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 247 through 250 removed outlier: 4.080A pdb=" N ALA A 250 " --> pdb=" O MET A 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 261 through 273 removed outlier: 3.776A pdb=" N CYS A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 299 Processing helix chain 'A' and resid 300 through 326 removed outlier: 3.599A pdb=" N ALA A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Proline residue: A 317 - end of helix removed outlier: 3.553A pdb=" N TYR A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 325 " --> pdb=" O TRP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 405 through 414 removed outlier: 3.909A pdb=" N LYS A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 449 through 456 removed outlier: 3.699A pdb=" N GLN A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 removed outlier: 3.599A pdb=" N LEU A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 500 through 519 removed outlier: 3.823A pdb=" N ILE A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 30 removed outlier: 3.616A pdb=" N GLY B 24 " --> pdb=" O CYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 58 removed outlier: 3.840A pdb=" N VAL B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 113 through 129 removed outlier: 3.593A pdb=" N ASP B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 147 through 164 Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 269 through 285 Processing helix chain 'B' and resid 289 through 311 removed outlier: 3.573A pdb=" N VAL B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N HIS B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N MET B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 335 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 374 through 384 removed outlier: 4.120A pdb=" N LEU B 378 " --> pdb=" O ASP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 397 through 405 removed outlier: 3.820A pdb=" N SER B 401 " --> pdb=" O GLY B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 427 through 451 Processing helix chain 'B' and resid 453 through 457 removed outlier: 3.506A pdb=" N LEU B 457 " --> pdb=" O GLU B 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 79 removed outlier: 3.889A pdb=" N THR C 76 " --> pdb=" O PRO C 72 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR C 79 " --> pdb=" O CYS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 114 through 126 Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 182 through 189 Processing helix chain 'C' and resid 215 through 226 Processing helix chain 'C' and resid 240 through 246 Processing helix chain 'C' and resid 247 through 250 removed outlier: 4.044A pdb=" N ALA C 250 " --> pdb=" O MET C 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 247 through 250' Processing helix chain 'C' and resid 261 through 273 removed outlier: 3.717A pdb=" N CYS C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 299 Processing helix chain 'C' and resid 300 through 326 removed outlier: 3.608A pdb=" N ALA C 304 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Proline residue: C 317 - end of helix removed outlier: 3.555A pdb=" N TYR C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG C 325 " --> pdb=" O TRP C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 405 through 414 removed outlier: 3.909A pdb=" N LYS C 414 " --> pdb=" O GLU C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 448 Processing helix chain 'C' and resid 449 through 456 removed outlier: 3.695A pdb=" N GLN C 453 " --> pdb=" O SER C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 removed outlier: 3.603A pdb=" N LEU C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 500 through 519 removed outlier: 3.823A pdb=" N ILE C 504 " --> pdb=" O SER C 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 30 removed outlier: 3.605A pdb=" N GLY D 24 " --> pdb=" O CYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 58 removed outlier: 3.808A pdb=" N VAL D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 113 through 129 removed outlier: 3.531A pdb=" N ASP D 122 " --> pdb=" O SER D 118 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 147 through 164 Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 246 through 258 Processing helix chain 'D' and resid 268 through 285 removed outlier: 4.349A pdb=" N ASN D 272 " --> pdb=" O VAL D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 311 removed outlier: 3.579A pdb=" N VAL D 293 " --> pdb=" O PRO D 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N HIS D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N MET D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 335 Processing helix chain 'D' and resid 354 through 364 Processing helix chain 'D' and resid 374 through 384 removed outlier: 4.125A pdb=" N LEU D 378 " --> pdb=" O ASP D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 396 No