Starting phenix.real_space_refine on Wed Jun 3 12:10:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r8d_53810/06_2026/9r8d_53810.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r8d_53810/06_2026/9r8d_53810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r8d_53810/06_2026/9r8d_53810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r8d_53810/06_2026/9r8d_53810.map" model { file = "/net/cci-nas-00/data/ceres_data/9r8d_53810/06_2026/9r8d_53810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r8d_53810/06_2026/9r8d_53810.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 8 5.16 5 C 2936 2.51 5 N 864 2.21 5 O 888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4696 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "G" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 1.35, per 1000 atoms: 0.29 Number of scatterers: 4696 At special positions: 0 Unit cell: (123.6, 102.176, 40.376, 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 8 16.00 O 888 8.00 N 864 7.00 C 2936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 192.6 milliseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1072 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 55.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.374A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLN C 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N TYR G 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.750A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 317 through 318 removed outlier: 6.445A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS C 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 321 through 330 removed outlier: 6.744A pdb=" N SER A 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU E 325 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N GLY C 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N LEU A 325 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N ILE C 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN A 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N HIS C 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS C 321 " --> pdb=" O CYS G 322 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER G 324 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLY C 323 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N GLY G 326 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N LEU C 325 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N ILE G 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN C 327 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N HIS G 330 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N HIS C 329 " --> pdb=" O HIS G 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 336 through 345 removed outlier: 6.965A pdb=" N VAL E 337 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLU A 338 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL E 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS A 340 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N SER E 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU A 342 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU C 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N VAL C 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N LYS G 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N VAL C 339 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N GLU G 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N SER C 341 " --> pdb=" O GLU G 342 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU G 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS C 343 " --> pdb=" O LEU G 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 349 through 362 removed outlier: 6.836A pdb=" N VAL E 350 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN A 351 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER E 352 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS A 353 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE E 354 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLY A 355 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N LEU C 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER A 356 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASN C 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N VAL C 350 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N LYS G 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N SER C 352 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N GLY G 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE C 354 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N LEU G 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER C 356 " --> pdb=" O LEU G 357 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASN G 359 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP C 358 " --> pdb=" O ASN G 359 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N THR G 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE C 360 " --> pdb=" O THR G 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 369 through 379 removed outlier: 6.665A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS C 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLU G 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE C 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N HIS G 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR C 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU G 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS C 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE G 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR C 377 " --> pdb=" O PHE G 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 306 through 310 removed outlier: 6.397A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN D 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TYR H 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL D 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 313 through 314 removed outlier: 6.556A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL D 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 317 through 318 removed outlier: 6.603A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS D 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 321 through 324 removed outlier: 6.753A pdb=" N SER B 324 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS D 321 " --> pdb=" O CYS H 322 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER H 324 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY D 323 " --> pdb=" O SER H 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 328 through 330 removed outlier: 6.708A pdb=" N HIS B 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N HIS D 329 " --> pdb=" O HIS H 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 336 through 346 removed outlier: 6.495A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU F 344 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N LYS B 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 10.619A pdb=" N PHE F 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS D 343 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU B 344 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP D 345 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE B 346 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS H 343 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU D 344 " --> pdb=" O LYS H 343 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP H 345 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE D 346 " --> pdb=" O ASP H 345 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 351 through 362 removed outlier: 6.725A pdb=" N SER F 352 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 353 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE F 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY B 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N LEU D 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER B 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASN D 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N SER D 352 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N GLY H 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE D 354 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N LEU H 357 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER D 356 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASN H 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP D 358 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THR H 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE D 360 " --> pdb=" O THR H 361 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 369 through 371 removed outlier: 6.454A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 374 through 379 removed outlier: 6.674A pdb=" N HIS B 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR F 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ARG F 379 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE B 378 " --> pdb=" O ARG F 379 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 222 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: 0.58 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 970 1.33 - 1.45: 1097 1.45 - 1.57: 2693 1.57 - 1.70: 0 1.70 - 1.82: 8 Bond restraints: 4768 Sorted by residual: bond pdb=" CB ILE G 371 " pdb=" CG1 ILE G 371 " ideal model delta sigma weight residual 1.530 1.462 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CB ILE C 371 " pdb=" CG1 ILE C 371 " ideal model delta sigma weight residual 1.530 1.462 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CB ILE E 371 " pdb=" CG1 ILE E 371 " ideal model delta sigma weight residual 1.530 1.462 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" CB ILE A 371 " pdb=" CG1 ILE A 371 " ideal model delta sigma weight residual 1.530 1.463 0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" CA SER F 316 " pdb=" CB SER F 316 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.54e-02 4.22e+03 9.37e+00 ... (remaining 4763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 5526 2.48 - 4.97: 751 4.97 - 7.45: 75 7.45 - 9.94: 20 9.94 - 12.42: 4 Bond angle restraints: 6376 Sorted by residual: angle pdb=" CA THR D 361 " pdb=" CB THR D 361 " pdb=" OG1 THR D 361 " ideal model delta sigma weight residual 109.60 97.18 12.42 1.50e+00 4.44e-01 6.86e+01 angle pdb=" CA THR H 361 " pdb=" CB THR H 361 " pdb=" OG1 THR H 361 " ideal model delta sigma weight residual 109.60 97.18 12.42 1.50e+00 4.44e-01 6.86e+01 angle pdb=" CA THR B 361 " pdb=" CB THR B 361 " pdb=" OG1 THR B 361 " ideal model delta sigma weight residual 109.60 97.19 12.41 1.50e+00 4.44e-01 6.85e+01 angle pdb=" CA THR F 361 " pdb=" CB THR F 361 " pdb=" OG1 THR F 361 " ideal model delta sigma weight residual 109.60 97.19 12.41 1.50e+00 4.44e-01 6.84e+01 angle pdb=" CA THR G 361 " pdb=" CB THR G 361 " pdb=" OG1 THR G 361 " ideal model delta sigma weight residual 109.60 100.79 8.81 1.50e+00 4.44e-01 3.45e+01 ... (remaining 6371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.69: 