Starting phenix.real_space_refine on Sun May 3 09:00:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o79_70191/05_2026/9o79_70191.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o79_70191/05_2026/9o79_70191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o79_70191/05_2026/9o79_70191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o79_70191/05_2026/9o79_70191.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o79_70191/05_2026/9o79_70191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o79_70191/05_2026/9o79_70191.map" } resolution = 2.55 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 3600 2.51 5 N 1060 2.21 5 O 1080 1.98 5 H 6000 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11750 Number of models: 1 Model: "" Number of chains: 10 Chain: "F" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "N" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "O" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "H" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "P" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "I" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "Q" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "J" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "R" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 2.37, per 1000 atoms: 0.20 Number of scatterers: 11750 At special positions: 0 Unit cell: (153.562, 84.2858, 46.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 1080 8.00 N 1060 7.00 C 3600 6.00 H 6000 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 370.3 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1320 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 49.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 306 through 310 removed outlier: 6.622A pdb=" N GLN F 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TYR G 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL F 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN G 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N TYR J 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL G 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 313 through 314 removed outlier: 6.841A pdb=" N VAL F 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL G 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 317 through 322 removed outlier: 6.298A pdb=" N LYS F 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N SER G 320 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR F 319 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N CYS G 322 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS F 321 " --> pdb=" O CYS G 322 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS G 317 " --> pdb=" O VAL J 318 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N SER J 320 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR G 319 " --> pdb=" O SER J 320 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N CYS J 322 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS G 321 " --> pdb=" O CYS J 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 325 through 330 removed outlier: 6.838A pdb=" N GLY H 326 " --> pdb=" O LEU I 325 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN I 327 " --> pdb=" O GLY H 326 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY F 326 " --> pdb=" O LEU H 325 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN H 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N LEU F 325 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N ILE G 328 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN F 327 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N HIS G 330 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS F 329 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N LEU G 325 " --> pdb=" O GLY J 326 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N ILE J 328 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN G 327 " --> pdb=" O ILE J 328 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N HIS J 330 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS G 329 " --> pdb=" O HIS J 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 336 through 340 removed outlier: 6.565A pdb=" N GLN F 336 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL G 339 " --> pdb=" O GLN F 336 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU F 338 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN G 336 " --> pdb=" O VAL J 337 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL J 339 " --> pdb=" O GLN G 336 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU G 338 " --> pdb=" O VAL J 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 343 through 346 removed outlier: 6.378A pdb=" N LYS