Starting phenix.real_space_refine on Tue Mar 3 18:52:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p6c_13225/03_2026/7p6c_13225.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p6c_13225/03_2026/7p6c_13225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p6c_13225/03_2026/7p6c_13225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p6c_13225/03_2026/7p6c_13225.map" model { file = "/net/cci-nas-00/data/ceres_data/7p6c_13225/03_2026/7p6c_13225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p6c_13225/03_2026/7p6c_13225.cif" } resolution = 2.5 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= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 5060 2.51 5 N 1520 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8120 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.88, per 1000 atoms: 0.11 Number of scatterers: 8120 At special positions: 0 Unit cell: (106.142, 114.139, 49.436, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1520 8.00 N 1520 7.00 C 5060 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: 0.69 Conformation dependent library (CDL) restraints added in 323.8 milliseconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 274 through 280 removed outlier: 6.825A pdb=" N LYS B 274 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE C 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN B 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN C 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS A 274 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE B 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLN A 276 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASN B 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 278 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 283 through 284 removed outlier: 6.209A pdb=" N ASP B 283 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP A 283 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 287 through 292 removed outlier: 6.444A pdb=" N VAL A 287 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LYS D 290 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N SER A 289 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N GLY D 292 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N CYS A 291 " --> pdb=" O GLY D 292 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 287 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LYS E 290 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER D 289 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLY E 292 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS D 291 " --> pdb=" O GLY E 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 297 through 298 removed outlier: 6.277A pdb=" N ILE A 297 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE D 297 " --> pdb=" O LYS E 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 305 through 310 removed outlier: 6.625A pdb=" N SER B 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE C 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N TYR C 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 305 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE B 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.817A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.274A pdb=" N VAL A 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LYS D 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N SER A 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL D 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LYS E 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER D 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.698A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE D 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.317A pdb=" N VAL A 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LYS D 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL A 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU D 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER A 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU D 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS A 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE D 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL D 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LYS E 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL D 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLU E 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER D 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LEU E 344 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS D 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE E 346 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP D 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 349 through 354 removed outlier: 6.573A pdb=" N VAL B 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LYS C 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER B 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LYS B 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER A 352 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.871A pdb=" N ASP B 358 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASN C 359 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP A 358 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN B 359 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N LEU A 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N ILE D 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN A 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N HIS D 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N LEU D 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ILE E 360 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN D 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N HIS E 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR D 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.815A pdb=" N LYS B 370 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS A 370 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU D 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE D 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS D 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N GLU E 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE D 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N HIS E 