Starting phenix.real_space_refine on Wed Feb 12 16:44:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p6c_13225/02_2025/7p6c_13225.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p6c_13225/02_2025/7p6c_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_13225/02_2025/7p6c_13225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p6c_13225/02_2025/7p6c_13225.map" model { file = "/net/cci-nas-00/data/ceres_data/7p6c_13225/02_2025/7p6c_13225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p6c_13225/02_2025/7p6c_13225.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, E, D, G, F, I, H, J Time building chain proxies: 3.75, per 1000 atoms: 0.46 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: 1.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.39 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: 2.31 Time building geometry restraints manager: 2.13 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 5.300 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.620 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.780 ------------------------------------------------------------------------------- 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= 0.344 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.005 0.001 HIS H 330 PHE 0.007 0.002 PHE G 346 TYR 0.008 0.002 TYR H 310 ARG 0.001 0.000 ARG I 379 *********************** 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 : 0.811 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 347 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7541 (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: 0.6985 (t70) REVERT: C 347 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7588 (mptp) 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: 0.7029 (t70) REVERT: D 347 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7611 (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: 0.6871 (t70) REVERT: E 347 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7693 (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: 0.6633 (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: 1.2148 time to fit residues: 334.0206 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 : 0.967 ------------------------------------------------------------------------------- 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 84 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.133070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.113805 restraints weight = 8868.629| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.47 r_work: 0.3562 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 8230 Z= 0.447 Angle : 0.690 5.231 10990 Z= 0.364 Chirality : 0.053 0.138 1230 Planarity : 0.004 0.025 1410 Dihedral : 6.302 30.575 1109 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.51 % Allowed : 18.28 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.17), 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 HIS 0.004 0.002 HIS J 299 PHE 0.008 0.001 PHE B 378 TYR 0.009 0.003 TYR J 310 ARG 0.004 0.001 ARG E 379 *********************** 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 243 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.914 Fit side-chains REVERT: A 274 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6933 (ttmm) REVERT: A 347 LYS cc_start: 0.8579 (mtpt) cc_final: 0.7753 (mptp) REVERT: B 274 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6885 (ttmm) REVERT: B 281 LYS cc_start: 0.7488 (mttt) cc_final: 0.7195 (mttm) REVERT: B 288 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: B 293 SER cc_start: 0.8346 (p) cc_final: 0.8058 (m) REVERT: B 347 LYS cc_start: 0.8565 (mtpt) cc_final: 0.7739 (mptp) REVERT: C 274 LYS cc_start: 0.7646 (mtmt) cc_final: 0.7335 (ttmm) REVERT: C 340 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7508 (mtpp) REVERT: C 345 ASP cc_start: 0.7922 (t70) cc_final: 0.7626 (t70) REVERT: C 347 LYS cc_start: 0.8503 (mtpt) cc_final: 0.7724 (mptp) REVERT: C 376 LEU cc_start: 0.8765 (mp) cc_final: 0.8143 (tp) REVERT: D 274 LYS cc_start: 0.7093 (mtmt) cc_final: 0.6671 (ttmm) REVERT: D 340 LYS cc_start: 0.7504 (mttt) cc_final: 0.6910 (mtpp) REVERT: D 345 ASP cc_start: 0.7912 (t70) cc_final: 0.7653 (t70) REVERT: D 347 LYS cc_start: 0.8552 (mtpt) cc_final: 0.7839 (mtmp) REVERT: E 274 LYS cc_start: 0.6978 (mtmt) cc_final: 0.6586 (ttmm) REVERT: E 347 LYS cc_start: 0.8512 (mtpt) cc_final: 0.7790 (mppt) REVERT: F 345 ASP cc_start: 0.7898 (t70) cc_final: 0.7648 (t70) REVERT: F 347 LYS cc_start: 0.8461 (mtpt) cc_final: 0.7769 (mptp) REVERT: G 274 LYS cc_start: 0.7264 (mtmt) cc_final: 0.6621 (mttp) REVERT: G 277 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7990 (mp) REVERT: G 283 ASP cc_start: 0.7581 (t0) cc_final: 0.7365 (t0) REVERT: G 347 LYS cc_start: 0.8501 (mtpt) cc_final: 0.7716 (mptp) REVERT: H 293 SER cc_start: 0.8020 (p) cc_final: 0.7664 (m) REVERT: H 345 ASP cc_start: 0.7888 (t70) cc_final: 0.7395 (t70) REVERT: H 347 LYS cc_start: 0.8465 (mtpt) cc_final: 0.7786 (mptp) REVERT: I 274 LYS cc_start: 0.7166 (mtmt) cc_final: 0.6804 (ttmm) REVERT: I 345 ASP cc_start: 0.7866 (t70) cc_final: 0.7646 (t70) REVERT: I 347 LYS cc_start: 0.8552 (mtpt) cc_final: 0.7938 (mtmp) REVERT: J 293 SER cc_start: 0.8037 (p) cc_final: 0.7733 (m) REVERT: J 347 LYS cc_start: 0.8610 (mtpt) cc_final: 0.7943 (mtmp) REVERT: J 376 LEU cc_start: 0.8688 (mp) cc_final: 0.7983 (tp) outliers start: 14 outliers final: 7 residues processed: 235 average time/residue: 1.3895 time to fit residues: 343.4319 Evaluate side-chains 224 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 215 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN D 288 GLN E 296 ASN F 296 ASN H 288 GLN I 288 GLN J 288 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.134251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.115176 restraints weight = 9038.745| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.48 r_work: 0.3585 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8230 Z= 0.298 Angle : 0.603 5.312 10990 Z= 0.314 Chirality : 0.051 0.136 1230 Planarity : 0.003 0.024 1410 Dihedral : 5.922 14.546 1100 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.58 % Allowed : 17.20 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.17), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.13), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 299 PHE 0.007 0.001 PHE B 378 TYR 0.010 0.003 TYR J 310 ARG 0.006 0.000 ARG E 379 *********************** 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: 24 poor density : 218 time to evaluate : 0.924 Fit side-chains REVERT: A 274 LYS cc_start: 0.7234 (mtmt) cc_final: 0.6935 (ttmm) REVERT: A 347 LYS cc_start: 0.8480 (mtpt) cc_final: 0.7736 (mtmp) REVERT: B 274 LYS cc_start: 0.7266 (mtmt) cc_final: 0.6905 (ttmm) REVERT: B 281 LYS cc_start: 0.7451 (mttt) cc_final: 0.7175 (mttm) REVERT: B 288 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: B 293 SER cc_start: 0.8313 (p) cc_final: 0.8032 (m) REVERT: B 347 LYS cc_start: 0.8492 (mtpt) cc_final: 0.7735 (mtmp) REVERT: B 351 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: C 274 LYS cc_start: 0.7669 (mtmt) cc_final: 0.7371 (ttmm) REVERT: C 347 LYS cc_start: 0.8476 (mtpt) cc_final: 0.7765 (mtmp) REVERT: C 376 LEU cc_start: 0.8753 (mp) cc_final: 0.8116 (tp) REVERT: D 274 LYS cc_start: 0.7032 (mtmt) cc_final: 0.6680 (ttmm) REVERT: D 