F 343 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE G 346 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP F 345 " --> pdb=" O PHE G 346 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS G 343 " --> pdb=" O LEU J 344 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE J 346 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP G 345 " --> pdb=" O PHE J 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 351 through 356 removed outlier: 6.807A pdb=" N SER H 356 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER F 356 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN F 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE G 354 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS F 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER G 356 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLY F 355 " --> pdb=" O SER G 356 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN G 351 " --> pdb=" O SER J 352 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE J 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS G 353 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER J 356 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY G 355 " --> pdb=" O SER J 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 359 through 362 removed outlier: 6.635A pdb=" N ASN H 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS I 362 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR H 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN F 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N HIS H 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR F 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 369 through 371 removed outlier: 6.595A pdb=" N LYS F 370 " --> pdb=" O ILE H 371 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS F 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS G 369 " --> pdb=" O LYS J 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 374 through 378 removed outlier: 6.511A pdb=" N LYS F 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE G 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR F 377 " --> pdb=" O PHE G 378 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS G 375 " --> pdb=" O LEU J 376 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE J 378 " --> pdb=" O LYS G 375 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR G 377 " --> pdb=" O PHE J 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 306 through 310 removed outlier: 6.672A pdb=" N GLN N 307 " --> pdb=" O ILE O 308 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TYR O 310 " --> pdb=" O GLN N 307 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL N 309 " --> pdb=" O TYR O 310 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN O 307 " --> pdb=" O ILE R 308 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N TYR R 310 " --> pdb=" O GLN O 307 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL O 309 " --> pdb=" O TYR R 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 313 through 314 removed outlier: 6.728A pdb=" N VAL N 313 " --> pdb=" O ASP O 314 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL O 313 " --> pdb=" O ASP R 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 317 through 322 removed outlier: 6.305A pdb=" N LYS N 317 " --> pdb=" O VAL O 318 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N SER O 320 " --> pdb=" O LYS N 317 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR N 319 " --> pdb=" O SER O 320 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N CYS O 322 " --> pdb=" O THR N 319 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS N 321 " --> pdb=" O CYS O 322 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS O 317 " --> pdb=" O VAL R 318 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N SER R 320 " --> pdb=" O LYS O 317 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR O 319 " --> pdb=" O SER R 320 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N CYS R 322 " --> pdb=" O THR O 319 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS O 321 " --> pdb=" O CYS R 322 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 325 through 330 removed outlier: 6.848A pdb=" N GLY P 326 " --> pdb=" O LEU Q 325 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN Q 327 " --> pdb=" O GLY P 326 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY N 326 " --> pdb=" O LEU P 325 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN P 327 " --> pdb=" O GLY N 326 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N LEU N 325 " --> pdb=" O GLY O 326 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N ILE O 328 " --> pdb=" O LEU N 325 