2652 13.69 - 27.38: 188 27.38 - 41.07: 44 41.07 - 54.75: 8 54.75 - 68.44: 12 Dihedral angle restraints: 2904 sinusoidal: 1216 harmonic: 1688 Sorted by residual: dihedral pdb=" CA GLY H 326 " pdb=" C GLY H 326 " pdb=" N ASN H 327 " pdb=" CA ASN H 327 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA GLY F 326 " pdb=" C GLY F 326 " pdb=" N ASN F 327 " pdb=" CA ASN F 327 " ideal model delta harmonic sigma weight residual 180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLY B 326 " pdb=" C GLY B 326 " pdb=" N ASN B 327 " pdb=" CA ASN B 327 " ideal model delta harmonic sigma weight residual -180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 2901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 343 0.061 - 0.121: 204 0.121 - 0.182: 125 0.182 - 0.242: 28 0.242 - 0.302: 12 Chirality restraints: 712 Sorted by residual: chirality pdb=" CA ASP E 348 " pdb=" N ASP E 348 " pdb=" C ASP E 348 " pdb=" CB ASP E 348 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASP A 348 " pdb=" N ASP A 348 " pdb=" C ASP A 348 " pdb=" CB ASP A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA ASP C 348 " pdb=" N ASP C 348 " pdb=" C ASP C 348 " pdb=" CB ASP C 348 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 709 not shown) Planarity restraints: 816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 350 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.73e+00 pdb=" C VAL F 350 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL F 350 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN F 351 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 350 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.70e+00 pdb=" C VAL H 350 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL H 350 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN H 351 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 350 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C VAL B 350 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL B 350 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN B 351 " -0.016 2.00e-02 2.50e+03 ... (remaining 813 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 1699 2.91 - 3.41: 4114 3.41 - 3.91: 7735 3.91 - 4.40: 8274 4.40 - 4.90: 16318 Nonbonded interactions: 38140 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.415 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.416 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.416 3.040 nonbonded pdb=" OD1 ASP H 314 " pdb=" OG SER H 316 " model vdw 2.416 3.040 nonbonded pdb=" OG SER D 316 " pdb=" NZ LYS D 370 " model vdw 2.490 3.120 ... (remaining 38135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 5.730 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.250 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.010 0.068 4768 Z= 0.610 Angle : 1.788 12.424 6376 Z= 1.129 Chirality : 0.098 0.302 712 Planarity : 0.010 0.050 816 Dihedral : 11.471 68.442 1832 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.49 % Allowed : 5.97 % Favored : 92.54 % Cbeta Deviations : 1.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.17), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.004 ARG E 379 TYR 0.012 0.006 TYR F 310 PHE 0.017 0.005 PHE E 346 HIS 0.016 0.005 HIS H 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00981 / 0.61 ( 4768) covalent geometry : angle 1.78782 / 1.13 ( 6376) hydrogen bonds : bond 0.17367 / 10.95 ( 74) hydrogen bonds : angle 7.53054 / 4.99 ( 222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8582 (mttt) cc_final: 0.8188 (tttt) REVERT: A 353 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8244 (tttt) REVERT: A 371 ILE cc_start: 0.8653 (pt) cc_final: 0.8372 (mt) REVERT: C 317 LYS cc_start: 0.8510 (mttt) cc_final: 0.8199 (tttt) REVERT: C 371 ILE cc_start: 0.8692 (pt) cc_final: 0.8481 (mt) REVERT: E 317 LYS cc_start: 0.8553 (mttt) cc_final: 0.8271 (pttt) REVERT: E 343 LYS cc_start: 0.7972 (mttt) cc_final: 0.7748 (mmpt) REVERT: E 369 LYS cc_start: 0.8728 (tttt) cc_final: 0.8424 (ttmt) REVERT: F 340 LYS cc_start: 0.8175 (mttt) cc_final: 0.7426 (tppt) REVERT: F 370 LYS cc_start: 0.8491 (tttt) cc_final: 0.7536 (pttt) REVERT: G 317 LYS cc_start: 0.8555 (mttt) cc_final: 0.8341 (tttt) REVERT: G 369 LYS cc_start: 0.8825 (tttt) cc_final: 0.8615 (ttmt) REVERT: H 347 LYS cc_start: 0.7419 (mttt) cc_final: 0.6662 (pmtt) outliers start: 8 outliers final: 0 residues processed: 167 average time/residue: 0.7009 time to fit residues: 120.2229 Evaluate side-chains 112 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.0570 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 330 HIS A 362 HIS B 330 HIS B 362 HIS C 327 ASN C 329 HIS C 330 HIS C 362 HIS D 327 ASN D 330 HIS D 362 HIS E 327 ASN E 330 HIS E 362 HIS F 329 HIS F 330 HIS F 362 HIS G 327 ASN G 329 HIS G 362 HIS H 329 HIS H 362 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.131427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.095353 restraints weight = 5947.543| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.51 r_work: 0.3568 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4768 Z= 0.190 Angle : 0.711 8.123 6376 Z= 0.346 Chirality : 0.049 0.152 712 Planarity : 0.003 0.026 816 Dihedral : 5.158 17.974 632 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.04 % Allowed : 18.10 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 349 TYR 0.016 0.003 TYR C 310 PHE 0.014 0.002 PHE G 346 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 4768) covalent geometry : angle 0.71090 / 0.35 ( 6376) hydrogen bonds : bond 0.03027 / 2.02 ( 74) hydrogen bonds : angle 5.57270 / 3.61 ( 222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8016 (mtpm) cc_final: 0.7501 (mtmt) REVERT: A 356 SER cc_start: 0.8489 (p) cc_final: 0.8279 (m) REVERT: B 371 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7762 (mt) REVERT: C 311 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8123 (mtpp) REVERT: C 347 LYS cc_start: 0.7826 (mtpm) cc_final: 0.7548 (mtmm) REVERT: D 370 LYS cc_start: 0.8653 (tttm) cc_final: 0.8353 (tmtt) REVERT: D 371 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7699 (mt) REVERT: E 343 LYS cc_start: 0.7760 (mttt) cc_final: 0.7478 (mmpt) REVERT: E 349 ARG cc_start: 0.7147 (mtt90) cc_final: 0.6894 (mtt90) REVERT: E 369 LYS cc_start: 0.8506 (tttt) cc_final: 0.8136 (tmtt) REVERT: F 347 LYS cc_start: 0.6657 (mmmt) cc_final: 0.6191 (mppt) REVERT: F 349 ARG cc_start: 0.6960 (mpp80) cc_final: 0.5733 (mmm160) REVERT: F 356 SER cc_start: 0.7940 (t) cc_final: 0.7492 (p) REVERT: G 343 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7277 (pmtt) REVERT: H 314 ASP cc_start: 0.8491 (t0) cc_final: 0.8119 (t0) REVERT: H 347 LYS cc_start: 0.6926 (mttt) cc_final: 0.6479 (pmtt) REVERT: H 369 LYS cc_start: 0.8924 (ttmp) cc_final: 0.8639 (ttmm) outliers start: 27 outliers final: 13 residues processed: 148 average time/residue: 0.6985 time to fit residues: 106.3027 Evaluate side-chains 102 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain G residue 356 SER Chi-restraints excluded: chain G residue 371 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 51 optimal weight: 0.0770 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS C 362 HIS ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.134738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.098641 restraints weight = 5752.312| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.38 r_work: 0.3575 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 4768 Z= 0.282 Angle : 0.810 8.358 6376 Z= 0.392 Chirality : 0.052 0.144 712 Planarity : 0.003 0.020 816 Dihedral : 5.671 17.322 632 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.34 % Allowed : 20.15 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.26), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 349 TYR 0.017 0.004 TYR A 310 PHE 0.010 0.002 PHE A 346 HIS 0.006 0.002 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.28 ( 4768) covalent geometry : angle 0.80998 / 0.39 ( 6376) hydrogen bonds : bond 0.03271 / 2.21 ( 74) hydrogen bonds : angle 5.52720 / 3.51 ( 222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8517 (mttt) REVERT: A 357 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7431 (mt) REVERT: A 379 ARG cc_start: 0.7280 (mmm-85) cc_final: 0.6824 (tmt170) REVERT: B 370 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8352 (tptp) REVERT: C 379 ARG cc_start: 0.7433 (mmm-85) cc_final: 0.6884 (tmt170) REVERT: D 347 LYS cc_start: 0.6927 (mtpt) cc_final: 0.6436 (mppt) REVERT: D 353 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8252 (ttmt) REVERT: E 343 LYS cc_start: 0.7901 (mttt) cc_final: 0.7610 (mmpt) REVERT: E 379 ARG cc_start: 0.7218 (mmm-85) cc_final: 0.6834 (tmm160) REVERT: F 347 LYS cc_start: 0.7022 (mmmt) cc_final: 0.6552 (mppt) REVERT: F 349 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.5632 (mmp-170) REVERT: F 353 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8120 (ttmm) REVERT: F 356 SER cc_start: 0.7719 (t) cc_final: 0.7248 (p) REVERT: F 370 LYS cc_start: 0.8734 (tttt) cc_final: 0.7514 (pttt) REVERT: G 325 LEU cc_start: 0.8461 (mp) cc_final: 0.8227 (mt) REVERT: G 343 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7427 (pmtt) REVERT: G 379 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.6583 (ttp80) REVERT: H 314 ASP cc_start: 0.8526 (t0) cc_final: 0.8137 (t0) REVERT: H 340 LYS cc_start: 0.3550 (OUTLIER) cc_final: 0.2405 (pptt) REVERT: H 347 LYS cc_start: 0.6976 (mttt) cc_final: 0.6626 (pmtt) REVERT: H 369 LYS cc_start: 0.8987 (ttmp) cc_final: 0.8681 (ttmm) outliers start: 34 outliers final: 17 residues processed: 122 average time/residue: 0.6906 time to fit residues: 86.6753 Evaluate side-chains 121 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain G residue 356 SER Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain H residue 340 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN G 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.123481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.089000 restraints weight = 6029.719| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.43 r_work: 0.3503 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4768 Z= 0.207 Angle : 0.738 8.688 6376 Z= 0.347 Chirality : 0.049 0.138 712 Planarity : 0.003 0.018 816 Dihedral : 5.416 16.509 632 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 7.09 % Allowed : 23.32 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.28), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 349 TYR 0.015 0.003 TYR E 310 PHE 0.012 0.002 PHE A 346 HIS 0.005 0.002 HIS G 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 ( 4768) covalent geometry : angle 0.73769 / 0.35 ( 6376) hydrogen bonds : bond 0.02642 / 1.80 ( 74) hydrogen bonds : angle 5.35488 / 3.39 ( 222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7441 (mt) REVERT: A 379 ARG cc_start: 0.7347 (mmm-85) cc_final: 0.6858 (tmt170) REVERT: B 370 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8280 (tptp) REVERT: B 371 