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR D 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU E 376 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS D 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE E 378 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR D 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 274 through 280 removed outlier: 6.823A pdb=" N LYS G 274 " --> pdb=" O VAL H 275 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE H 277 " --> pdb=" O LYS G 274 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLN G 276 " --> pdb=" O ILE H 277 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASN H 279 " --> pdb=" O GLN G 276 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE G 278 " --> pdb=" O ASN H 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS F 274 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE G 277 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLN F 276 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASN G 279 " --> pdb=" O GLN F 276 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE F 278 " --> pdb=" O ASN G 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 283 through 284 removed outlier: 6.206A pdb=" N ASP G 283 " --> pdb=" O LEU H 284 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP F 283 " --> pdb=" O LEU G 284 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 287 through 292 removed outlier: 6.440A pdb=" N VAL F 287 " --> pdb=" O GLN I 288 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS I 290 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N SER F 289 " --> pdb=" O LYS I 290 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLY I 292 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS F 291 " --> pdb=" O GLY I 292 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL I 287 " --> pdb=" O GLN J 288 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LYS J 290 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N SER I 289 " --> pdb=" O LYS J 290 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N GLY J 292 " --> pdb=" O SER I 289 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS I 291 " --> pdb=" O GLY J 292 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 297 through 298 removed outlier: 6.270A pdb=" N ILE F 297 " --> pdb=" O LYS I 298 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE I 297 " --> pdb=" O LYS J 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 305 through 310 removed outlier: 6.627A pdb=" N SER G 305 " --> pdb=" O VAL H 306 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE H 308 " --> pdb=" O SER G 305 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN G 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N TYR H 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL G 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER F 305 " --> pdb=" O VAL G 306 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE G 308 " --> pdb=" O SER F 305 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN F 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N TYR G 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL F 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 313 through 314 removed outlier: 6.819A pdb=" N VAL G 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL F 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 317 through 322 removed outlier: 6.278A pdb=" N VAL F 318 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LYS I 321 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER F 320 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL I 318 " --> pdb=" O THR J 319 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LYS J 321 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER I 320 " --> pdb=" O LYS J 321 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 328 through 330 removed outlier: 6.696A pdb=" N ILE F 328 " --> pdb=" O HIS I 329 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE I 328 " --> pdb=" O HIS J 329 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 337 through 346 removed outlier: 6.311A pdb=" N VAL F 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LYS I 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL F 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLU I 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER F 341 " --> pdb=" O GLU I 342 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LEU I 344 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS F 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE I 346 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP F 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL I 337 " --> pdb=" O GLU J 338 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LYS J 340 " --> pdb=" O VAL I 337 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL I 339 " --> pdb=" O LYS J 340 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLU J 342 " --> pdb=" O VAL I 339 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER I 341 " --> pdb=" O GLU J 342 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU J 344 " --> pdb=" O SER I 341 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS I 343 " --> pdb=" O LEU J 344 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE J 346 " --> pdb=" O LYS I 343 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASP I 345 " --> pdb=" O PHE J 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 349 through 354 removed outlier: 6.563A pdb=" N VAL G 350 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LYS H 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER G 352 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL F 350 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LYS G 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER F 352 " --> pdb=" O LYS G 353 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 357 through 362 removed outlier: 6.862A pdb=" N ASP G 358 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN H 359 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP F 358 " --> pdb=" O LEU G 357 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN G 359 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N LEU F 357 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N ILE I 360 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN F 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N