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN N 327 " --> pdb=" O ILE O 328 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N HIS O 330 " --> pdb=" O ASN N 327 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS N 329 " --> pdb=" O HIS O 330 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N LEU O 325 " --> pdb=" O GLY R 326 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N ILE R 328 " --> pdb=" O LEU O 325 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN O 327 " --> pdb=" O ILE R 328 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N HIS R 330 " --> pdb=" O ASN O 327 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS O 329 " --> pdb=" O HIS R 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 336 through 340 removed outlier: 6.534A pdb=" N GLN N 336 " --> pdb=" O VAL O 337 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL O 339 " --> pdb=" O GLN N 336 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU N 338 " --> pdb=" O VAL O 339 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN O 336 " --> pdb=" O VAL R 337 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL R 339 " --> pdb=" O GLN O 336 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU O 338 " --> pdb=" O VAL R 339 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 343 through 346 removed outlier: 6.301A pdb=" N LYS N 343 " --> pdb=" O LEU O 344 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N PHE O 346 " --> pdb=" O LYS N 343 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP N 345 " --> pdb=" O PHE O 346 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS O 343 " --> pdb=" O LEU R 344 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE R 346 " --> pdb=" O LYS O 343 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP O 345 " --> pdb=" O PHE R 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 351 through 356 removed outlier: 6.816A pdb=" N SER P 356 " --> pdb=" O GLY Q 355 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER N 356 " --> pdb=" O GLY P 355 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN N 351 " --> pdb=" O SER O 352 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE O 354 " --> pdb=" O GLN N 351 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS N 353 " --> pdb=" O ILE O 354 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER O 356 " --> pdb=" O LYS N 353 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLY N 355 " --> pdb=" O SER O 356 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN O 351 " --> pdb=" O SER R 352 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ILE R 354 " --> pdb=" O GLN O 351 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LYS O 353 " --> pdb=" O ILE R 354 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER R 356 " --> pdb=" O LYS O 353 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY O 355 " --> pdb=" O SER R 356 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 359 through 362 removed outlier: 6.620A pdb=" N ASN P 359 " --> pdb=" O ILE Q 360 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N HIS Q 362 " --> pdb=" O ASN P 359 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR P 361 " --> pdb=" O HIS Q 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 369 through 377 removed outlier: 6.448A pdb=" N LYS N 369 " --> pdb=" O LYS O 370 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N GLU O 372 " --> pdb=" O LYS N 369 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE N 371 " --> pdb=" O GLU O 372 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N HIS O 374 " --> pdb=" O ILE N 371 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR N 373 " --> pdb=" O HIS O 374 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU O 376 " --> pdb=" O THR N 373 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS N 375 " --> pdb=" O LEU O 376 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE O 378 " --> pdb=" O LYS N 375 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR N 377 " --> pdb=" O PHE O 378 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS O 369 " --> pdb=" O LYS R 370 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLU R 372 " --> pdb=" O LYS O 369 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE O 371 " --> pdb=" O GLU R 372 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N HIS R 374 " --> pdb=" O ILE O 371 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR O 373 " --> pdb=" O HIS R 374 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU R 376 " --> pdb=" O THR O 373 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS O 375 " --> pdb=" O LEU R 376 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 5990 1.12 - 1.29: 