340 LYS cc_start: 0.7499 (mttt) cc_final: 0.6893 (mtpp) REVERT: D 347 LYS cc_start: 0.8508 (mtpt) cc_final: 0.7775 (mtmp) REVERT: E 274 LYS cc_start: 0.6935 (mtmt) cc_final: 0.6618 (ttmm) REVERT: E 277 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8262 (mp) REVERT: F 347 LYS cc_start: 0.8487 (mtpt) cc_final: 0.7758 (mtmp) REVERT: G 274 LYS cc_start: 0.7213 (mtmt) cc_final: 0.6915 (ttmm) REVERT: G 283 ASP cc_start: 0.7638 (t0) cc_final: 0.7397 (t0) REVERT: G 347 LYS cc_start: 0.8464 (mtpt) cc_final: 0.7752 (mtmp) REVERT: H 274 LYS cc_start: 0.7596 (mtmt) cc_final: 0.7259 (ttmm) REVERT: H 347 LYS cc_start: 0.8470 (mtpt) cc_final: 0.7791 (mtmp) REVERT: I 274 LYS cc_start: 0.7137 (mtmt) cc_final: 0.6813 (ttmm) REVERT: I 345 ASP cc_start: 0.7871 (t70) cc_final: 0.7646 (t70) REVERT: I 347 LYS cc_start: 0.8519 (mtpt) cc_final: 0.7857 (mtmp) REVERT: J 347 LYS cc_start: 0.8608 (mtpt) cc_final: 0.7909 (mtmp) REVERT: J 376 LEU cc_start: 0.8678 (mp) cc_final: 0.7941 (tp) outliers start: 24 outliers final: 10 residues processed: 230 average time/residue: 1.3566 time to fit residues: 328.4206 Evaluate side-chains 227 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 288 GLN 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 F 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 284 LEU 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 79 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 63 optimal weight: 0.0040 chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 overall best weight: 2.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN E 276 GLN E 296 ASN F 296 ASN H 288 GLN J 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.135170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.116162 restraints weight = 8920.716| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.48 r_work: 0.3609 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8230 Z= 0.228 Angle : 0.560 5.362 10990 Z= 0.290 Chirality : 0.050 0.132 1230 Planarity : 0.003 0.027 1410 Dihedral : 5.739 14.243 1100 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.37 % Allowed : 16.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 299 PHE 0.006 0.001 PHE B 378 TYR 0.010 0.002 TYR J 310 ARG 0.007 0.000 ARG E 379 *********************** 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 241 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 1.034 Fit side-chains REVERT: A 274 LYS cc_start: 0.7186 (mtmt) cc_final: 0.6956 (ttmm) REVERT: A 277 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7757 (mt) REVERT: A 347 LYS cc_start: 0.8469 (mtpt) cc_final: 0.7702 (mtmp) REVERT: B 274 LYS cc_start: 0.7222 (mtmt) cc_final: 0.6895 (ttmm) REVERT: B 281 LYS cc_start: 0.7449 (mttt) cc_final: 0.7189 (mttm) REVERT: B 288 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: B 347 LYS cc_start: 0.8509 (mtpt) cc_final: 0.7750 (mtmp) REVERT: B 351 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: C 274 LYS cc_start: 0.7636 (mtmt) cc_final: 0.7335 (ttmm) REVERT: C 347 LYS cc_start: 0.8482 (mtpt) cc_final: 0.7777 (mtmp) REVERT: D 274 LYS cc_start: 0.7014 (mtmt) cc_final: 0.6699 (ttmm) REVERT: D 347 LYS cc_start: 0.8514 (mtpt) cc_final: 0.7786 (mtmp) REVERT: E 274 LYS cc_start: 0.6921 (mtmt) cc_final: 0.6651 (ttmm) REVERT: E 277 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8246 (mp) REVERT: F 347 LYS cc_start: 0.8491 (mtpt) cc_final: 0.7758 (mtmp) REVERT: G 274 LYS cc_start: 0.7220 (mtmt) cc_final: 0.6896 (ttmm) REVERT: G 277 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7956 (mp) REVERT: G 283 ASP cc_start: 0.7685 (t0) cc_final: 0.7455 (t0) REVERT: G 347 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7706 (mtmp) REVERT: H 274 LYS cc_start: 0.7518 (mtmt) cc_final: 0.7222 (ttmm) REVERT: H 347 LYS cc_start: 0.8453 (mtpt) cc_final: 0.7799 (mtmp) REVERT: I 274 LYS cc_start: 0.7126 (mtmt) cc_final: 0.6847 (ttmm) REVERT: I 345 ASP cc_start: 0.7861 (t70) cc_final: 0.7595 (t70) REVERT: I 347 LYS cc_start: 0.8530 (mtpt) cc_final: 0.7866 (mtmp) REVERT: J 347 LYS cc_start: 0.8622 (mtpt) cc_final: 0.7924 (mtmp) REVERT: J 376 LEU cc_start: 0.8676 (mp) cc_final: 0.7927 (tp) outliers start: 22 outliers final: 11 residues processed: 228 average time/residue: 1.3756 time to fit residues: 329.8709 Evaluate side-chains 231 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 288 GLN 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 F 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 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 12 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 296 ASN 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 = 0.3960 r_free = 0.3960 target = 0.133156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.114096 restraints weight = 8876.658| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.47 r_work: 0.3574 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8230 Z= 0.364 Angle : 0.634 5.985 10990 Z= 0.330 Chirality : 0.051 0.131 1230 Planarity : 0.003 0.032 1410 Dihedral : 6.009 15.261 1100 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.80 % Allowed : 15.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 299 PHE 0.008 0.001 PHE B 378 TYR 0.010 0.003 TYR D 310 ARG 0.007 0.001 ARG J 379 *********************** 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: 26 poor density : 222 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6951 (ttmm) REVERT: B 274 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6946 (ttmm) REVERT: B 281 LYS cc_start: 0.7503 (mttt) cc_final: 0.7234 (mttm) REVERT: B 293 SER cc_start: 0.8356 (p) cc_final: 0.8044 (m) REVERT: B 347 LYS cc_start: 0.8523 (mtpt) cc_final: 0.7753 (mtmp) REVERT: B 351 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: C 274 LYS cc_start: 0.7705 (mtmt) cc_final: 0.7368 (ttmm) REVERT: C 347 LYS cc_start: 0.8492 (mtpt) cc_final: 0.7755 (mtmp) REVERT: D 274 LYS cc_start: 0.7098 (mtmt) cc_final: 0.6736 (ttmm) REVERT: D 347 LYS cc_start: 0.8528 (mtpt) cc_final: 0.7820 (mtmp) REVERT: E 274 LYS cc_start: 0.6939 (mtmt) cc_final: 0.6669 (ttmm) REVERT: E 277 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8279 (mp) REVERT: E 347 LYS cc_start: 0.8524 (mtpt) cc_final: 0.7886 (mtmp) REVERT: G 274 LYS cc_start: 0.7232 (mtmt) cc_final: 0.6899 (ttmm) REVERT: G 277 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7950 (mp) REVERT: G 281 LYS cc_start: 0.7508 (mttt) cc_final: 0.7283 (mttm) REVERT: G 283 ASP cc_start: 0.7691 (t0) cc_final: 0.7457 (t0) REVERT: G 347 LYS cc_start: 0.8445 (mtpt) cc_final: 0.7736 (mtmp) REVERT: H 274 LYS cc_start: 0.7604 (mtmt) cc_final: 0.7285 (ttmm) REVERT: H 293 SER cc_start: 0.7939 (p) cc_final: 0.7637 (m) REVERT: H 347 LYS cc_start: 0.8489 (mtpt) cc_final: 0.7828 (mtmp) REVERT: I 274 LYS cc_start: 0.7140 (mtmt) cc_final: 0.6831 (ttmm) REVERT: I 345 ASP cc_start: 0.7859 (t70) cc_final: 0.7642 (t70) REVERT: I 347 LYS cc_start: 0.8568 (mtpt) cc_final: 0.7910 (mtmp) REVERT: J 347 LYS cc_start: 0.8597 (mtpt) cc_final: 0.7880 (mtmp) outliers start: 26 outliers final: 13 residues processed: 233 average time/residue: 1.3579 time to fit residues: 333.0228 Evaluate side-chains 230 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F 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 59 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN D 288 GLN E 296 ASN F 296 ASN J 288 GLN J 