HIS I 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR F 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N LEU I 357 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N ILE J 360 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN I 359 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N HIS J 362 " --> pdb=" O ASN I 359 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR I 361 " --> pdb=" O HIS J 362 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 369 through 378 removed outlier: 6.808A pdb=" N LYS G 370 " --> pdb=" O LYS H 369 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS F 370 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS F 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLU I 372 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE F 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N HIS I 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR F 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU I 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS F 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE I 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR F 377 " --> pdb=" O PHE I 378 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS I 369 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N GLU J 372 " --> pdb=" O LYS I 369 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE I 371 " --> pdb=" O GLU J 372 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N HIS J 374 " --> pdb=" O ILE I 371 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR I 373 " --> pdb=" O HIS J 374 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU J 376 " --> pdb=" O THR I 373 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS I 375 " --> pdb=" O LEU J 376 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE J 378 " --> pdb=" O LYS I 375 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR I 377 " --> pdb=" O PHE J 378 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 612 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: 1.24 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2710 1.34 - 1.46: 1245 1.46 - 1.58: 4255 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 8230 Sorted by residual: bond pdb=" N ILE F 371 " pdb=" CA ILE F 371 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.24e-02 6.50e+03 7.73e+00 bond pdb=" N ILE D 371 " pdb=" CA ILE D 371 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.56e+00 bond pdb=" N ILE E 371 " pdb=" CA ILE E 371 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.42e+00 bond pdb=" N ILE B 371 " pdb=" CA ILE B 371 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.37e+00 bond pdb=" N ILE C 371 " pdb=" CA ILE C 371 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.34e+00 ... (remaining 8225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 9229 0.99 - 1.98: 1359 1.98 - 2.98: 329 2.98 - 3.97: 43 3.97 - 4.96: 30 Bond angle restraints: 10990 Sorted by residual: angle pdb=" CA ILE I 371 " pdb=" C ILE I 371 " pdb=" O ILE I 371 " ideal model delta sigma weight residual 120.53 117.72 2.81 1.07e+00 8.73e-01 6.90e+00 angle pdb=" CA ILE G 371 " pdb=" C ILE G 371 " pdb=" O ILE G 371 " ideal model delta sigma weight residual 120.53 117.74 2.79 1.07e+00 8.73e-01 6.81e+00 angle pdb=" CA ILE A 371 " pdb=" C ILE A 371 " pdb=" O ILE A 371 " ideal model delta sigma weight residual 120.53 117.74 2.79 1.07e+00 8.73e-01 6.81e+00 angle pdb=" CA ILE B 371 " pdb=" C ILE B 371 " pdb=" O ILE B 371 " ideal model delta sigma weight residual 120.53 117.74 2.79 1.07e+00 8.73e-01 6.80e+00 angle pdb=" CA ILE C 371 " pdb=" C ILE C 371 " pdb=" O ILE C 371 " ideal model delta sigma weight residual 120.53 117.74 2.79 1.07e+00 8.73e-01 6.80e+00 ... (remaining 10985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.13: 4200 13.13 - 26.25: 479 26.25 - 39.38: 281 39.38 - 52.51: 80 52.51 - 65.63: 10 Dihedral angle restraints: 5050 sinusoidal: 2110 harmonic: 2940 Sorted by residual: dihedral pdb=" CG LYS B 340 " pdb=" CD LYS B 340 " pdb=" CE LYS B 340 " pdb=" NZ LYS B 340 " ideal model delta sinusoidal sigma weight residual 180.00 132.86 47.14 3 1.50e+01 4.44e-03 8.45e+00 dihedral pdb=" CG LYS D 340 " pdb=" CD LYS D 340 " pdb=" CE LYS D 340 " pdb=" NZ LYS D 340 " ideal model delta sinusoidal sigma weight residual 180.00 132.89 47.11 3 1.50e+01 4.44e-03 8.44e+00 dihedral pdb=" CG LYS F 340 " pdb=" CD LYS F 340 " pdb=" CE LYS F 340 " pdb=" NZ LYS F 340 " ideal model delta sinusoidal sigma weight residual 180.00 132.89 47.11 3 1.50e+01 4.44e-03 8.44e+00 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 752 0.043 - 0.086: 184 0.086 - 0.129: 284 0.129 - 0.172: 0 0.172 - 0.214: 10 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CA ILE H 371 " pdb=" N ILE H 371 " pdb=" C ILE H 371 " pdb=" CB ILE H 371 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE E 371 " pdb=" N ILE E 371 " pdb=" C ILE E 371 " pdb=" CB ILE E 371 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE I 371 " pdb=" N ILE I 371 " pdb=" C ILE I 371 " pdb=" CB ILE I 371 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1227 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 300 " -0.014 5.00e-02 4.00e+02 2.09e-02 7.00e-01 pdb=" N PRO D 301 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO D 301 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO D 301 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 300 " -0.014 5.00e-02 4.00e+02 2.09e-02 6.99e-01 pdb=" N PRO J 301 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO J 301 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO J 301 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 300 " -0.014 5.00e-02 4.00e+02 2.08e-02 6.93e-01 pdb=" N PRO A 301 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " -0.012 5.00e-02 4.00e+02 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1669 2.81 - 3.33: 6711 3.33 - 3.85: 14379 3.85 - 4.38: 16376 4.38 - 4.90: 31438 Nonbonded interactions: 70573 Sorted by model distance: nonbonded pdb=" OG1 THR A 373 " pdb=" OG1 THR B 361 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR I 361 " pdb=" OG1 THR J 373 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR F 373 " pdb=" OG1 THR G 361 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR A 361 " pdb=" OG1 THR D 373 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR G 373 " pdb=" OG1 