960 1.29 - 1.46: 1656 1.46 - 1.63: 3224 1.63 - 1.80: 10 Bond restraints: 11840 Sorted by residual: bond pdb=" N ASP O 345 " pdb=" H ASP O 345 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ASP P 345 " pdb=" H ASP P 345 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ASP R 345 " pdb=" H ASP R 345 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASP R 348 " pdb=" H ASP R 348 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ILE R 371 " pdb=" H ILE R 371 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 11835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 17702 2.39 - 4.77: 2852 4.77 - 7.16: 960 7.16 - 9.54: 66 9.54 - 11.93: 10 Bond angle restraints: 21590 Sorted by residual: angle pdb=" CA ASP Q 348 " pdb=" CB ASP Q 348 " pdb=" CG ASP Q 348 " ideal model delta sigma weight residual 112.60 120.25 -7.65 1.00e+00 1.00e+00 5.85e+01 angle pdb=" CA ASP O 348 " pdb=" CB ASP O 348 " pdb=" CG ASP O 348 " ideal model delta sigma weight residual 112.60 120.22 -7.62 1.00e+00 1.00e+00 5.81e+01 angle pdb=" CA ASP N 348 " pdb=" CB ASP N 348 " pdb=" CG ASP N 348 " ideal model delta sigma weight residual 112.60 120.21 -7.61 1.00e+00 1.00e+00 5.79e+01 angle pdb=" CA ASP P 348 " pdb=" CB ASP P 348 " pdb=" CG ASP P 348 " ideal model delta sigma weight residual 112.60 120.20 -7.60 1.00e+00 1.00e+00 5.78e+01 angle pdb=" CA ASP R 348 " pdb=" CB ASP R 348 " pdb=" CG ASP R 348 " ideal model delta sigma weight residual 112.60 120.18 -7.58 1.00e+00 1.00e+00 5.74e+01 ... (remaining 21585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.80: 4617 13.80 - 27.59: 418 27.59 - 41.38: 130 41.38 - 55.17: 115 55.17 - 68.97: 160 Dihedral angle restraints: 5440 sinusoidal: 3110 harmonic: 2330 Sorted by residual: dihedral pdb=" CA LYS I 347 " pdb=" C LYS I 347 " pdb=" N ASP I 348 " pdb=" CA ASP I 348 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA LYS J 347 " pdb=" C LYS J 347 " pdb=" N ASP J 348 " pdb=" CA ASP J 348 " ideal model delta harmonic sigma weight residual 180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA LYS H 347 " pdb=" C LYS H 347 " pdb=" N ASP H 348 " pdb=" CA ASP H 348 " ideal model delta harmonic sigma weight residual -180.00 -152.29 -27.71 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 5437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 640 0.088 - 0.175: 226 0.175 - 0.263: 9 0.263 - 0.351: 0 0.351 - 0.438: 5 Chirality restraints: 880 Sorted by residual: chirality pdb=" CA ASP G 348 " pdb=" N ASP G 348 " pdb=" C ASP G 348 " pdb=" CB ASP G 348 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA ASP F 348 " pdb=" N ASP F 348 " pdb=" C ASP F 348 " pdb=" CB ASP F 348 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CA ASP H 348 " pdb=" N ASP H 348 " pdb=" C ASP H 348 " pdb=" CB ASP H 348 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.74e+00 ... (remaining 877 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 310 " 0.080 2.00e-02 2.50e+03 3.50e-02 3.68e+01 pdb=" CG TYR Q 310 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 310 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 310 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 310 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR Q 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR Q 310 " 0.069 2.00e-02 2.50e+03 pdb=" HD1 TYR Q 310 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR Q 310 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 TYR Q 310 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 TYR Q 310 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 310 " 0.080 2.00e-02 2.50e+03 3.49e-02 3.65e+01 pdb=" CG TYR O 310 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR O 310 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR O 310 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR O 310 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR O 310 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR O 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR O 310 " 0.069 2.00e-02 2.50e+03 pdb=" HD1 TYR O 310 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR O 310 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR O 310 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR O 310 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 310 " 0.080 2.00e-02 2.50e+03 3.49e-02 3.65e+01 pdb=" CG TYR R 310 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR R 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR R 310 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR R 310 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR R 310 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR R 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 