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7502 (mt) REVERT: C 356 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8048 (t) REVERT: C 372 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: C 379 ARG cc_start: 0.7416 (mmm-85) cc_final: 0.6876 (tmt170) REVERT: D 349 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.6435 (mpp80) REVERT: D 353 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8256 (ttmm) REVERT: D 372 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: E 343 LYS cc_start: 0.7975 (mttt) cc_final: 0.7692 (mmpt) REVERT: E 353 LYS cc_start: 0.8627 (ttmm) cc_final: 0.7986 (tttt) REVERT: E 379 ARG cc_start: 0.7314 (mmm-85) cc_final: 0.6392 (mmt-90) REVERT: F 347 LYS cc_start: 0.7011 (mmmt) cc_final: 0.6521 (mppt) REVERT: F 349 ARG cc_start: 0.6859 (mpp80) cc_final: 0.5614 (mmm160) REVERT: F 353 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8109 (ttmm) REVERT: F 370 LYS cc_start: 0.8683 (tttt) cc_final: 0.7438 (pttt) REVERT: G 343 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7417 (pmtt) REVERT: G 372 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8395 (mt-10) REVERT: G 379 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.6661 (ttp80) REVERT: H 314 ASP cc_start: 0.8546 (t0) cc_final: 0.8175 (t0) REVERT: H 340 LYS cc_start: 0.3597 (OUTLIER) cc_final: 0.2360 (pptt) REVERT: H 347 LYS cc_start: 0.7193 (mttt) cc_final: 0.6736 (pmtt) REVERT: H 349 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.5654 (ppt170) REVERT: H 369 LYS cc_start: 0.8962 (ttmp) cc_final: 0.8734 (ttmm) outliers start: 38 outliers final: 15 residues processed: 124 average time/residue: 0.7393 time to fit residues: 94.2263 Evaluate side-chains 121 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain H residue 340 LYS Chi-restraints excluded: chain H residue 349 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 49 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 53 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.124542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.089515 restraints weight = 6232.701| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.59 r_work: 0.3510 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4768 Z= 0.137 Angle : 0.660 9.119 6376 Z= 0.306 Chirality : 0.048 0.133 712 Planarity : 0.002 0.017 816 Dihedral : 5.040 15.859 632 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 6.16 % Allowed : 24.63 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.29), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 349 TYR 0.013 0.003 TYR E 310 PHE 0.011 0.001 PHE A 346 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 4768) covalent geometry : angle 0.65969 / 0.31 ( 6376) hydrogen bonds : bond 0.02234 / 1.53 ( 74) hydrogen bonds : angle 5.18571 / 3.31 ( 222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8148 (tt0) cc_final: 0.7473 (mt-10) REVERT: A 379 ARG cc_start: 0.7320 (mmm-85) cc_final: 0.6768 (tmt170) REVERT: B 370 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8264 (tptp) REVERT: B 371 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7342 (mt) REVERT: B 375 LYS cc_start: 0.8659 (tmtp) cc_final: 0.8277 (tmtp) REVERT: C 316 SER cc_start: 0.9294 (p) cc_final: 0.9036 (p) REVERT: C 356 SER cc_start: 0.8627 (p) cc_final: 0.7993 (t) REVERT: C 379 ARG cc_start: 0.7438 (mmm-85) cc_final: 0.6656 (tmt170) REVERT: D 353 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8262 (ttmm) REVERT: D 371 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7589 (mt) REVERT: D 372 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: E 343 LYS cc_start: 0.7965 (mttt) cc_final: 0.7642 (mmpt) REVERT: E 353 LYS cc_start: 0.8583 (ttmm) cc_final: 0.7964 (tttt) REVERT: E 379 ARG cc_start: 0.7336 (mmm-85) cc_final: 0.6278 (mmt180) REVERT: F 347 LYS cc_start: 0.7028 (mmmt) cc_final: 0.6490 (mppt) REVERT: F 349 ARG cc_start: 0.6855 (mpp80) cc_final: 0.5486 (mmp-170) REVERT: F 353 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7999 (ttmm) REVERT: F 357 LEU cc_start: 0.8271 (tt) cc_final: 0.7967 (tp) REVERT: F 370 LYS cc_start: 0.8646 (tttt) cc_final: 0.7373 (pttt) REVERT: G 325 LEU cc_start: 0.8242 (mp) cc_final: 0.7912 (mt) REVERT: G 372 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: H 314 ASP cc_start: 0.8528 (t0) cc_final: 0.8137 (t0) REVERT: H 336 GLN cc_start: 0.8582 (mt0) cc_final: 0.8344 (mt0) REVERT: H 340 LYS cc_start: 0.3658 (OUTLIER) cc_final: 0.2319 (pptt) REVERT: H 347 LYS cc_start: 0.7179 (mttt) cc_final: 0.6757 (pptt) REVERT: H 349 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.5685 (ppt170) REVERT: H 369 LYS cc_start: 0.8894 (ttmp) cc_final: 0.8663 (ttmm) outliers start: 33 outliers final: 13 residues processed: 122 average time/residue: 0.6721 time to fit residues: 84.2816 Evaluate side-chains 120 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain H residue 340 LYS Chi-restraints excluded: chain H residue 349 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 24 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 48 optimal weight: 0.0970 chunk 51 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 19 optimal weight: 6.9990 overall best weight: 3.