THR H 361 " model vdw 2.286 3.040 ... (remaining 70568 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.940 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 : 0.005 0.040 8230 Z= 0.321 Angle : 0.803 4.959 10990 Z= 0.486 Chirality : 0.061 0.214 1230 Planarity : 0.003 0.021 1410 Dihedral : 15.343 65.635 3190 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.43 % Allowed : 13.87 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.05 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.13), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 379 TYR 0.008 0.002 TYR H 310 PHE 0.007 0.002 PHE G 346 HIS 0.005 0.001 HIS H 330 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 8230) covalent geometry : angle 0.80265 (10990) hydrogen bonds : bond 0.09104 ( 204) hydrogen bonds : angle 7.05052 ( 612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 260 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7528 (mptp) REVERT: B 281 LYS cc_start: 0.7364 (mttt) cc_final: 0.7070 (mttm) REVERT: B 288 GLN cc_start: 0.8306 (tt0) cc_final: 0.8034 (tt0) REVERT: B 345 ASP cc_start: 0.7269 (t70) cc_final: 0.6876 (t70) REVERT: B 347 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7580 (mptp) REVERT: C 288 GLN cc_start: 0.8392 (tt0) cc_final: 0.8186 (tt0) REVERT: C 345 ASP cc_start: 0.7372 (t70) cc_final: 0.6911 (t70) REVERT: C 347 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7553 (mppt) REVERT: C 376 LEU cc_start: 0.8635 (mp) cc_final: 0.7928 (tp) REVERT: D 288 GLN cc_start: 0.8322 (tt0) cc_final: 0.8070 (tt0) REVERT: D 345 ASP cc_start: 0.7369 (t70) cc_final: 0.7028 (t70) REVERT: D 347 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7609 (mppt) REVERT: E 340 LYS cc_start: 0.7583 (mtpt) cc_final: 0.6983 (mtpm) REVERT: E 345 ASP cc_start: 0.7412 (t70) cc_final: 0.6870 (t70) REVERT: E 347 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7692 (mppt) REVERT: F 340 LYS cc_start: 0.7410 (mtpt) cc_final: 0.6807 (mtpp) REVERT: F 345 ASP cc_start: 0.7307 (t70) cc_final: 0.6632 (t70) REVERT: F 347 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7501 (mppt) REVERT: G 345 ASP cc_start: 0.7388 (t70) cc_final: 0.6827 (t70) REVERT: G 347 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7504 (mppt) REVERT: H 345 ASP cc_start: 0.7378 (t70) cc_final: 0.7002 (t70) REVERT: H 347 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7651 (mppt) REVERT: I 345 ASP cc_start: 0.7302 (t70) cc_final: 0.6841 (t70) REVERT: I 347 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7577 (mppt) REVERT: I 351 GLN cc_start: 0.8121 (tt0) cc_final: 0.7914 (tt0) REVERT: J 347 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7632 (mptp) outliers start: 4 outliers final: 3 residues processed: 260 average time/residue: 0.5528 time to fit residues: 151.7298 Evaluate side-chains 222 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 219 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain I residue 342 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 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 296 ASN E 296 ASN F 296 ASN G 296 ASN H 288 GLN I 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.137703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.118765 restraints weight = 8847.236| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.48 r_work: 0.3638 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8230 Z= 0.116 Angle : 0.534 4.391 10990 Z= 0.279 Chirality : 0.050 0.136 1230 Planarity : 0.003 0.027 1410 Dihedral : 5.624 23.408 1109 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.97 % Allowed : 17.42 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.98 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 379 TYR 0.009 0.002 TYR J 310 PHE 0.004 0.001 PHE B 378 HIS 0.002 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8230) covalent geometry : angle 0.53357 (10990) hydrogen bonds : bond 0.02358 ( 204) hydrogen bonds : angle 5.34486 ( 612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8508 (mtpt) cc_final: 0.7699 (mptp) REVERT: B 281 LYS cc_start: 0.7381 (mttt) cc_final: 0.7103 (mttp) REVERT: B 288 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: B 345 ASP cc_start: 0.7719 (t70) cc_final: 0.7465 (t70) REVERT: B 347 LYS cc_start: 0.8475 (mtpt) cc_final: 0.7714 (mptp) REVERT: C 288 GLN cc_start: 0.8701 (tt0) cc_final: 0.8485 (tt0) REVERT: C 340 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7540 (mtpp) REVERT: C 345 ASP cc_start: 0.7806 (t70) cc_final: 0.7412 (t70) REVERT: C 347 LYS cc_start: 0.8435 (mtpt) cc_final: 0.7688 (mptp) REVERT: C 376 LEU cc_start: 0.8781 (mp) cc_final: 0.8115 (tp) REVERT: D 345 ASP cc_start: 0.7884 (t70) cc_final: 0.7655 (t70) REVERT: D 347 LYS cc_start: 0.8433 (mtpt) cc_final: 0.7848 (mtmp) REVERT: E 340 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7455 (mtpm) REVERT: E 347 LYS cc_start: 0.8460 (mtpt) cc_final: 0.7791 (mptp) REVERT: F 340 LYS cc_start: 0.7822 (mtpt) cc_final: 0.7294 (mtpp) REVERT: F 345 ASP cc_start: 0.7794 (t70) cc_final: 0.7441 (t70) REVERT: F 347 LYS cc_start: 0.8419 (mtpt) cc_final: 0.7749 (mptp) REVERT: G 283 ASP cc_start: 0.7513 (t0) cc_final: 0.7306 (t0) REVERT: G 347 LYS cc_start: 0.8400 (mtpt) cc_final: 0.7651 (mptp) REVERT: H 345 ASP cc_start: 0.7833 (t70) cc_final: 0.7597 (t70) REVERT: H 347 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7777 (mtmp) REVERT: I 347 LYS cc_start: 0.8461 (mtpt) cc_final: 0.7909 (mtmp) REVERT: J 347 LYS cc_start: 0.8511 (mtpt) cc_final: 0.7915 (mtmp) outliers start: 9 outliers final: 7 residues processed: 218 average time/residue: 0.6086 time to fit residues: 139.5588 Evaluate side-chains 217 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN E 296 ASN F 296 ASN G 296 ASN H 288 GLN I 288 GLN I 296 ASN J 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.133831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.114647 restraints weight = 8963.130| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.47 r_work: 0.3577 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8230 Z= 0.236 Angle : 0.633 4.725 10990 Z= 0.333 Chirality : 0.051 0.134 1230 Planarity : 0.003 0.024 1410 Dihedral : 5.929 14.916 1100 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.04 % Allowed : 16.34 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.86 