310 " 0.069 2.00e-02 2.50e+03 pdb=" HD1 TYR R 310 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR R 310 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 TYR R 310 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR R 310 " 0.001 2.00e-02 2.50e+03 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 838 2.15 - 2.76: 19761 2.76 - 3.38: 32059 3.38 - 3.99: 45494 3.99 - 4.60: 62368 Nonbonded interactions: 160520 Sorted by model distance: nonbonded pdb=" OD1 ASP O 314 " pdb=" HG SER O 316 " model vdw 1.542 2.450 nonbonded pdb=" OD1 ASP P 314 " pdb=" HG SER P 316 " model vdw 1.542 2.450 nonbonded pdb=" OD1 ASP N 314 " pdb=" HG SER N 316 " model vdw 1.542 2.450 nonbonded pdb=" OD1 ASP R 314 " pdb=" HG SER R 316 " model vdw 1.542 2.450 nonbonded pdb=" OD1 ASP Q 314 " pdb=" HG SER Q 316 " model vdw 1.542 2.450 ... (remaining 160515 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 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.060 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.930 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 : 0.011 0.040 5840 Z= 0.697 Angle : 1.961 7.647 7820 Z= 1.299 Chirality : 0.084 0.438 880 Planarity : 0.010 0.042 1000 Dihedral : 11.171 57.605 2250 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.76 % Allowed : 1.06 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.26), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 349 TYR 0.075 0.030 TYR Q 310 PHE 0.019 0.007 PHE P 346 HIS 0.006 0.002 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.01090 ( 5840) covalent geometry : angle 1.96083 ( 7820) hydrogen bonds : bond 0.09781 ( 138) hydrogen bonds : angle 7.43443 ( 414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 0.341 Fit side-chains REVERT: F 340 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8226 (tmtm) REVERT: F 343 LYS cc_start: 0.8549 (mttp) cc_final: 0.8123 (mtpp) REVERT: F 375 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8253 (ttpt) REVERT: N 338 GLU cc_start: 0.8589 (tt0) cc_final: 0.8351 (tm-30) REVERT: N 340 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8148 (tmtm) REVERT: N 342 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8094 (mt-10) REVERT: N 343 LYS cc_start: 0.8546 (mttp) cc_final: 0.8259 (mmtt) REVERT: G 340 LYS cc_start: 0.8485 (ttmm) cc_final: 0.8111 (tmtm) REVERT: G 343 LYS cc_start: 0.8551 (mttp) cc_final: 0.7916 (mtpp) REVERT: O 317 LYS cc_start: 0.8404 (mttm) cc_final: 0.8018 (mtpt) REVERT: H 340 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8199 (tmtm) REVERT: H 343 LYS cc_start: 0.8485 (mttp) cc_final: 0.7897 (mtpp) REVERT: H 348 ASP cc_start: 0.8331 (p0) cc_final: 0.8040 (p0) REVERT: H 351 GLN cc_start: 0.8482 (mt0) cc_final: 0.8211 (mt0) REVERT: H 375 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8269 (ttmm) REVERT: P 317 LYS cc_start: 0.8349 (mttm) cc_final: 0.7972 (mtpt) REVERT: P 338 GLU cc_start: 0.8623 (tt0) cc_final: 0.8287 (tm-30) REVERT: P 340 LYS cc_start: 0.8497 (mtpp) cc_final: 0.8026 (tttm) REVERT: P 343 LYS cc_start: 0.8533 (mttp) cc_final: 0.7927 (mtpp) REVERT: P 351 GLN cc_start: 0.8562 (mt0) cc_final: 0.8347 (mt0) REVERT: I 321 LYS cc_start: 0.8831 (mttp) cc_final: 0.8625 (mttm) REVERT: I 340 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8115 (tptp) REVERT: I 343 LYS cc_start: 0.8510 (mttp) cc_final: 0.7879 (mtpp) REVERT: I 347 LYS cc_start: 0.8137 (mttp) cc_final: 0.7786 (mttm) REVERT: Q 317 LYS cc_start: 0.8488 (mttm) cc_final: 0.7972 (mtpt) REVERT: Q 321 LYS cc_start: 0.8863 (mttp) cc_final: 0.8618 (mttm) REVERT: Q 338 GLU cc_start: 0.8666 (tt0) cc_final: 0.8406 (tm-30) REVERT: Q 340 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8117 (ttpp) REVERT: Q 343 LYS cc_start: 0.8517 (mttp) cc_final: 0.7771 (mtpp) REVERT: Q 348 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7740 (t70) REVERT: J 314 ASP cc_start: 0.8753 (t0) cc_final: 0.8383 (t0) REVERT: J 340 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8438 (tmtt) REVERT: J 343 LYS cc_start: 0.8607 (mttp) cc_final: 0.8129 (mtpp) REVERT: J 375 LYS cc_start: 0.8940 (ttpt) cc_final: 0.8717 (ttmm) REVERT: R 317 LYS cc_start: 0.8733 (mttm) cc_final: 0.8378 (mtpt) REVERT: R 340 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8117 (mtmm) REVERT: R 343 LYS cc_start: 0.8954 (mttp) cc_final: 0.8342 (mtpp) outliers start: 5 outliers final: 4 residues processed: 184 average time/residue: 1.8944 time to fit residues: 358.9001 Evaluate side-chains 149 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 348 ASP Chi-restraints excluded: chain O residue 348 ASP Chi-restraints excluded: chain P residue 348 ASP Chi-restraints excluded: chain Q residue 348 ASP