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.134609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.115745 restraints weight = 8885.528| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.46 r_work: 0.3603 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8230 Z= 0.254 Angle : 0.579 6.964 10990 Z= 0.299 Chirality : 0.050 0.130 1230 Planarity : 0.003 0.035 1410 Dihedral : 5.822 14.272 1100 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.47 % Allowed : 16.02 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 299 PHE 0.008 0.001 PHE I 378 TYR 0.010 0.002 TYR D 310 ARG 0.008 0.001 ARG J 379 *********************** 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 240 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7151 (mtmt) cc_final: 0.6925 (ttmm) REVERT: B 274 LYS cc_start: 0.7276 (mtmt) cc_final: 0.6960 (ttmm) REVERT: B 347 LYS cc_start: 0.8511 (mtpt) cc_final: 0.7755 (mtmp) REVERT: B 351 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: C 274 LYS cc_start: 0.7677 (mtmt) cc_final: 0.7367 (ttmm) REVERT: C 347 LYS cc_start: 0.8475 (mtpt) cc_final: 0.7763 (mtmp) REVERT: D 274 LYS cc_start: 0.7069 (mtmt) cc_final: 0.6731 (ttmm) REVERT: D 284 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8531 (mt) REVERT: D 347 LYS cc_start: 0.8517 (mtpt) cc_final: 0.7832 (mtmp) REVERT: E 274 LYS cc_start: 0.6886 (mtmt) cc_final: 0.6635 (ttmm) REVERT: E 277 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8246 (mp) REVERT: E 347 LYS cc_start: 0.8515 (mtpt) cc_final: 0.7785 (mtmm) REVERT: F 347 LYS cc_start: 0.8489 (mtpt) cc_final: 0.7782 (mtmp) REVERT: G 274 LYS cc_start: 0.7226 (mtmt) cc_final: 0.6947 (ttmm) REVERT: G 277 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7943 (mp) REVERT: G 281 LYS cc_start: 0.7510 (mttt) cc_final: 0.7307 (mttm) REVERT: G 283 ASP cc_start: 0.7723 (t0) cc_final: 0.7490 (t0) REVERT: G 347 LYS cc_start: 0.8433 (mtpt) cc_final: 0.7731 (mtmp) REVERT: H 274 LYS cc_start: 0.7542 (mtmt) cc_final: 0.7255 (ttmm) REVERT: H 347 LYS cc_start: 0.8471 (mtpt) cc_final: 0.7816 (mtmp) REVERT: I 274 LYS cc_start: 0.7142 (mtmt) cc_final: 0.6862 (ttmm) REVERT: I 345 ASP cc_start: 0.7864 (t70) cc_final: 0.7614 (t70) REVERT: I 347 LYS cc_start: 0.8580 (mtpt) cc_final: 0.7878 (mtmp) REVERT: J 347 LYS cc_start: 0.8620 (mtpt) cc_final: 0.7889 (mtmp) outliers start: 23 outliers final: 11 residues processed: 224 average time/residue: 1.4026 time to fit residues: 330.1286 Evaluate side-chains 228 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 284 LEU 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 F 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 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 82 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 43 optimal weight: 0.0470 chunk 69 optimal weight: 0.0070 chunk 47 optimal weight: 7.9990 overall best weight: 4.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.133691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.114770 restraints weight = 8925.769| |-----------------------------------------------------------------------------| 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: 0.3480 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1842 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= 0.305 Angle : 0.609 7.557 10990 Z= 0.315 Chirality : 0.051 0.129 1230 Planarity : 0.003 0.038 1410 Dihedral : 5.938 15.104 1100 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 299 PHE 0.008 0.001 PHE B 378 TYR 0.010 0.003 TYR D 310 ARG 0.009 0.001 ARG J 379 *********************** 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 232 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7191 (mtmt) cc_final: 