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.13), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 379 TYR 0.010 0.003 TYR J 310 PHE 0.007 0.001 PHE B 378 HIS 0.004 0.001 HIS J 299 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 8230) covalent geometry : angle 0.63289 (10990) hydrogen bonds : bond 0.02567 ( 204) hydrogen bonds : angle 5.31355 ( 612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 0.409 Fit side-chains REVERT: A 274 LYS cc_start: 0.7244 (mtmt) cc_final: 0.6933 (ttmm) REVERT: A 347 LYS cc_start: 0.8500 (mtpt) cc_final: 0.7770 (mtmp) REVERT: B 274 LYS cc_start: 0.7276 (mtmt) cc_final: 0.6901 (ttmm) REVERT: B 281 LYS cc_start: 0.7443 (mttt) cc_final: 0.7148 (mttm) REVERT: B 293 SER cc_start: 0.8357 (p) cc_final: 0.8050 (m) REVERT: B 345 ASP cc_start: 0.7827 (t70) cc_final: 0.7550 (t70) REVERT: B 347 LYS cc_start: 0.8551 (mtpt) cc_final: 0.7784 (mtmp) REVERT: C 274 LYS cc_start: 0.7650 (mtmt) cc_final: 0.7369 (ttmm) REVERT: C 340 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7502 (mtpp) REVERT: C 347 LYS cc_start: 0.8502 (mtpt) cc_final: 0.7820 (mtmp) REVERT: C 376 LEU cc_start: 0.8765 (mp) cc_final: 0.8138 (tp) REVERT: D 274 LYS cc_start: 0.7059 (mtmt) cc_final: 0.6701 (ttmm) REVERT: D 345 ASP cc_start: 0.7900 (t70) cc_final: 0.7666 (t70) REVERT: D 347 LYS cc_start: 0.8446 (mtpt) cc_final: 0.7779 (mtmp) REVERT: E 274 LYS cc_start: 0.6906 (mtmt) cc_final: 0.6569 (ttmm) REVERT: E 277 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8282 (mp) REVERT: E 340 LYS cc_start: 0.7929 (mtpt) cc_final: 0.7415 (mtpm) REVERT: E 347 LYS cc_start: 0.8487 (mtpt) cc_final: 0.7773 (mppt) REVERT: F 274 LYS cc_start: 0.7104 (mtmt) cc_final: 0.6741 (ttmm) REVERT: F 340 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7294 (mtpp) REVERT: F 345 ASP cc_start: 0.7872 (t70) cc_final: 0.7665 (t70) REVERT: F 347 LYS cc_start: 0.8484 (mtpt) cc_final: 0.7719 (mptp) REVERT: G 274 LYS cc_start: 0.7253 (mtmt) cc_final: 0.6933 (ttmm) REVERT: G 277 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7945 (mp) REVERT: G 283 ASP cc_start: 0.7611 (t0) cc_final: 0.7387 (t0) REVERT: G 347 LYS cc_start: 0.8488 (mtpt) cc_final: 0.7705 (mptp) REVERT: H 293 SER cc_start: 0.7989 (p) cc_final: 0.7645 (m) REVERT: H 345 ASP cc_start: 0.7849 (t70) cc_final: 0.7457 (t70) REVERT: H 347 LYS cc_start: 0.8473 (mtpt) cc_final: 0.7742 (mptp) REVERT: I 274 LYS cc_start: 0.7161 (mtmt) cc_final: 0.6813 (ttmm) REVERT: I 347 LYS cc_start: 0.8510 (mtpt) cc_final: 0.7913 (mtmp) REVERT: J 347 LYS cc_start: 0.8574 (mtpt) cc_final: 0.7898 (mtmp) REVERT: J 376 LEU cc_start: 0.8679 (mp) cc_final: 0.7968 (tp) outliers start: 19 outliers final: 7 residues processed: 233 average time/residue: 0.6416 time to fit residues: 156.9775 Evaluate side-chains 222 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN C 288 GLN E 296 ASN F 296 ASN H 288 GLN I 288 GLN J 288 GLN J 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.134728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.115686 restraints weight = 9076.714| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.49 r_work: 0.3598 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8230 Z= 0.168 Angle : 0.575 5.521 10990 Z= 0.299 Chirality : 0.050 0.132 1230 Planarity : 0.003 0.027 1410 Dihedral : 5.770 14.341 1100 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.80 % Allowed : 16.67 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.88 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 379 TYR 0.010 0.002 TYR J 310 PHE 0.006 0.001 PHE B 378 HIS 0.003 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8230) covalent geometry : angle 0.57451 (10990) hydrogen bonds : bond 0.02203 ( 204) hydrogen bonds : angle 5.06347 ( 612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.321 Fit side-chains REVERT: A 274 LYS cc_start: 0.7176 (mtmt) cc_final: 0.6914 (ttmm) REVERT: A 277 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7766 (mt) REVERT: A 347 LYS cc_start: 0.8491 (mtpt) cc_final: 0.7626 (mptp) REVERT: B 274 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6915 (ttmm) REVERT: B 281 LYS cc_start: 0.7409 (mttt) cc_final: 0.7122 (mttm) REVERT: B 293 SER cc_start: 0.8300 (p) cc_final: 0.8021 (m) REVERT: B 345 ASP cc_start: 0.7802 (t70) cc_final: 0.7352 (t70) REVERT: B 347 LYS cc_start: 0.8526 (mtpt) cc_final: 0.7716 (mptp) REVERT: B 351 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: C 274 LYS cc_start: 0.7630 (mtmt) cc_final: 0.7349 (ttmm) REVERT: C 340 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7488 (mtpp) REVERT: C 347 LYS cc_start: 0.8478 (mtpt) cc_final: 0.7658 (mttm) REVERT: C 376 LEU cc_start: 0.8713 (mp) cc_final: 0.8103 (tp) REVERT: D 274 LYS cc_start: 0.6997 (mtmt) cc_final: 0.6687 (ttmm) REVERT: D 347 LYS cc_start: 0.8500 (mtpt) cc_final: 0.7789 (mtmp) REVERT: E 274 LYS cc_start: 0.6913 (mtmt) cc_final: 0.6626 (ttmm) REVERT: E 340 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7436 (mtpm) REVERT: F 274 LYS cc_start: 0.7088 (mtmt) cc_final: 0.6746 (ttmm) REVERT: F 347 LYS cc_start: 0.8481 (mtpt) cc_final: 0.7745 (mtmp) REVERT: G 274 LYS cc_start: 0.7245 (mtmt) cc_final: 0.6902 (ttmm) REVERT: G 277 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7936 (mp) REVERT: G 283 ASP cc_start: 0.7653 (t0) cc_final: 0.7425 (t0) REVERT: G 347 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7716 (mtmp) REVERT: H 274 LYS cc_start: 0.7563 (mtmt) cc_final: 0.7264 (ttmm) REVERT: H 347 LYS cc_start: 0.8487 (mtpt) cc_final: 0.7807 (mtmp) REVERT: I 274 LYS cc_start: 0.7122 (mtmt) cc_final: 0.6797 (ttmm) REVERT: I 347 LYS cc_start: 0.8491 (mtpt) cc_final: 0.7845 (mtmp) REVERT: J 347 LYS cc_start: 0.8565 (mtpt) cc_final: 0.7885 (mtmp) REVERT: J 376 LEU cc_start: 0.8673 (mp) cc_final: 0.7936 (tp) outliers start: 26 outliers final: 10 residues processed: 232 average time/residue: 0.6390 time to fit residues: 155.8723 Evaluate side-chains 229 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 216 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN E 296 ASN F 296 ASN H 288 GLN I 351 GLN J 288 GLN J 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.133878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.114814 restraints weight = 8989.694| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.47 r_work: 0.3588 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8230 Z= 0.198 