Chi-restraints excluded: chain R residue 348 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN I 351 GLN Q 351 GLN J 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.118200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.099580 restraints weight = 21521.018| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.89 r_work: 0.3595 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5840 Z= 0.125 Angle : 0.621 5.892 7820 Z= 0.334 Chirality : 0.051 0.131 880 Planarity : 0.003 0.022 1000 Dihedral : 7.049 21.830 790 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.61 % Allowed : 6.97 % Favored : 92.42 % 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: -1.71 (0.25), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 349 TYR 0.012 0.002 TYR H 310 PHE 0.007 0.001 PHE P 346 HIS 0.009 0.002 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5840) covalent geometry : angle 0.62132 ( 7820) hydrogen bonds : bond 0.02660 ( 138) hydrogen bonds : angle 4.74952 ( 414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.336 Fit side-chains REVERT: F 340 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8193 (tmtm) REVERT: F 375 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8494 (ttmm) REVERT: N 338 GLU cc_start: 0.8862 (tt0) cc_final: 0.8513 (tm-30) REVERT: N 340 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8239 (tmtm) REVERT: G 340 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8176 (tmtm) REVERT: G 343 LYS cc_start: 0.8727 (mttp) cc_final: 0.8110 (mtpp) REVERT: H 340 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8183 (tttm) REVERT: H 351 GLN cc_start: 0.8311 (mt0) cc_final: 0.7978 (mt0) REVERT: H 375 LYS cc_start: 0.8595 (ttpt) cc_final: 0.8305 (ttmt) REVERT: P 317 LYS cc_start: 0.8411 (mttm) cc_final: 0.8119 (mtmt) REVERT: P 338 GLU cc_start: 0.8852 (tt0) cc_final: 0.8619 (tt0) REVERT: P 340 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8155 (tttt) REVERT: P 343 LYS cc_start: 0.8849 (mttp) cc_final: 0.8262 (mtpp) REVERT: P 351 GLN cc_start: 0.8438 (mt0) cc_final: 0.8196 (mt0) REVERT: P 372 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: I 321 LYS cc_start: 0.8714 (mttp) cc_final: 0.8428 (mttp) REVERT: I 338 GLU cc_start: 0.8784 (tt0) cc_final: 0.8469 (tm-30) REVERT: I 343 LYS cc_start: 0.8712 (mttp) cc_final: 0.8101 (mtpp) REVERT: Q 317 LYS cc_start: 0.8597 (mttm) cc_final: 0.8199 (mtpt) REVERT: Q 321 LYS cc_start: 0.8709 (mttp) cc_final: 0.8398 (mttm) REVERT: Q 340 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8284 (ttpp) REVERT: Q 343 LYS cc_start: 0.8855 (mttp) cc_final: 0.8130 (mtpp) REVERT: Q 344 LEU cc_start: 0.9454 (mp) cc_final: 0.9035 (mp) REVERT: J 340 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8393 (tmmt) REVERT: J 343 LYS cc_start: 0.8674 (mttp) cc_final: 0.8229 (mtpp) REVERT: R 314 ASP cc_start: 0.8382 (t70) cc_final: 0.7758 (t0) REVERT: R 343 LYS cc_start: 0.8989 (mttp) cc_final: 0.8413 (mtpp) outliers start: 4 outliers final: 1 residues processed: 142 average time/residue: 2.0517 time to fit residues: 299.3701 Evaluate side-chains 115 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 372 GLU Chi-restraints excluded: chain I residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN G 307 GLN G 351 GLN O 351 GLN Q 351 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.115868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.096791 restraints weight = 20991.914| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.90 r_work: 0.3529 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5840 Z= 0.131 Angle : 0.577 6.374 7820 Z= 0.304 Chirality : 0.051 0.128 880 Planarity : 0.004 0.036 1000 Dihedral : 6.265 17.838 780 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.61 % Allowed : 12.27 % Favored : 87.12 % 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: -1.88 (0.25), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 349 TYR 0.011 0.002 TYR H 310 PHE 0.005 0.001 PHE J 378 HIS 0.007 0.002 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5840) covalent geometry : angle 0.57738 ( 7820) hydrogen bonds : bond 0.02414 ( 138) hydrogen bonds : angle 4.22486 ( 414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.358 Fit side-chains REVERT: F 340 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8155 (tmtm) REVERT: F 375 LYS cc_start: 0.8831 (ttpt) cc_final: 0.8580 (ttpt) REVERT: N 340 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8184 (tmtm) REVERT: G 340 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8178 (tmtm) REVERT: H 340 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8094 (tttm) REVERT: P 317 LYS cc_start: 0.8343 (mttm) cc_final: 0.8059 (mtmt) REVERT: P 338 