H-bonds generated for 'chain 'D' and resid 394 through 396' Processing helix chain 'D' and resid 397 through 405 removed outlier: 3.823A pdb=" N SER D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 424 Processing helix chain 'D' and resid 427 through 451 Processing helix chain 'D' and resid 453 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 165 removed outlier: 6.467A pdb=" N MET A 132 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 98 " --> pdb=" O HIS A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 236 removed outlier: 6.973A pdb=" N ILE A 205 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N PHE A 235 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TYR A 207 " --> pdb=" O PHE A 235 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 204 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL A 254 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASN A 206 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN A 253 " --> pdb=" O LEU A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 354 through 355 removed outlier: 6.502A pdb=" N LYS A 330 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N PHE A 403 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS A 332 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 402 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.887A pdb=" N THR B 6 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL B 316 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU B 342 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 318 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU B 344 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG B 315 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU B 392 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 317 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 391 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.513A pdb=" N LEU B 137 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 202 removed outlier: 6.899A pdb=" N ILE B 173 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU B 202 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 175 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASN B 174 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR B 238 " --> pdb=" O VAL B 262 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 162 through 166 removed outlier: 6.445A pdb=" N MET C 132 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N CYS C 166 " --> pdb=" O MET C 132 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 134 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE C 98 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 230 through 236 removed outlier: 6.968A pdb=" N ILE C 205 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N PHE C 235 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR C 207 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN C 253 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 354 through 355 removed outlier: 6.521A pdb=" N LYS C 330 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE C 403 " --> pdb=" O LYS C 330 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS C 332 " --> pdb=" O PHE C 403 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE C 402 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 6 through 7 removed outlier: 6.888A pdb=" N THR D 6 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL D 316 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU D 342 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE D 318 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU D 344 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG D 315 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU D 392 " --> pdb=" O ARG D 315 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA D 317 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE D 391 " --> pdb=" O VAL D 409 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.508A pdb=" N LEU D 137 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 199 through 202 removed outlier: 6.899A pdb=" N ILE D 173 " --> pdb=" O ASN D 200 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU D 202 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU D 175 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN D 174 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR D 238 " --> pdb=" O VAL D 262 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 609 hydrogen bonds defined for protein. 