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.122833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.088055 restraints weight = 6213.258| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.48 r_work: 0.3477 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4768 Z= 0.198 Angle : 0.719 9.015 6376 Z= 0.337 Chirality : 0.049 0.133 712 Planarity : 0.003 0.021 816 Dihedral : 5.371 15.657 632 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.16 % Allowed : 25.56 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.29), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 349 TYR 0.016 0.003 TYR E 310 PHE 0.011 0.002 PHE A 346 HIS 0.004 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 4768) covalent geometry : angle 0.71924 / 0.34 ( 6376) hydrogen bonds : bond 0.02617 / 1.83 ( 74) hydrogen bonds : angle 5.12792 / 3.35 ( 222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8163 (tt0) cc_final: 0.7538 (mt-10) REVERT: A 379 ARG cc_start: 0.7427 (mmm-85) cc_final: 0.6992 (tmm160) REVERT: B 370 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8325 (tptp) REVERT: B 375 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8335 (tmtp) REVERT: C 356 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8120 (t) REVERT: C 372 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: C 379 ARG cc_start: 0.7514 (mmm-85) cc_final: 0.6966 (tmm160) REVERT: D 353 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8297 (ttmm) REVERT: D 372 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: E 343 LYS cc_start: 0.8019 (mttt) cc_final: 0.7733 (mmpt) REVERT: E 353 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8060 (tttt) REVERT: E 379 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.6215 (mmt180) REVERT: F 347 LYS cc_start: 0.7095 (mmmt) cc_final: 0.6580 (mppt) REVERT: F 349 ARG cc_start: 0.6844 (mpp80) cc_final: 0.5467 (mmp-170) REVERT: F 353 LYS cc_start: 0.8225 (ttmt) cc_final: 0.8010 (ttmm) REVERT: F 357 LEU cc_start: 0.8225 (tt) cc_final: 0.7988 (tp) REVERT: F 370 LYS cc_start: 0.8702 (tttt) cc_final: 0.7462 (pttt) REVERT: G 343 LYS cc_start: 0.8336 (ttpp) cc_final: 0.7478 (pmtt) REVERT: G 379 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.6631 (ttp80) REVERT: H 314 ASP cc_start: 0.8540 (t0) cc_final: 0.8159 (t0) REVERT: H 336 GLN cc_start: 0.8637 (mt0) cc_final: 0.8413 (mt0) REVERT: H 340 LYS cc_start: 0.3697 (OUTLIER) cc_final: 0.2233 (pptt) REVERT: H 347 LYS cc_start: 0.7197 (mttt) cc_final: 0.6755 (pptt) REVERT: H 349 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.5709 (ppt170) REVERT: H 370 LYS cc_start: 0.8845 (tmtp) cc_final: 0.8569 (tptp) outliers start: 33 outliers final: 20 residues processed: 127 average time/residue: 0.6902 time to fit residues: 90.0467 Evaluate side-chains 127 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain H residue 340 LYS Chi-restraints excluded: chain H residue 349 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 2 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.121482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.086900 restraints weight = 6194.827| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.55 r_work: 0.3468 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 4768 Z= 0.249 Angle : 0.772 9.187 6376 Z= 0.366 Chirality : 0.050 0.135 712 Planarity : 0.003 0.016 816 Dihedral : 5.594 16.113 632 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 6.72 % Allowed : 26.31 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.28), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 349 TYR 0.020 0.004 TYR E 310 PHE 0.012 0.002 PHE A 346 HIS 0.005 0.002 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 ( 4768) covalent geometry : angle 0.77162 / 0.37 ( 6376) hydrogen bonds : bond 0.02898 / 2.03 ( 74) hydrogen bonds : angle 5.19852 / 3.46 ( 222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 356 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8254 (m) REVERT: A 379 ARG cc_start: 0.7381 (mmm-85) cc_final: 0.6895 (tmt170) REVERT: B 347 LYS cc_start: 0.6814 (mtpt) cc_final: 0.6164 (mmpt) REVERT: B 356 SER cc_start: 0.7686 (t) cc_final: 0.7374 (p) REVERT: B 370 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8397 (tptp) REVERT: C 343 LYS cc_start: 0.8092 (mtpm) cc_final: 0.7653 (ttpp) REVERT: C 356 SER cc_start: 0.8664 (p) cc_final: 0.8060 (t) REVERT: C 372 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: C 379 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.6966 (tmm160) REVERT: D 353 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8291 (ttmm) REVERT: E 343 LYS cc_start: 0.7962 (mttt) cc_final: 0.7641 (mmpt) REVERT: E 353 LYS cc_start: 0.8621 (ttmm) cc_final: 0.7969 (tttt) REVERT: E 372 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8473 (tt0) REVERT: E 379 ARG cc_start: 0.7178 (mmm-85) cc_final: 0.6145 (mmp-170) REVERT: F 349 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.5598 (mmm160) REVERT: F 357 LEU cc_start: 0.8152 (tt) cc_final: 0.7929 (tp) REVERT: F 370 LYS cc_start: 0.8739 (tttt) cc_final: 0.7477 (pttt) REVERT: G 343 LYS cc_start: 0.8344 (ttpp) cc_final: 0.7506 (pmtt) REVERT: G 372 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: G 379 ARG cc_start: 0.7874 (mmm-85) cc_final: 0.6651 (ttp80) REVERT: H 314 ASP cc_start: 0.8574 (t0) cc_final: 0.8181 (t0) REVERT: H 340 LYS cc_start: 0.3754 (OUTLIER) cc_final: 0.2182 (pptt) REVERT: H 347 LYS cc_start: 0.7242 (mttt) cc_final: 0.6774 (pptt) REVERT: H 349 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.5951 (ppt170) outliers start: 36 outliers final: 20 residues processed: 127 average time/residue: 0.6867 time to fit residues: 89.6761 Evaluate side-chains 130 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 356 SER Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain H residue 340 LYS