Angle : 0.602 6.224 10990 Z= 0.313 Chirality : 0.051 0.130 1230 Planarity : 0.003 0.025 1410 Dihedral : 5.880 14.723 1100 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.26 % Allowed : 16.99 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.86 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.13), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 379 TYR 0.010 0.003 TYR J 310 PHE 0.007 0.001 PHE B 378 HIS 0.003 0.001 HIS G 299 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 8230) covalent geometry : angle 0.60222 (10990) hydrogen bonds : bond 0.02265 ( 204) hydrogen bonds : angle 5.00762 ( 612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 0.319 Fit side-chains REVERT: A 274 LYS cc_start: 0.7202 (mtmt) cc_final: 0.6949 (ttmm) REVERT: A 277 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7794 (mt) REVERT: A 347 LYS cc_start: 0.8532 (mtpt) cc_final: 0.7639 (mptp) REVERT: B 274 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6964 (ttmm) REVERT: B 293 SER cc_start: 0.8329 (p) cc_final: 0.8034 (m) REVERT: B 345 ASP cc_start: 0.7840 (t70) cc_final: 0.7363 (t70) REVERT: B 347 LYS cc_start: 0.8546 (mtpt) cc_final: 0.7727 (mptp) REVERT: B 351 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: C 274 LYS cc_start: 0.7676 (mtmt) cc_final: 0.7367 (ttmm) REVERT: C 347 LYS cc_start: 0.8515 (mtpt) cc_final: 0.7653 (mttm) REVERT: C 376 LEU cc_start: 0.8701 (mp) cc_final: 0.8103 (tp) REVERT: D 274 LYS cc_start: 0.7065 (mtmt) cc_final: 0.6744 (ttmm) REVERT: D 347 LYS cc_start: 0.8527 (mtpt) cc_final: 0.7834 (mtmp) REVERT: E 274 LYS cc_start: 0.6894 (mtmt) cc_final: 0.6652 (ttmm) REVERT: E 277 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8275 (mp) REVERT: E 340 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7443 (mtpm) REVERT: F 274 LYS cc_start: 0.7110 (mtmt) cc_final: 0.6839 (ttmm) REVERT: F 345 ASP cc_start: 0.7683 (t70) cc_final: 0.7228 (t70) REVERT: F 347 LYS cc_start: 0.8487 (mtpt) cc_final: 0.7721 (mttp) REVERT: G 274 LYS cc_start: 0.7250 (mtmt) cc_final: 0.6946 (ttmm) REVERT: G 277 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7927 (mp) REVERT: G 281 LYS cc_start: 0.7467 (mttt) cc_final: 0.7240 (mttm) REVERT: G 283 ASP cc_start: 0.7706 (t0) cc_final: 0.7475 (t0) REVERT: G 347 LYS cc_start: 0.8460 (mtpt) cc_final: 0.7641 (mptp) REVERT: H 274 LYS cc_start: 0.7600 (mtmt) cc_final: 0.7296 (ttmm) REVERT: H 293 SER cc_start: 0.7919 (p) cc_final: 0.7625 (m) REVERT: H 345 ASP cc_start: 0.7680 (t70) cc_final: 0.7196 (t70) REVERT: H 347 LYS cc_start: 0.8483 (mtpt) cc_final: 0.7736 (mttm) REVERT: I 274 LYS cc_start: 0.7112 (mtmt) cc_final: 0.6814 (ttmm) REVERT: I 347 LYS cc_start: 0.8551 (mtpt) cc_final: 0.7923 (mtmp) REVERT: J 347 LYS cc_start: 0.8596 (mtpt) cc_final: 0.7905 (mtmp) outliers start: 21 outliers final: 11 residues processed: 235 average time/residue: 0.6342 time to fit residues: 156.7401 Evaluate side-chains 234 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN E 296 ASN F 296 ASN H 288 GLN J 288 GLN J 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.132459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.113513 restraints weight = 8963.674| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.46 r_work: 0.3567 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8230 Z= 0.276 Angle : 0.670 6.638 10990 Z= 0.349 Chirality : 0.052 0.131 1230 Planarity : 0.003 0.024 1410 Dihedral : 6.108 16.590 1100 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.47 % Allowed : 16.13 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.79 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.13), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 379 TYR 0.010 0.003 TYR D 310 PHE 0.008 0.001 PHE B 378 HIS 0.004 0.001 HIS J 299 Details of bonding type rmsd covalent geometry : bond 0.00632 ( 8230) covalent geometry : angle 0.67043 (10990) hydrogen bonds : bond 0.02531 ( 204) hydrogen bonds : angle 5.14673 ( 612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.517 Fit side-chains REVERT: A 274 LYS cc_start: 0.7271 (mtmt) cc_final: 0.7014 (ttmm) REVERT: A 277 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7821 (mt) REVERT: A 347 LYS cc_start: 0.8590 (mtpt) cc_final: 0.7657 (mptp) REVERT: B 274 LYS cc_start: 0.7304 (mtmt) cc_final: 0.6955 (ttmm) REVERT: B 281 LYS cc_start: 0.7572 (mttt) cc_final: 0.7300 (mttm) REVERT: B 293 SER cc_start: 0.8374 (p) cc_final: 0.8067 (m) REVERT: B 347 LYS cc_start: 0.8548 (mtpt) cc_final: 0.7718 (mttp) REVERT: B 351 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: C 274 LYS cc_start: 0.7724 (mtmt) cc_final: 0.7394 (ttmm) REVERT: C 347 LYS cc_start: 0.8532 (mtpt) cc_final: 0.7675 (mttm) REVERT: D 274 LYS cc_start: 0.7124 (mtmt) cc_final: 0.6756 (ttmm) REVERT: D 347 LYS cc_start: 0.8553 (mtpt) cc_final: 0.7839 (mtmp) REVERT: E 274 LYS cc_start: 0.6940 (mtmt) cc_final: 0.6677 (ttmm) REVERT: E 277 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8263 (mp) REVERT: E 347 LYS cc_start: 0.8522 (mtpt) cc_final: 0.7907 (mtmp) REVERT: F 274 LYS cc_start: 0.7164 (mtmt) cc_final: 0.6845 (ttmm) REVERT: G 274 LYS cc_start: 0.7266 (mtmt) cc_final: 0.7018 (mtpm) REVERT: G 277 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7976 (mp) REVERT: G 281 LYS cc_start: 0.7536 (mttt) cc_final: 0.7306 (mttm) REVERT: G 283 ASP cc_start: 0.7719 (t0) cc_final: 0.7491 (t0) REVERT: G 347 LYS cc_start: 0.8494 (mtpt) cc_final: 0.7775 (mtmp) REVERT: H 274 LYS cc_start: 0.7625 (mtmt) cc_final: 0.7306 (ttmm) REVERT: H 293 SER cc_start: 0.8010 (p) cc_final: 0.7660 (m) REVERT: H 345 ASP cc_start: 0.7721 (t70) cc_final: 0.7375 (t70) REVERT: H 347 LYS cc_start: 0.8488 (mtpt) cc_final: 0.7782 (mttp) REVERT: I 274 LYS cc_start: 0.7140 (mtmt) cc_final: 0.6787 (ttmm) REVERT: I 347 LYS cc_start: 0.8571 (mtpt) cc_final: 0.7937 (mtmp) outliers start: 23 outliers final: 12 residues processed: 232 average time/residue: 0.6286 time to fit residues: 153.3129 Evaluate side-chains 232 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 216 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN E 296 ASN F 296 ASN J 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.134236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.115382 restraints weight = 9039.503| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.47 r_work: 0.3599 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8230 