1761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.53: 12240 1.53 - 1.86: 1368 1.86 - 2.19: 0 2.19 - 2.52: 26 2.52 - 2.85: 10 Bond restraints: 13644 Sorted by residual: bond pdb="FE6 CLF D 501 " pdb="FE7 CLF D 501 " ideal model delta sigma weight residual 2.200 2.845 -0.645 2.00e-02 2.50e+03 1.04e+03 bond pdb="FE5 CLF D 501 " pdb="FE7 CLF D 501 " ideal model delta sigma weight residual 2.200 2.813 -0.613 2.00e-02 2.50e+03 9.40e+02 bond pdb="FE1 CLF B 501 " pdb="FE3 CLF B 501 " ideal model delta sigma weight residual 2.200 2.793 -0.593 2.00e-02 2.50e+03 8.80e+02 bond pdb="FE2 CLF B 501 " pdb="FE3 CLF B 501 " ideal model delta sigma weight residual 2.200 2.753 -0.553 2.00e-02 2.50e+03 7.64e+02 bond pdb="FE7 CLF D 501 " pdb="FE8 CLF D 501 " ideal model delta sigma weight residual 2.200 2.734 -0.534 2.00e-02 2.50e+03 7.13e+02 ... (remaining 13639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.73: 18396 6.73 - 13.46: 6 13.46 - 20.20: 1 20.20 - 26.93: 0 26.93 - 33.66: 2 Bond angle restraints: 18405 Sorted by residual: angle pdb=" S1 CLF B 501 " pdb="FE2 CLF B 501 " pdb="FE4 CLF B 501 " ideal model delta sigma weight residual 90.00 56.34 33.66 3.00e+00 1.11e-01 1.26e+02 angle pdb=" S1 CLF B 501 " pdb="FE2 CLF B 501 " pdb="FE1 CLF B 501 " ideal model delta sigma weight residual 90.00 57.54 32.46 3.00e+00 1.11e-01 1.17e+02 angle pdb=" N LEU A 340 " pdb=" CA LEU A 340 " pdb=" C LEU A 340 " ideal model delta sigma weight residual 114.04 104.59 9.45 1.24e+00 6.50e-01 5.81e+01 angle pdb=" S1 CLF B 501 " pdb="FE2 CLF B 501 " pdb="FE3 CLF B 501 " ideal model delta sigma weight residual 90.00 108.05 -18.05 3.00e+00 1.11e-01 3.62e+01 angle pdb=" N GLU C 489 " pdb=" CA GLU C 489 " pdb=" C GLU C 489 " ideal model delta sigma weight residual 112.92 107.21 5.71 1.23e+00 6.61e-01 2.15e+01 ... (remaining 18400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 7148 17.72 - 35.45: 734 35.45 - 53.17: 201 53.17 - 70.89: 58 70.89 - 88.62: 7 Dihedral angle restraints: 8148 sinusoidal: 3284 harmonic: 4864 Sorted by residual: dihedral pdb=" CA TRP A 343 " pdb=" C TRP A 343 " pdb=" N ALA A 344 " pdb=" CA ALA A 344 " ideal model delta harmonic sigma weight residual 180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA HIS B 394 " pdb=" C HIS B 394 " pdb=" N SER B 395 " pdb=" CA SER B 395 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA HIS D 394 " pdb=" C HIS D 394 " pdb=" N SER D 395 " pdb=" CA SER D 395 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1582 0.058 - 0.116: 406 0.116 - 0.175: 40 0.175 - 0.233: 8 0.233 - 0.291: 2 Chirality restraints: 2038 Sorted by residual: chirality pdb=" CA LEU A 340 " pdb=" N LEU A 340 " pdb=" C LEU A 340 " pdb=" CB LEU A 340 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ASP A 78 " pdb=" N ASP A 78 " pdb=" C ASP A 78 " pdb=" CB ASP A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA CYS C 332 " pdb=" N CYS C 332 " pdb=" C CYS C 332 " pdb=" CB CYS C 332 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2035 not shown) Planarity restraints: 2356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 158 " 0.414 9.50e-02 1.11e+02 1.86e-01 2.11e+01 pdb=" NE ARG A 158 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 158 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 158 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 158 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 80 " 0.384 9.50e-02 1.11e+02 1.72e-01 1.83e+01 pdb=" NE ARG D 80 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 80 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 80 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 80 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 158 " 0.283 9.50e-02 1.11e+02 1.27e-01 9.87e+00 pdb=" NE ARG C 158 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG C 158 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 158 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 158 " 0.009 2.00e-02 2.50e+03 ... (remaining 2353 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 155 2.66 - 3.22: 11933 3.22 - 3.78: 22228 3.78 - 4.34: 32612 4.34 - 4.90: 50823 Nonbonded interactions: 117751 Sorted by model distance: nonbonded pdb=" OE1 GLU A 410 " pdb=" OG SER B 54 " model vdw 2.094 3.040 nonbonded pdb=" OE1 GLU C 410 " pdb=" OG SER D 54 " model vdw 2.099 3.040 nonbonded pdb=" O LYS C 55 " pdb=" OG1 THR C 60 " model vdw 2.142 3.040 nonbonded pdb=" O LYS A 55 " pdb=" OG1 THR A 60 " model vdw 2.152 3.040 nonbonded pdb=" NE2 GLN B 21 " pdb=" O VAL B 145 " model vdw 2.211 3.120 ... (remaining 117746 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.950 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 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 : 0.017 0.645 13652 Z= 0.843 Angle : 0.816 33.661 18405 Z= 0.460 Chirality : 0.051 0.291 2038 Planarity : 0.008 0.186 2356 Dihedral : 16.172 88.617 5012 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.63 % Allowed : 13.34 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.25 % 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: -0.23 (0.19), residues: 1648 helix: 0.45 (0.17), residues: 848 sheet: 0.12 (0.37), residues: 176 loop : -0.96 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 80 TYR 0.027 0.003 TYR C 241 PHE 0.020 0.002 PHE C 284 TRP 0.030 0.003 TRP A 80 HIS 0.006 0.001 HIS D 394 Details of bonding