0.6958 (ttmm) REVERT: A 277 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7774 (mt) REVERT: B 274 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6959 (ttmm) REVERT: B 281 LYS cc_start: 0.7503 (mttt) cc_final: 0.7230 (mttm) REVERT: B 293 SER cc_start: 0.8326 (p) cc_final: 0.8034 (m) REVERT: B 347 LYS cc_start: 0.8524 (mtpt) cc_final: 0.7769 (mtmp) REVERT: B 351 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: C 274 LYS cc_start: 0.7693 (mtmt) cc_final: 0.7368 (ttmm) REVERT: C 347 LYS cc_start: 0.8489 (mtpt) cc_final: 0.7785 (mtmp) REVERT: D 274 LYS cc_start: 0.7116 (mtmt) cc_final: 0.6764 (ttmm) REVERT: D 347 LYS cc_start: 0.8534 (mtpt) cc_final: 0.7840 (mtmp) REVERT: E 274 LYS cc_start: 0.6915 (mtmt) cc_final: 0.6667 (ttmm) REVERT: E 277 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8255 (mp) REVERT: E 347 LYS cc_start: 0.8529 (mtpt) cc_final: 0.7806 (mtmm) REVERT: G 274 LYS cc_start: 0.7231 (mtmt) cc_final: 0.6950 (ttmm) REVERT: G 277 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7975 (mp) REVERT: G 281 LYS cc_start: 0.7560 (mttt) cc_final: 0.7281 (mttm) REVERT: G 283 ASP cc_start: 0.7755 (t0) cc_final: 0.7519 (t0) REVERT: G 347 LYS cc_start: 0.8469 (mtpt) cc_final: 0.7735 (mtmp) REVERT: H 274 LYS cc_start: 0.7560 (mtmt) cc_final: 0.7251 (ttmm) REVERT: H 347 LYS cc_start: 0.8493 (mtpt) cc_final: 0.7784 (mttp) REVERT: I 274 LYS cc_start: 0.7137 (mtmt) cc_final: 0.6842 (ttmm) REVERT: I 345 ASP cc_start: 0.7861 (t70) cc_final: 0.7639 (t70) REVERT: I 347 LYS cc_start: 0.8586 (mtpt) cc_final: 0.7927 (mtmp) outliers start: 18 outliers final: 11 residues processed: 219 average time/residue: 1.4274 time to fit residues: 328.7394 Evaluate side-chains 227 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 F 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 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 49 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 D 288 GLN E 296 ASN F 296 ASN H 288 GLN 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 = 0.3960 r_free = 0.3960 target = 0.132831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.113843 restraints weight = 9015.134| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.47 r_work: 0.3574 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8230 Z= 0.364 Angle : 0.642 7.702 10990 Z= 0.333 Chirality : 0.051 0.133 1230 Planarity : 0.003 0.035 1410 Dihedral : 6.048 16.292 1100 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.04 % Allowed : 16.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.003 0.001 HIS I 299 PHE 0.008 0.001 PHE B 378 TYR 0.010 0.003 TYR I 310 ARG 0.008 0.001 ARG J 379 *********************** 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 231 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7224 (mtmt) cc_final: 0.6953 (ttmm) REVERT: A 277 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7793 (mt) REVERT: B 274 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6947 (ttmm) REVERT: B 281 LYS cc_start: 0.7499 (mttt) cc_final: 0.7221 (mttm) REVERT: B 293 SER cc_start: 0.8342 (p) cc_final: 0.8044 (m) REVERT: B 347 LYS cc_start: 0.8556 (mtpt) cc_final: 0.7773 (mtmp) REVERT: B 351 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: C 274 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7379 (ttmm) REVERT: C 347 LYS cc_start: 0.8508 (mtpt) cc_final: 0.7806 (mtmp) REVERT: D 274 LYS cc_start: 0.7123 (mtmt) cc_final: 0.6750 (ttmm) REVERT: D 347 LYS cc_start: 0.8532 (mtpt) cc_final: 0.7833 (mtmp) REVERT: E 274 LYS cc_start: 0.6911 (mtmt) cc_final: 0.6650 (ttmm) REVERT: E 277 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8297 (mp) REVERT: E 347 LYS cc_start: 0.8540 (mtpt) cc_final: 0.7801 (mtmm) REVERT: G 274 LYS cc_start: 0.7224 (mtmt) cc_final: 0.6914 (ttmm) REVERT: G 277 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7982 (mp) REVERT: G 283 ASP cc_start: 0.7768 (t0) cc_final: 0.7531 (t0) REVERT: G 347 LYS cc_start: 0.8479 (mtpt) cc_final: 0.7732 (mtmp) REVERT: H 274 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7252 (ttmm) REVERT: H 293 SER cc_start: 0.7962 (p) cc_final: 0.7674 (m) REVERT: H 347 LYS cc_start: 0.8495 (mtpt) cc_final: 0.7777 (mttp) REVERT: I 274 LYS cc_start: 0.7143 (mtmt) cc_final: 0.6827 (ttmm) REVERT: I 345 ASP cc_start: 0.7872 (t70) cc_final: 0.7653 (t70) REVERT: I 347 LYS cc_start: 0.8574 (mtpt) cc_final: 0.7924 (mtmp) outliers start: 19 outliers final: 11 residues processed: 219 average time/residue: 1.3865 time to fit residues: 319.3766 Evaluate side-chains 224 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 F 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 D 288 GLN E 296 ASN F 296 ASN 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 = 0.3972 r_free = 0.3972 target = 0.133639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.114643 restraints weight = 9084.149| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.48 r_work: 0.3586 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8230 Z= 0.310 Angle : 0.610 6.007 10990 Z= 0.316 Chirality : 0.051 0.134 1230 Planarity : 0.003 0.041 1410 Dihedral : 5.970 15.457 1100 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.04 % Allowed : 16.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.003 0.001 HIS G 299 PHE 0.007 0.001 PHE B 378 TYR 0.011 0.003 TYR D 310 ARG 0.009 0.001 ARG E 379 *********************** 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 233 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7200 (mtmt) cc_final: 0.6938 (ttmm) REVERT: A 277 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7745 (mt) REVERT: B 274 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6934 (ttmm) REVERT: B 281 LYS cc_start: 0.7470 (mttt) cc_final: 0.7191 (mttm) REVERT: B 293 SER cc_start: 0.8306 (p) cc_final: 0.8017 (m) REVERT: B 347 LYS cc_start: 0.8521 (mtpt) cc_final: 0.7743 (mtmp) REVERT: B 351 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: C 274 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7378 (ttmm) REVERT: C 347 LYS cc_start: 0.8507 (mtpt) cc_final: 0.7791 (mtmp) REVERT: D 274 LYS cc_start: 0.7109 (mtmt) cc_final: 0.6753 (ttmm) REVERT: D 347 LYS cc_start: 0.8520 (mtpt) cc_final: 0.7821 (mtmp) REVERT: E 274 LYS cc_start: 0.6877 (mtmt) cc_final: 0.6634 (ttmm) REVERT: E 277 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8266 (mp) REVERT: E 347 LYS cc_start: 0.8522 (mtpt) cc_final: 0.7786 (mtmm) REVERT: G 274 LYS cc_start: 0.7245 (mtmt) cc_final: 0.6922 (ttmm) REVERT: G 277 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7993 (mp) REVERT: G 283 ASP cc_start: 0.7783 (t0) cc_final: 0.7546 (t0) REVERT: G 347 LYS cc_start: 0.8476 (mtpt) cc_final: 0.7710 (mtmp) REVERT: H 274 LYS cc_start: 0.7573 (mtmt) cc_final: 0.7258 (ttmm) REVERT: H 347 LYS cc_start: 0.8490 (mtpt) cc_final: 0.7775 (mttp) REVERT: I 274 LYS cc_start: 0.7135 (mtmt) cc_final: 0.6839 (ttmm) REVERT: I 345 ASP cc_start: 0.7869 (t70) cc_final: 0.7627 (t70) REVERT: I 347 LYS cc_start: 0.8564 (mtpt) cc_final: 0.7901 (mtmp) outliers start: 19 outliers final: 12 residues processed: 220 average time/residue: 1.3755 time to fit residues: 318.5739 Evaluate side-chains 227 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 F 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 96 optimal weight: 0.0970 chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 46 optimal weight: 