Z= 0.174 Angle : 0.590 7.281 10990 Z= 0.304 Chirality : 0.051 0.131 1230 Planarity : 0.003 0.030 1410 Dihedral : 5.876 14.631 1100 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.83 % Allowed : 17.20 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.80 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.13), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 379 TYR 0.011 0.003 TYR J 310 PHE 0.008 0.001 PHE I 378 HIS 0.003 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8230) covalent geometry : angle 0.58992 (10990) hydrogen bonds : bond 0.02136 ( 204) hydrogen bonds : angle 4.87722 ( 612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.264 Fit side-chains REVERT: A 274 LYS cc_start: 0.7212 (mtmt) cc_final: 0.6970 (ttmm) REVERT: A 277 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7736 (mt) REVERT: A 347 LYS cc_start: 0.8551 (mtpt) cc_final: 0.7645 (mptp) REVERT: B 274 LYS cc_start: 0.7280 (mtmt) cc_final: 0.6973 (ttmm) REVERT: B 281 LYS cc_start: 0.7466 (mttt) cc_final: 0.7203 (mttm) REVERT: B 293 SER cc_start: 0.8310 (p) cc_final: 0.8033 (m) REVERT: B 345 ASP cc_start: 0.7813 (t70) cc_final: 0.7405 (t70) REVERT: B 347 LYS cc_start: 0.8530 (mtpt) cc_final: 0.7720 (mttp) REVERT: B 351 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: C 274 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7394 (ttmm) REVERT: C 347 LYS cc_start: 0.8490 (mtpt) cc_final: 0.7655 (mttm) REVERT: D 274 LYS cc_start: 0.7062 (mtmt) cc_final: 0.6747 (ttmm) REVERT: D 347 LYS cc_start: 0.8539 (mtpt) cc_final: 0.7831 (mtmp) REVERT: E 274 LYS cc_start: 0.6871 (mtmt) cc_final: 0.6634 (ttmm) REVERT: E 277 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8253 (mp) REVERT: E 347 LYS cc_start: 0.8511 (mtpt) cc_final: 0.7796 (mtmm) REVERT: F 274 LYS cc_start: 0.7100 (mtmt) cc_final: 0.6776 (ttmm) REVERT: G 274 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6968 (ttmm) REVERT: G 277 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7961 (mp) REVERT: G 281 LYS cc_start: 0.7520 (mttt) cc_final: 0.7299 (mttm) REVERT: G 283 ASP cc_start: 0.7744 (t0) cc_final: 0.7518 (t0) REVERT: G 347 LYS cc_start: 0.8443 (mtpt) cc_final: 0.7717 (mtmp) REVERT: H 274 LYS cc_start: 0.7558 (mtmt) cc_final: 0.7286 (ttmm) REVERT: H 345 ASP cc_start: 0.7638 (t70) cc_final: 0.7248 (t70) REVERT: H 347 LYS cc_start: 0.8489 (mtpt) cc_final: 0.7798 (mttp) REVERT: I 274 LYS cc_start: 0.7124 (mtmt) cc_final: 0.6806 (ttmm) REVERT: I 347 LYS cc_start: 0.8572 (mtpt) cc_final: 0.7938 (mtmp) REVERT: J 347 LYS cc_start: 0.8598 (mtpt) cc_final: 0.7888 (mtmp) outliers start: 17 outliers final: 11 residues processed: 226 average time/residue: 0.6592 time to fit residues: 156.1661 Evaluate side-chains 234 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 69 optimal weight: 0.0870 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 overall best weight: 2.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN E 276 GLN E 296 ASN F 296 ASN H 288 GLN I 296 ASN J 288 GLN J 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.135838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.117121 restraints weight = 8911.587| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.47 r_work: 0.3659 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8230 Z= 0.126 Angle : 0.552 7.457 10990 Z= 0.282 Chirality : 0.050 0.131 1230 Planarity : 0.003 0.033 1410 Dihedral : 5.646 14.710 1100 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.94 % Allowed : 16.67 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.81 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 379 TYR 0.011 0.002 TYR E 310 PHE 0.007 0.001 PHE I 378 HIS 0.002 0.000 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8230) covalent geometry : angle 0.55150 (10990) hydrogen bonds : bond 0.01893 ( 204) hydrogen bonds : angle 4.67661 ( 612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.340 Fit side-chains REVERT: A 277 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7769 (mt) REVERT: A 347 LYS cc_start: 0.8552 (mtpt) cc_final: 0.7621 (mtmm) REVERT: B 274 LYS cc_start: 0.7251 (mtmt) cc_final: 0.6982 (ttmm) REVERT: B 345 ASP cc_start: 0.7788 (t70) cc_final: 0.7547 (t70) REVERT: B 347 LYS cc_start: 0.8550 (mtpt) cc_final: 0.7815 (mtmp) REVERT: B 351 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: C 274 LYS cc_start: 0.7631 (mtmt) cc_final: 0.7379 (ttmm) REVERT: C 347 LYS cc_start: 0.8494 (mtpt) cc_final: 0.7810 (mtmp) REVERT: D 274 LYS cc_start: 0.7050 (mtmt) cc_final: 0.6792 (ttmm) REVERT: D 347 LYS cc_start: 0.8523 (mtpt) cc_final: 0.7796 (mtmp) REVERT: E 277 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8257 (mp) REVERT: E 347 LYS cc_start: 0.8494 (mtpt) cc_final: 0.7767 (mppt) REVERT: F 274 LYS cc_start: 0.7068 (mtmt) cc_final: 0.6789 (ttmm) REVERT: F 347 LYS cc_start: 0.8481 (mtpt) cc_final: 0.7784 (mtmp) REVERT: G 274 LYS cc_start: 0.7266 (mtmt) cc_final: 0.6979 (ttmm) REVERT: G 277 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7985 (mp) REVERT: G 283 ASP cc_start: 0.7806 (t0) cc_final: 0.7582 (t0) REVERT: G 347 LYS cc_start: 0.8415 (mtpt) cc_final: 0.7747 (mtmp) REVERT: H 274 LYS cc_start: 0.7496 (mtmt) cc_final: 0.7222 (ttmm) REVERT: H 345 ASP cc_start: 0.7579 (t70) cc_final: 0.6991 (t70) REVERT: H 347 LYS cc_start: 0.8457 (mtpt) cc_final: 0.7782 (mtmt) REVERT: I 274 LYS cc_start: 0.7134 (mtmt) cc_final: 0.6862 (ttmm) REVERT: I 347 LYS cc_start: 0.8569 (mtpt) cc_final: 0.7926 (mtmp) REVERT: J 347 LYS cc_start: 0.8607 (mtpt) cc_final: 0.7873 (mttm) outliers start: 18 outliers final: 10 residues processed: 227 average time/residue: 0.6637 time to fit residues: 157.9853 Evaluate side-chains 229 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 0.0170 chunk 15 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 overall best weight: 4.