type rmsd covalent geometry : bond 0.01682 (13644) covalent geometry : angle 0.81601 (18405) hydrogen bonds : bond 0.14346 ( 609) hydrogen bonds : angle 7.27648 ( 1761) Misc. bond : bond 0.06909 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 178 time to evaluate : 0.571 Fit side-chains REVERT: B 154 LYS cc_start: 0.8124 (mttt) cc_final: 0.7876 (tptp) REVERT: B 309 MET cc_start: 0.8997 (tpt) cc_final: 0.8456 (tpt) REVERT: D 154 LYS cc_start: 0.8093 (mttt) cc_final: 0.7871 (tptp) REVERT: D 309 MET cc_start: 0.9003 (tpt) cc_final: 0.8456 (tpt) REVERT: D 421 MET cc_start: 0.8486 (mmm) cc_final: 0.8189 (mmm) outliers start: 9 outliers final: 7 residues processed: 185 average time/residue: 0.6837 time to fit residues: 137.0122 Evaluate side-chains 181 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 174 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 340 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN B 26 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 26 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.156725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116349 restraints weight = 11467.256| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.28 r_work: 0.3121 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13652 Z= 0.111 Angle : 0.591 28.948 18405 Z= 0.285 Chirality : 0.043 0.129 2038 Planarity : 0.004 0.043 2356 Dihedral : 5.178 58.111 1812 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.83 % Allowed : 13.20 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.25 % 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: 0.39 (0.20), residues: 1648 helix: 1.02 (0.17), residues: 862 sheet: 0.07 (0.39), residues: 162 loop : -0.68 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 259 TYR 0.014 0.001 TYR A 241 PHE 0.012 0.001 PHE A 126 TRP 0.012 0.001 TRP A 80 HIS 0.003 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00238 (13644) covalent geometry : angle 0.59073 (18405) hydrogen bonds : bond 0.03907 ( 609) hydrogen bonds : angle 5.47930 ( 1761) Misc. bond : bond 0.01190 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.530 Fit side-chains REVERT: A 426 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.8509 (m90) REVERT: B 154 LYS cc_start: 0.8496 (mttt) cc_final: 0.7776 (tptp) REVERT: B 309 MET cc_start: 0.8952 (tpt) cc_final: 0.8611 (tpt) REVERT: B 353 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8051 (mtmt) REVERT: D 154 LYS cc_start: 0.8490 (mttt) cc_final: 0.7766 (tptp) REVERT: D 196 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8333 (mt-10) REVERT: D 309 MET cc_start: 0.8993 (tpt) cc_final: 0.8688 (tpt) outliers start: 26 outliers final: 12 residues processed: 204 average time/residue: 0.6807 time to fit residues: 150.6893 Evaluate side-chains 190 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 196 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 34 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 135 HIS ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 26 GLN D 135 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.113094 restraints weight = 11477.202| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.31 r_work: 0.3050 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13652 Z= 0.180 Angle : 0.642 28.847 18405 Z= 0.314 Chirality : 0.045 0.129 2038 Planarity : 0.004 0.036 2356 Dihedral : 5.299 55.543 1808 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.67 % Allowed : 12.78 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.25 % 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: 0.25 (0.20), residues: 1648 helix: 0.94 (0.17), residues: 860 sheet: -0.06 (0.38), residues: 162 loop : -0.76 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 423 TYR 0.021 0.002 TYR C 241 PHE 0.014 0.002 PHE A 126 TRP 0.013 0.002 TRP D 179 HIS 0.004 0.001 HIS D 394 Details of bonding type rmsd covalent geometry : bond 0.00420 (13644) covalent geometry : angle 0.64170 (18405) hydrogen bonds : bond 0.04509 ( 609) hydrogen bonds : angle 5.49724 ( 1761) Misc. bond : bond 0.02623 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.424 Fit side-chains REVERT: A 426 HIS cc_start: 0.9213 (OUTLIER) cc_final: 0.8675 (m90) REVERT: B 154 LYS cc_start: 0.8545 (mttt) cc_final: 0.7811 (tptp) REVERT: B 353 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8185 (mtmt) REVERT: D 154 LYS cc_start: 0.8544 (mttt) cc_final: 0.7822 (tptp) REVERT: D 196 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8405 (mt-10) REVERT: D 309 MET cc_start: 0.9039 (tpt) cc_final: 0.8733 (tpt) REVERT: D 353 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8271 (mtmt) outliers start: 38 outliers final: 13 residues processed: 199 average time/residue: 0.6868 time to fit residues: 147.9178 Evaluate side-chains 195 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 120 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 135 HIS ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 26 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.151606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110031 restraints weight = 11478.862| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.31 r_work: 0.3029 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13652 Z= 0.288 Angle : 0.732 28.836 18405 Z= 0.366 Chirality : 0.051 0.149 2038 Planarity : 0.005 0.035 2356 Dihedral : 5.685 48.886 1808 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.18 % Allowed : 13.41 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 1648 helix: 0.62 (0.17), residues: 862 sheet: -0.23 (0.36), residues: 174 loop : -0.84 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 423 TYR 0.027 0.003 TYR C 241 PHE 0.019 0.003 PHE B 163 TRP 0.017 0.003 TRP D 179 HIS 0.006 0.001 HIS D 394 Details of bonding type rmsd covalent geometry : bond 0.00690 (13644) covalent geometry : angle 0.73196 (18405) hydrogen bonds : bond 0.05344 ( 609) hydrogen bonds : angle 5.72684 ( 1761) Misc. bond : bond 0.03257 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.520 Fit side-chains REVERT: A 426 HIS cc_start: 0.9270 (OUTLIER) cc_final: 0.8748 (m90) REVERT: C 426 HIS cc_start: 0.9222 (OUTLIER) cc_final: 0.8771 (m90) REVERT: D 154 LYS cc_start: 0.8565 (mttt) cc_final: 0.7900 (mtpp) REVERT: D 196 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8427 (mt-10) outliers start: 31 outliers final: 14 residues processed: 192 average time/residue: 0.6579 time to fit residues: 137.0530 Evaluate side-chains 190 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 104 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN D 21 GLN D 26 GLN D 135 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.156661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115487 restraints weight = 11397.508| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.31 r_work: 0.3102 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13652 Z= 0.112 Angle : 0.590 28.835 18405 Z= 0.283 Chirality : 0.043 0.132 2038 Planarity : 0.004 0.033 2356 Dihedral : 5.027 48.456 1806 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.47 % Allowed : 14.19 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.25 % 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: 0.37 (0.20), residues: 1648 helix: 1.04 (0.17), residues: 866 sheet: -0.15 (0.37), residues: 162 loop : -0.69 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 10 TYR 0.015 0.001 TYR A 241 PHE 0.011 0.001 PHE A 126 TRP 0.012 0.001 TRP D 376 HIS 0.003 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00243 (13644) covalent geometry : angle 0.58978 (18405) hydrogen bonds : bond 0.03813 ( 609) hydrogen bonds : angle 5.27384 ( 1761) Misc. bond : bond 0.01286 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.559 Fit side-chains REVERT: A 426 HIS cc_start: 0.9100 (OUTLIER) cc_final: 0.8521 (m90) REVERT: B 11 GLU cc_start: 0.7240 (mt-10) cc_final: 0.7026 (mt-10) REVERT: B 353 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8115 (mtmt) REVERT: C 117 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7755 (ttmt) REVERT: C 426 HIS cc_start: 0.9014 (OUTLIER) cc_final: 0.8493 (m90) REVERT: D 154 LYS cc_start: 0.8512 (mttt) cc_final: 0.7775 (tptp) REVERT: D 196 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: D 309 MET cc_start: 0.8922 (tpt) cc_final: 0.8621 (tpt) REVERT: D 353 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8113 (mtmt) outliers start: 21 outliers final: 10 residues processed: 191 average time/residue: 0.6912 time to fit residues: 142.9264 Evaluate side-chains 192 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 92 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 26 GLN D 135 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.154758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.113272 restraints weight = 11376.398| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.30 r_work: 0.3071 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13652 Z= 0.174 Angle : 0.637 28.840 18405 Z= 0.311 Chirality : 0.045 0.129 2038 Planarity : 0.004 0.033 2356 Dihedral : 5.212 46.188 1806 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.76 % Allowed : 13.97 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.25 % 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: 0.25 (0.20), residues: 1648 helix: 1.01 (0.17), residues: 852 sheet: -0.21 (0.37), residues: 162 loop : -0.80 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 84 TYR 0.020 0.002 TYR C 241 PHE 0.014 0.002 PHE A 126 TRP 0.011 0.002 TRP B 376 HIS 0.005 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00407 (13644) covalent geometry : angle 0.63728 (18405) hydrogen bonds : bond 0.04372 ( 609) hydrogen bonds : angle 5.37541 ( 1761) Misc. bond : bond 0.02092 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.523 Fit side-chains REVERT: A 426 HIS