0.0060 chunk 89 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 overall best weight: 4.6200 ------------------------------------------------------------------------------- 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 D 288 GLN E 296 ASN F 296 ASN 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 = 0.3967 r_free = 0.3967 target = 0.133231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.114269 restraints weight = 8873.162| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.46 r_work: 0.3582 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8230 Z= 0.342 Angle : 0.631 6.082 10990 Z= 0.327 Chirality : 0.051 0.134 1230 Planarity : 0.003 0.037 1410 Dihedral : 6.031 16.085 1100 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.83 % Allowed : 16.88 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 299 PHE 0.008 0.001 PHE B 378 TYR 0.010 0.003 TYR D 310 ARG 0.008 0.001 ARG E 379 ********************** 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 229 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7184 (mtmt) cc_final: 0.6939 (ttmm) REVERT: A 277 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7774 (mt) REVERT: B 274 LYS cc_start: 0.7273 (mtmt) cc_final: 0.6946 (ttmm) REVERT: B 281 LYS cc_start: 0.7501 (mttt) cc_final: 0.7219 (mttm) REVERT: B 293 SER cc_start: 0.8317 (p) cc_final: 0.8029 (m) REVERT: B 347 LYS cc_start: 0.8529 (mtpt) cc_final: 0.7753 (mtmp) REVERT: B 351 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: C 274 LYS cc_start: 0.7698 (mtmt) cc_final: 0.7367 (ttmm) REVERT: C 347 LYS cc_start: 0.8502 (mtpt) cc_final: 0.7794 (mtmp) REVERT: D 274 LYS cc_start: 0.7107 (mtmt) cc_final: 0.6738 (ttmm) REVERT: D 347 LYS cc_start: 0.8526 (mtpt) cc_final: 0.7824 (mtmp) REVERT: E 274 LYS cc_start: 0.6887 (mtmt) cc_final: 0.6636 (ttmm) REVERT: E 277 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8299 (mp) REVERT: E 347 LYS cc_start: 0.8515 (mtpt) cc_final: 0.7787 (mtmm) REVERT: G 274 LYS cc_start: 0.7254 (mtmt) cc_final: 0.6921 (ttmm) REVERT: G 277 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8007 (mp) REVERT: G 283 ASP cc_start: 0.7822 (t0) cc_final: 0.7584 (t0) REVERT: G 347 LYS cc_start: 0.8489 (mtpt) cc_final: 0.7727 (mtmp) REVERT: H 274 LYS cc_start: 0.7572 (mtmt) cc_final: 0.7242 (ttmm) REVERT: H 347 LYS cc_start: 0.8481 (mtpt) cc_final: 0.7770 (mttp) REVERT: I 274 LYS cc_start: 0.7142 (mtmt) cc_final: 0.6834 (ttmm) REVERT: I 345 ASP cc_start: 0.7894 (t70) cc_final: 0.7669 (t70) REVERT: I 347 LYS cc_start: 0.8565 (mtpt) cc_final: 0.7902 (mtmp) outliers start: 17 outliers final: 12 residues processed: 217 average time/residue: 1.3920 time to fit residues: 317.2951 Evaluate side-chains 226 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 F 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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 D 288 GLN E 296 ASN F 296 ASN I 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 = 0.3970 r_free = 0.3970 target = 0.133432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.114463 restraints weight = 9011.952| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.47 r_work: 0.3584 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8230 Z= 0.322 Angle : 0.621 7.020 10990 Z= 0.321 Chirality : 0.051 0.135 1230 Planarity : 0.003 0.035 1410 Dihedral : 6.007 15.828 1100 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.04 % Allowed : 16.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 299 PHE 0.007 0.001 PHE B 378 TYR 0.011 0.003 TYR D 310 ARG 0.008 0.001 ARG J 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7417.01 seconds wall clock time: 132 minutes 5.99 seconds (7925.99 seconds total)