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN E 296 ASN F 296 ASN H 288 GLN I 296 ASN J 288 GLN J 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.133557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.114602 restraints weight = 8970.572| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.47 r_work: 0.3589 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8230 Z= 0.204 Angle : 0.620 7.588 10990 Z= 0.318 Chirality : 0.051 0.132 1230 Planarity : 0.003 0.040 1410 Dihedral : 5.907 15.632 1100 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.72 % Allowed : 17.20 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.77 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 379 TYR 0.010 0.003 TYR D 310 PHE 0.007 0.001 PHE I 378 HIS 0.003 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8230) covalent geometry : angle 0.62016 (10990) hydrogen bonds : bond 0.02187 ( 204) hydrogen bonds : angle 4.83221 ( 612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.334 Fit side-chains REVERT: A 277 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7765 (mt) REVERT: A 347 LYS cc_start: 0.8554 (mtpt) cc_final: 0.7649 (mptp) REVERT: B 274 LYS cc_start: 0.7266 (mtmt) cc_final: 0.6948 (ttmm) REVERT: B 281 LYS cc_start: 0.7487 (mttt) cc_final: 0.7214 (mttm) REVERT: B 293 SER cc_start: 0.8303 (p) cc_final: 0.8036 (m) REVERT: B 345 ASP cc_start: 0.7823 (t70) cc_final: 0.7441 (t70) REVERT: B 347 LYS cc_start: 0.8531 (mtpt) cc_final: 0.7684 (mttm) REVERT: B 351 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: C 274 LYS cc_start: 0.7673 (mtmt) cc_final: 0.7369 (ttmm) REVERT: C 347 LYS cc_start: 0.8497 (mtpt) cc_final: 0.7790 (mtmp) REVERT: D 274 LYS cc_start: 0.7063 (mtmt) cc_final: 0.6759 (ttmm) REVERT: D 347 LYS cc_start: 0.8517 (mtpt) cc_final: 0.7812 (mtmp) REVERT: E 277 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8250 (mp) REVERT: E 347 LYS cc_start: 0.8537 (mtpt) cc_final: 0.7788 (mtmm) REVERT: F 274 LYS cc_start: 0.7095 (mtmt) cc_final: 0.6774 (ttmm) REVERT: G 274 LYS cc_start: 0.7238 (mtmt) cc_final: 0.6955 (ttmm) REVERT: G 277 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7940 (mp) REVERT: G 283 ASP cc_start: 0.7801 (t0) cc_final: 0.7573 (t0) REVERT: G 347 LYS cc_start: 0.8434 (mtpt) cc_final: 0.7712 (mtmp) REVERT: H 274 LYS cc_start: 0.7549 (mtmt) cc_final: 0.7272 (ttmm) REVERT: H 345 ASP cc_start: 0.7644 (t70) cc_final: 0.7265 (t70) REVERT: H 347 LYS cc_start: 0.8487 (mtpt) cc_final: 0.7790 (mttp) REVERT: I 274 LYS cc_start: 0.7124 (mtmt) cc_final: 0.6809 (ttmm) REVERT: I 347 LYS cc_start: 0.8566 (mtpt) cc_final: 0.7919 (mtmp) outliers start: 16 outliers final: 10 residues processed: 217 average time/residue: 0.6721 time to fit residues: 152.9836 Evaluate side-chains 224 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN E 276 GLN E 296 ASN F 296 ASN I 296 ASN J 288 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.132235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.113263 restraints weight = 9000.360| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.47 r_work: 0.3598 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8230 Z= 0.272 Angle : 0.678 7.653 10990 Z= 0.351 Chirality : 0.052 0.135 1230 Planarity : 0.003 0.037 1410 Dihedral : 6.118 16.352 1100 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.72 % Allowed : 17.20 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.71 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 379 TYR 0.010 0.003 TYR D 310 PHE 0.008 0.001 PHE I 378 HIS 0.004 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00623 ( 8230) covalent geometry : angle 0.67809 (10990) hydrogen bonds : bond 0.02473 ( 204) hydrogen bonds : angle 5.05153 ( 612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.351 Fit side-chains REVERT: A 277 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7810 (mt) REVERT: A 347 LYS cc_start: 0.8615 (mtpt) cc_final: 0.7712 (mptp) REVERT: B 274 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6977 (ttmm) REVERT: B 281 LYS cc_start: 0.7526 (mttt) cc_final: 0.7251 (mttm) REVERT: B 293 SER cc_start: 0.8349 (p) cc_final: 0.8056 (m) REVERT: B 347 LYS cc_start: 0.8551 (mtpt) cc_final: 0.7737 (mttp) REVERT: B 351 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: C 274 LYS cc_start: 0.7693 (mtmt) cc_final: 0.7370 (ttmm) REVERT: C 347 LYS cc_start: 0.8522 (mtpt) cc_final: 0.7698 (mttm) REVERT: D 274 LYS cc_start: 0.7126 (mtmt) cc_final: 0.6808 (ttmm) REVERT: D 347 LYS cc_start: 0.8561 (mtpt) cc_final: 0.7853 (mtmp) REVERT: E 277 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8318 (mp) REVERT: E 347 LYS cc_start: 0.8542 (mtpt) cc_final: 0.7830 (mtmm) REVERT: F 274 LYS cc_start: 0.7163 (mtmt) cc_final: 0.6869 (ttmm) REVERT: G 274 LYS cc_start: 0.7262 (mtmt) cc_final: 0.6952 (ttmm) REVERT: G 277 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8021 (mp) REVERT: G 283 ASP cc_start: 0.7778 (t0) cc_final: 0.7542 (t0) REVERT: G 347 LYS cc_start: 0.8494 (mtpt) cc_final: 0.7770 (mtmp) REVERT: H 274 LYS cc_start: 0.7640 (mtmt) cc_final: 0.7290 (ttmm) REVERT: H 293 SER cc_start: 0.7988 (p) cc_final: 0.7691 (m) REVERT: H 345 ASP cc_start: 0.7724 (t70) cc_final: 0.7355 (t70) REVERT: H 347 LYS cc_start: 0.8501 (mtpt) cc_final: 0.7814 (mttp) REVERT: I 274 LYS cc_start: 0.7134 (mtmt) cc_final: 0.6800 (ttmm) REVERT: I 347 LYS cc_start: 0.8569 (mtpt) cc_final: 0.7953 (mtmp) outliers start: 16 outliers final: 10 residues processed: 211 average time/residue: 0.6838 time to fit residues: 151.1852 Evaluate side-chains 220 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 0.0020 chunk 65 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 32 optimal weight: 0.0970 chunk 43 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 overall best weight: 3.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN E 296 ASN F 296 ASN G 288 GLN J 288 GLN J 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.134410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.115580 restraints weight = 8955.127| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.47 r_work: 0.3602 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8230 Z= 0.168 Angle : 0.597 7.595 10990 Z= 0.305 Chirality : 0.051 0.134 1230 Planarity : 0.003 0.035 1410 Dihedral : 5.872 15.436 1100 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.72 % Allowed : 17.10 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.73 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 379 TYR 0.010 0.002 TYR D 310 PHE 0.007 0.001 PHE F 378 HIS 0.003 0.001 HIS G 299 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8230) covalent geometry : angle 0.59668 (10990) hydrogen bonds : bond 0.02105 ( 204) hydrogen bonds : angle 4.82853 ( 612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3792.90 seconds wall clock time: 65 minutes 37.95 seconds (3937.95 seconds total)