cc_start: 0.9222 (OUTLIER) cc_final: 0.8679 (m90) REVERT: B 353 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8141 (mtmt) REVERT: C 83 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8409 (mmtp) REVERT: D 154 LYS cc_start: 0.8556 (mttt) cc_final: 0.7813 (tptp) REVERT: D 196 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: D 309 MET cc_start: 0.8957 (tpt) cc_final: 0.8680 (tpt) REVERT: D 353 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8128 (mtmt) outliers start: 25 outliers final: 9 residues processed: 189 average time/residue: 0.6624 time to fit residues: 135.6094 Evaluate side-chains 190 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 22 optimal weight: 0.0000 chunk 122 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 26 GLN D 135 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.112844 restraints weight = 11385.982| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.30 r_work: 0.3076 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13652 Z= 0.189 Angle : 0.652 28.845 18405 Z= 0.320 Chirality : 0.046 0.131 2038 Planarity : 0.004 0.032 2356 Dihedral : 5.282 46.587 1806 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.83 % Allowed : 14.12 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1648 helix: 0.93 (0.17), residues: 852 sheet: -0.25 (0.36), residues: 162 loop : -0.82 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.021 0.002 TYR C 241 PHE 0.015 0.002 PHE A 126 TRP 0.012 0.002 TRP D 179 HIS 0.005 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00444 (13644) covalent geometry : angle 0.65230 (18405) hydrogen bonds : bond 0.04520 ( 609) hydrogen bonds : angle 5.41977 ( 1761) Misc. bond : bond 0.02155 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.519 Fit side-chains REVERT: A 426 HIS cc_start: 0.9234 (OUTLIER) cc_final: 0.8681 (m90) REVERT: B 154 LYS cc_start: 0.8572 (mttt) cc_final: 0.7818 (tptp) REVERT: B 353 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8189 (mtmt) REVERT: C 117 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7825 (ttmt) REVERT: C 426 HIS cc_start: 0.9137 (OUTLIER) cc_final: 0.8698 (m90) REVERT: D 154 LYS cc_start: 0.8550 (mttt) cc_final: 0.7813 (tptp) REVERT: D 196 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8402 (mt-10) REVERT: D 309 MET cc_start: 0.8959 (tpt) cc_final: 0.8664 (tpt) REVERT: D 353 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8158 (mtmt) outliers start: 26 outliers final: 11 residues processed: 194 average time/residue: 0.7335 time to fit residues: 153.9701 Evaluate side-chains 191 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 93 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 26 GLN D 135 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.157171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116034 restraints weight = 11342.453| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.30 r_work: 0.3110 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13652 Z= 0.112 Angle : 0.587 28.837 18405 Z= 0.281 Chirality : 0.043 0.129 2038 Planarity : 0.004 0.033 2356 Dihedral : 4.887 45.796 1806 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.54 % Allowed : 14.33 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.25 % 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: 0.48 (0.20), residues: 1648 helix: 1.20 (0.17), residues: 854 sheet: -0.16 (0.38), residues: 162 loop : -0.69 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.015 0.001 TYR C 241 PHE 0.010 0.001 PHE A 126 TRP 0.011 0.001 TRP B 376 HIS 0.003 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00246 (13644) covalent geometry : angle 0.58726 (18405) hydrogen bonds : bond 0.03751 ( 609) hydrogen bonds : angle 5.17522 ( 1761) Misc. bond : bond 0.01332 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.569 Fit side-chains REVERT: A 117 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7806 (ttmm) REVERT: A 426 HIS cc_start: 0.9107 (OUTLIER) cc_final: 0.8515 (m90) REVERT: B 353 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8154 (mtmt) REVERT: C 426 HIS cc_start: 0.9027 (OUTLIER) cc_final: 0.8521 (m90) REVERT: D 154 LYS cc_start: 0.8496 (mttt) cc_final: 0.7781 (tptp) REVERT: D 196 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: D 309 MET cc_start: 0.8920 (tpt) cc_final: 0.8636 (tpt) REVERT: D 353 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8088 (mtmt) outliers start: 22 outliers final: 10 residues processed: 195 average time/residue: 0.6749 time to fit residues: 142.7490 Evaluate side-chains 197 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 92 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 43 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 26 GLN D 135 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.154711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113117 restraints weight = 11424.649| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.31 