Chi-restraints excluded: chain H residue 349 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.0470 chunk 25 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.122561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.087801 restraints weight = 6224.337| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.46 r_work: 0.3475 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4768 Z= 0.197 Angle : 0.745 9.602 6376 Z= 0.344 Chirality : 0.049 0.133 712 Planarity : 0.002 0.016 816 Dihedral : 5.392 16.224 632 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 6.90 % Allowed : 26.31 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.29), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 349 TYR 0.015 0.003 TYR E 310 PHE 0.011 0.002 PHE A 346 HIS 0.004 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 4768) covalent geometry : angle 0.74508 / 0.34 ( 6376) hydrogen bonds : bond 0.02623 / 1.85 ( 74) hydrogen bonds : angle 5.10647 / 3.44 ( 222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8149 (tt0) cc_final: 0.7514 (mt-10) REVERT: A 379 ARG cc_start: 0.7331 (mmm-85) cc_final: 0.6906 (tmt170) REVERT: B 347 LYS cc_start: 0.6953 (mtpt) cc_final: 0.6223 (mmpt) REVERT: B 356 SER cc_start: 0.7735 (t) cc_final: 0.7435 (p) REVERT: B 370 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8422 (tptp) REVERT: B 371 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7714 (mt) REVERT: B 375 LYS cc_start: 0.8660 (tmtp) cc_final: 0.8365 (tmtp) REVERT: C 316 SER cc_start: 0.9306 (p) cc_final: 0.9054 (p) REVERT: C 343 LYS cc_start: 0.8107 (mtpm) cc_final: 0.7651 (ttpp) REVERT: C 356 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8103 (t) REVERT: C 372 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: C 379 ARG cc_start: 0.7489 (mmm-85) cc_final: 0.6921 (tmt170) REVERT: D 353 LYS cc_start: 0.8560 (mtpt) cc_final: 0.8324 (ttmm) REVERT: E 343 LYS cc_start: 0.7978 (mttt) cc_final: 0.7711 (mmpt) REVERT: E 353 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8055 (tttt) REVERT: E 372 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8470 (tt0) REVERT: E 379 ARG cc_start: 0.7249 (mmm-85) cc_final: 0.6206 (mmp-170) REVERT: F 347 LYS cc_start: 0.7149 (mmmt) cc_final: 0.6578 (mppt) REVERT: F 349 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5531 (mmp-170) REVERT: F 357 LEU cc_start: 0.8195 (tt) cc_final: 0.7967 (tp) REVERT: F 370 LYS cc_start: 0.8694 (tttt) cc_final: 0.7468 (pttt) REVERT: G 343 LYS cc_start: 0.8369 (ttpp) cc_final: 0.7563 (pmtt) REVERT: G 372 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8314 (mt-10) REVERT: G 379 ARG cc_start: 0.7853 (mmm-85) cc_final: 0.6721 (ttp80) REVERT: H 314 ASP cc_start: 0.8549 (t0) cc_final: 0.8165 (t0) REVERT: H 340 LYS cc_start: 0.3878 (OUTLIER) cc_final: 0.2222 (pptt) REVERT: H 347 LYS cc_start: 0.7234 (mttt) cc_final: 0.6804 (pptt) REVERT: H 349 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.5760 (ppt170) REVERT: H 370 LYS cc_start: 0.8839 (tmtp) cc_final: 0.8580 (tptp) outliers start: 37 outliers final: 22 residues processed: 131 average time/residue: 0.6610 time to fit residues: 89.1377 Evaluate side-chains 133 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain H residue 340 LYS Chi-restraints excluded: chain H residue 349 ARG Chi-restraints excluded: chain H residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 46 optimal weight: 0.0020 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 42 optimal weight: 0.0770 chunk 32 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 overall best weight: 2.7750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.122039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.087296 restraints weight = 6322.826| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.54 r_work: 0.3472 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4768 Z= 0.175 Angle : 0.726 9.774 6376 Z= 0.336 Chirality : 0.048 0.127 712 Planarity : 0.002 0.019 816 Dihedral : 5.275 16.260 632 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.53 % Allowed : 27.24 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.29), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 349 TYR 0.014 0.003 TYR E 310 PHE 0.011 0.001 PHE A 346 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 ( 4768) covalent geometry : angle 0.72564 / 0.34 ( 6376) hydrogen bonds : bond 0.02479 / 1.73 ( 74) hydrogen bonds : angle 5.00629 / 3.36 ( 222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8162 (tt0) cc_final: 0.7499 (mt-10) REVERT: A 379 ARG cc_start: 0.7284 (mmm-85) cc_final: 0.6845 (tmt170) REVERT: B 347 LYS cc_start: 0.6868 (mtpt) cc_final: 0.6374 (mppt) REVERT: B 356 SER cc_start: 0.7676 (t) cc_final: 0.7383 (p) REVERT: B 370 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8391 (tptp) REVERT: B 371 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7658 (mt) REVERT: B 375 LYS cc_start: 0.8653 (tmtp) cc_final: 0.8356 (tmtp) REVERT: C 316 SER cc_start: 0.9307 (p) cc_final: 0.9058 (p) REVERT: C 343 LYS cc_start: 0.8054 (mtpm) cc_final: 0.7601 (ttpp) REVERT: C 356 SER cc_start: 0.8613 (OUTLIER) cc_final: 0.8040 (t) REVERT: C 372 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: C 379 ARG cc_start: 0.7563 (mmm-85) cc_final: 0.6855 (tmt170) REVERT: D 349 ARG cc_start: 0.6058 (mpp80) cc_final: 0.5825 (mpt180) REVERT: D 353 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8241 (ttmm) REVERT: E 343 LYS cc_start: 0.8005 (mttt) cc_final: 0.7685 (mmpt) REVERT: E 353 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8035 (tttt) REVERT: E 372 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8485 (tt0) REVERT: E 379 ARG cc_start: 0.7209 (mmm-85) cc_final: 0.6118 (mmp-170) REVERT: F 347 LYS cc_start: 0.7071 (mmmt) cc_final: 0.6515 (mppt) REVERT: F 349 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.5438 (mmp-170) REVERT: F 357 LEU cc_start: 0.8158 (tt) cc_final: 0.7944 (tp) REVERT: F 370 LYS cc_start: 0.8705 (tttt) cc_final: 0.7433 (pttt) REVERT: G 343 LYS cc_start: 0.8375 (ttpp) cc_final: 0.7523 (pmtt) REVERT: G 379 ARG cc_start: 0.7833 (mmm-85) cc_final: 0.6664 (ttp80) REVERT: H 314 ASP cc_start: 0.8554 (t0) cc_final: 0.8124 (t0) REVERT: H 340 LYS cc_start: 0.3711 (OUTLIER) cc_final: 0.2161 (pptt) REVERT: H 347 LYS cc_start: 0.7217 (mttt) cc_final: 0.6782 (pptt) REVERT: H 349 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.5891 (ppt170) outliers start: 35 outliers final: 23 residues processed: 131 average time/residue: 0.6857 time to fit residues: 92.3577 Evaluate side-chains 135 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain H residue 340 LYS Chi-restraints excluded: chain H residue 349 ARG Chi-restraints excluded: chain H residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.121175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.086345 restraints weight = 6372.990| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.56 r_work: 0.3461 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4768 Z= 0.208 Angle : 0.777 9.786 6376 Z= 0.359 Chirality : 0.049 0.130 712 Planarity : 0.003 0.017 816 Dihedral : 5.421 16.324 632 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.34 % Allowed : 27.61 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.29), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 349 TYR 0.015 0.003 TYR E 310 PHE 0.011 0.002 PHE A 346 HIS 0.004 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 ( 4768) covalent geometry : angle 0.77726 / 0.36 ( 6376) hydrogen bonds : bond 0.02707 / 1.92 ( 74) hydrogen bonds : angle 5.02549 / 3.33 ( 222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8137 (tt0) cc_final: 0.7453 (mt-10) REVERT: A 356 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8285 (m) REVERT: A 379 ARG cc_start: 0.7272 (mmm-85) cc_final: 0.6832 (tmt170) REVERT: B 347 LYS cc_start: 0.6856 (mtpt) cc_final: 0.6183 (mmpt) REVERT: B 356 SER cc_start: 0.7694 (t) cc_final: 0.7385 (p) REVERT: B 357 LEU cc_start: 0.7621 (tt) cc_final: 0.7403 (tp) REVERT: B 370 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8368 (tptp) REVERT: B 371 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7635 (mt) REVERT: B 375 LYS cc_start: 0.8660 (tmtp) cc_final: 0.8292 (tmtp) REVERT: C 316 SER cc_start: 0.9332 (p) cc_final: 0.9073 (p) REVERT: C 343 LYS cc_start: 0.8071 (mtpm) cc_final: 0.7623 (ttpp) REVERT: C 356 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8054 (t) REVERT: C 372 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: C 379 ARG cc_start: 0.7516 (mmm-85) cc_final: 0.6889 (tmt170) REVERT: D 347 LYS cc_start: 0.7073 (mtpp) cc_final: 0.6066 (mmpt) REVERT: D 349 ARG cc_start: 0.6055 (mpp80) cc_final: 0.5823 (mpt180) REVERT: D 353 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8250 (ttmm) REVERT: E 343 LYS cc_start: 0.8016 (mttt) cc_final: 0.7700 (mmpt) REVERT: E 351 GLN cc_start: 0.7557 (mt0) cc_final: 0.7225 (tt0) REVERT: E 353 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8049 (tttt) REVERT: E 379 ARG cc_start: 0.7199 (mmm-85) cc_final: 0.6075 (mmp-170) REVERT: F 349 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.5453 (mmp-170) REVERT: F 357 LEU cc_start: 0.8180 (tt) cc_final: 0.7936 (tp) REVERT: F 370 LYS cc_start: 0.8712 (tttt) cc_final: 0.7468 (pttt) REVERT: G 343 LYS cc_start: 0.8393 (ttpp) cc_final: 0.7549 (pmtt) REVERT: G 379 ARG cc_start: 0.7834 (mmm-85) cc_final: 0.6688 (ttp80) REVERT: H 314 ASP cc_start: 0.8556 (t0) cc_final: 0.8123 (t0) REVERT: H 340 LYS cc_start: 0.3788 (OUTLIER) cc_final: 0.2171 (pptt) REVERT: H 347 LYS cc_start: 0.7312 (mttt) cc_final: 0.6805 (pptt) REVERT: H 349 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.5879 (ppt170) REVERT: H 370 LYS cc_start: 0.8824 (tmtp) cc_final: 0.8563 (tptp) outliers start: 34 outliers final: 22 residues processed: 128 average time/residue: 0.7320 time to fit residues: 96.3015 Evaluate side-chains 136 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain H residue 340 LYS Chi-restraints excluded: chain H residue 349 ARG Chi-restraints excluded: chain H residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.121372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.086542 restraints weight = 6401.576| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.57 r_work: 0.3465 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4768 Z= 0.198 Angle : 0.778 9.768 6376 Z= 0.363 Chirality : 0.049 0.129 712 Planarity : 0.002 0.017 816 Dihedral : 5.400 16.323 632 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.72 % Allowed : 27.24 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.29), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 349 TYR 0.015 0.003 TYR E 310 PHE 0.011 0.002 PHE A 346 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 4768) covalent geometry : angle 0.77799 / 0.36 ( 6376) hydrogen bonds : bond 0.02703 / 1.92 ( 74) hydrogen bonds : angle 4.99864 / 3.30 ( 222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2488.92 seconds wall clock time: 43 minutes 17.70 seconds (2597.70 seconds total)