r_work: 0.3070 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13652 Z= 0.184 Angle : 0.647 28.844 18405 Z= 0.316 Chirality : 0.046 0.133 2038 Planarity : 0.004 0.033 2356 Dihedral : 5.062 43.144 1804 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.69 % Allowed : 14.33 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.25 % 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: 0.25 (0.20), residues: 1648 helix: 1.00 (0.17), residues: 852 sheet: -0.22 (0.37), residues: 162 loop : -0.80 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 84 TYR 0.021 0.002 TYR A 241 PHE 0.014 0.002 PHE A 126 TRP 0.011 0.002 TRP B 376 HIS 0.005 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00433 (13644) covalent geometry : angle 0.64709 (18405) hydrogen bonds : bond 0.04441 ( 609) hydrogen bonds : angle 5.37490 ( 1761) Misc. bond : bond 0.02166 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.429 Fit side-chains REVERT: A 426 HIS cc_start: 0.9236 (OUTLIER) cc_final: 0.8682 (m90) REVERT: B 353 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8156 (mtmt) REVERT: C 426 HIS cc_start: 0.9158 (OUTLIER) cc_final: 0.8647 (m90) REVERT: D 154 LYS cc_start: 0.8548 (mttt) cc_final: 0.7814 (tptp) REVERT: D 196 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8389 (mt-10) REVERT: D 309 MET cc_start: 0.8960 (tpt) cc_final: 0.8675 (tpt) REVERT: D 353 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8189 (mtmt) outliers start: 24 outliers final: 11 residues processed: 192 average time/residue: 0.6717 time to fit residues: 139.6122 Evaluate side-chains 193 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 39 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 26 GLN D 135 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.153091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.112183 restraints weight = 11425.767| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.28 r_work: 0.3061 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13652 Z= 0.247 Angle : 0.704 28.852 18405 Z= 0.350 Chirality : 0.049 0.135 2038 Planarity : 0.005 0.033 2356 Dihedral : 5.334 45.408 1804 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.33 % Allowed : 14.96 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.25 % 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: -0.01 (0.19), residues: 1648 helix: 0.74 (0.17), residues: 852 sheet: -0.29 (0.36), residues: 162 loop : -0.86 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 84 TYR 0.026 0.003 TYR A 241 PHE 0.017 0.002 PHE A 126 TRP 0.015 0.002 TRP D 179 HIS 0.006 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00588 (13644) covalent geometry : angle 0.70369 (18405) hydrogen bonds : bond 0.04965 ( 609) hydrogen bonds : angle 5.55319 ( 1761) Misc. bond : bond 0.02760 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.548 Fit side-chains REVERT: A 426 HIS cc_start: 0.9265 (OUTLIER) cc_final: 0.8765 (m90) REVERT: B 154 LYS cc_start: 0.8533 (mttt) cc_final: 0.7852 (mtpp) REVERT: B 353 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8229 (mtmt) REVERT: C 426 HIS cc_start: 0.9173 (OUTLIER) cc_final: 0.8728 (m90) REVERT: D 154 LYS cc_start: 0.8529 (mttt) cc_final: 0.7855 (mtpp) REVERT: D 196 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8395 (mt-10) REVERT: D 309 MET cc_start: 0.8954 (tpt) cc_final: 0.8662 (tpt) REVERT: D 353 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8190 (mtmt) outliers start: 19 outliers final: 10 residues processed: 186 average time/residue: 0.6618 time to fit residues: 133.4817 Evaluate side-chains 190 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 132 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 154 optimal weight: 0.0040 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 26 GLN D 135 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.156355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115018 restraints weight = 11331.044| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.31 r_work: 0.3085 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13652 Z= 0.123 Angle : 0.604 28.837 18405 Z= 0.291 Chirality : 0.043 0.128 2038 Planarity : 0.004 0.038 2356 Dihedral : 4.870 44.507 1804 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.05 % Allowed : 15.31 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1648 helix: 1.06 (0.17), residues: 852 sheet: -0.19 (0.38), residues: 162 loop : -0.77 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.016 0.001 TYR A 241 PHE 0.011 0.001 PHE A 126 TRP 0.013 0.001 TRP B 376 HIS 0.003 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00275 (13644) covalent geometry : angle 0.60363 (18405) hydrogen bonds : bond 0.03932 ( 609) hydrogen bonds : angle 5.25233 ( 1761) Misc. bond : bond 0.01547 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5109.85 seconds wall clock time: 87 minutes 44.21 seconds (5264.21 seconds total)