GLU cc_start: 0.8787 (tt0) cc_final: 0.8444 (tm-30) REVERT: P 340 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8078 (tttm) REVERT: P 343 LYS cc_start: 0.8807 (mttp) cc_final: 0.8175 (mtpp) REVERT: P 372 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8507 (mt-10) REVERT: I 338 GLU cc_start: 0.8733 (tt0) cc_final: 0.8494 (tm-30) REVERT: Q 317 LYS cc_start: 0.8510 (mttm) cc_final: 0.8083 (mtpt) REVERT: Q 321 LYS cc_start: 0.8825 (mttp) cc_final: 0.8490 (mttp) REVERT: Q 340 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8247 (ttpp) REVERT: Q 343 LYS cc_start: 0.8773 (mttp) cc_final: 0.7975 (mtpp) REVERT: J 314 ASP cc_start: 0.8784 (t0) cc_final: 0.8547 (t0) REVERT: J 340 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8376 (tmtt) REVERT: J 343 LYS cc_start: 0.8666 (mttp) cc_final: 0.8172 (mtpp) REVERT: R 314 ASP cc_start: 0.8587 (t70) cc_final: 0.7660 (t0) REVERT: R 340 LYS cc_start: 0.8627 (mtpm) cc_final: 0.8135 (mtmm) REVERT: R 343 LYS cc_start: 0.8881 (mttp) cc_final: 0.8317 (mtpp) outliers start: 4 outliers final: 2 residues processed: 120 average time/residue: 1.9164 time to fit residues: 236.8311 Evaluate side-chains 108 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 372 GLU Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain P residue 372 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN G 307 GLN Q 351 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.119067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.099079 restraints weight = 20891.172| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.91 r_work: 0.3572 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5840 Z= 0.099 Angle : 0.512 4.930 7820 Z= 0.271 Chirality : 0.050 0.125 880 Planarity : 0.004 0.028 1000 Dihedral : 5.672 15.379 780 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.45 % Allowed : 13.18 % Favored : 86.36 % 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: -1.95 (0.26), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 349 TYR 0.008 0.002 TYR H 310 PHE 0.004 0.001 PHE I 346 HIS 0.005 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 5840) covalent geometry : angle 0.51241 ( 7820) hydrogen bonds : bond 0.01962 ( 138) hydrogen bonds : angle 3.89569 ( 414) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: F 340 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8125 (tmtm) REVERT: F 375 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8597 (ttpt) REVERT: N 340 LYS cc_start: 0.8501 (mtpp) cc_final: 0.8140 (tmtm) REVERT: N 372 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: G 340 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8197 (tmtm) REVERT: G 342 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: H 340 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8035 (tttm) REVERT: P 317 LYS cc_start: 0.8296 (mttm) cc_final: 0.8030 (mtmt) REVERT: P 338 GLU cc_start: 0.8707 (tt0) cc_final: 0.8394 (tm-30) REVERT: P 340 LYS cc_start: 0.8379 (mtpp) cc_final: 0.8043 (tttm) REVERT: P 343 LYS cc_start: 0.8782 (mttp) cc_final: 0.8160 (mtpp) REVERT: P 372 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8491 (mt-10) REVERT: I 338 GLU cc_start: 0.8777 (tt0) cc_final: 0.8522 (tm-30) REVERT: Q 317 LYS cc_start: 0.8348 (mttm) cc_final: 0.7954 (mtpt) REVERT: Q 321 LYS cc_start: 0.8767 (mttp) cc_final: 0.8449 (mttm) REVERT: Q 340 LYS cc_start: 0.8463 (mtpp) cc_final: 0.8218 (ttpp) REVERT: Q 343 LYS cc_start: 0.8764 (mttp) cc_final: 0.7978 (mtpp) REVERT: J 314 ASP cc_start: 0.8783 (t0) cc_final: 0.8477 (t0) REVERT: J 340 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8369 (tmtt) REVERT: J 343 LYS cc_start: 0.8579 (mttp) cc_final: 0.8072 (mtpp) REVERT: R 314 ASP cc_start: 0.8569 (t70) cc_final: 0.8036 (t0) REVERT: R 343 LYS cc_start: 0.8631 (mttp) cc_final: 0.8117 (mtpp) outliers start: 3 outliers final: 0 residues processed: 113 average time/residue: 1.9077 time to fit residues: 222.0581 Evaluate side-chains 106 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 372 GLU Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain P residue 372 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 44 optimal weight: 0.0670 chunk 40 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN G 307 GLN Q 351 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.114639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.093702 restraints weight = 20904.624| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.89 r_work: 0.3486 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5840 Z= 0.216 Angle : 0.595 5.097 7820 Z= 0.315 Chirality : 0.050 0.128 880 Planarity : 0.004 0.036 1000 Dihedral : 6.062 18.032 780 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.91 % Allowed : 14.24 % Favored : 84.85 % 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 (0.26), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 349 TYR 0.013 0.003 TYR P 310 PHE 0.006 0.001 PHE H 378 HIS 0.007 0.002 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 5840) covalent geometry : angle 0.59535 ( 7820) hydrogen bonds : bond 0.02600 ( 138) hydrogen bonds : angle 4.20292 ( 414) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.339 Fit side-chains REVERT: F 340 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8142 (tmtm) REVERT: F 375 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8624 (ttpt) REVERT: N 372 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: G 340 LYS cc_start: 0.8662 (ttmm) cc_final: 0.8241 (tmtm) REVERT: G 342 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: H 340 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8065 (tttm) REVERT: P 338 GLU cc_start: 0.8711 (tt0) cc_final: 0.8396 (tm-30) REVERT: P 340 LYS cc_start: 0.8478 (mtpp) cc_final: 0.8073 (tttm) REVERT: P 343 LYS cc_start: 0.8697 (mttp) cc_final: 0.8055 (mtpp) REVERT: P 372 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8565 (mt-10) REVERT: I 338 GLU cc_start: 0.8726 (tt0) cc_final: 0.8441 (tm-30) REVERT: Q 317 LYS cc_start: 0.8380 (mttm) cc_final: 0.7955 (mtpt) REVERT: Q 321 LYS cc_start: 0.8740 (mttp) cc_final: 0.8401 (mttp) REVERT: Q 340 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8206 (ttpp) REVERT: Q 343 LYS cc_start: 0.8769 (mttp) cc_final: 0.7949 (mtpp) REVERT: J 314 ASP cc_start: 0.8973 (t0) cc_final: 0.8708 (t0) REVERT: J 340 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8387 (tmtt) REVERT: J 343 LYS cc_start: 0.8542 (mttp) cc_final: 0.8094 (mtpp) REVERT: R 314 ASP cc_start: 0.8716 (t70) cc_final: 0.8321 (t0) REVERT: R 340 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8143 (mtmm) outliers start: 6 outliers final: 1 residues processed: 112 average time/residue: 1.7699 time to fit residues: 204.3142 Evaluate side-chains 106 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 372 GLU Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain P residue 372 GLU Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN Q 351 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 GLN ** R 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.114950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.094281 restraints weight = 20950.073| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.90 r_work: 0.3498 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5840 Z= 0.186 Angle : 0.569 4.774 7820 Z= 0.301 Chirality : 0.050 0.127 880 Planarity : 0.004 0.040 1000 Dihedral : 5.957 17.372 780 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.91 % Allowed : 14.85 % Favored : 84.24 % 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 (0.26), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 349 TYR 0.012 0.002 TYR Q 310 PHE 0.005 0.001 PHE H 378 HIS 0.006 0.001 HIS Q 330 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 5840) covalent geometry : angle 0.56882 ( 7820) hydrogen bonds : bond 0.02478 ( 138) hydrogen bonds : angle 4.18450 ( 414) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.368 Fit side-chains REVERT: F 340 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8078 (tmtm) REVERT: F 375 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8666 (ttpt) REVERT: N 372 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: G 340 LYS cc_start: 0.8684 (ttmm) cc_final: 0.8241 (tmtm) REVERT: G 342 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: H 315 LEU cc_start: 0.9020 (mm) cc_final: 0.8813 (mt) REVERT: H 340 LYS cc_start: 0.8534 (ttmm) cc_final: 0.7987 (tttm) REVERT: P 338 GLU cc_start: 0.8709 (tt0) cc_final: 0.8405 (tm-30) REVERT: P 340 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8079 (tttm) REVERT: P 343 LYS cc_start: 0.8758 (mttp) cc_final: 0.8118 (mtpp) REVERT: P 372 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8545 (mt-10) REVERT: I 338 GLU cc_start: 0.8739 (tt0) cc_final: 0.8446 (tm-30) REVERT: I 349 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7151 (mtp85) REVERT: Q 317 LYS cc_start: 0.8400 (mttm) cc_final: 0.7973 (mtpt) REVERT: Q 321 LYS cc_start: 0.8768 (mttp) cc_final: 0.8554 (mttm) REVERT: Q 340 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8238 (ttpp) REVERT: Q 343 LYS cc_start: 0.8740 (mttp) cc_final: 0.7936 (mtpp) REVERT: J 340 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8340 (ttpp) REVERT: J 343 LYS cc_start: 0.8546 (mttp) cc_final: 0.8062 (mtpp) REVERT: R 314 ASP cc_start: 0.8731 (t70) cc_final: 0.8373 (t0) outliers start: 6 outliers final: 2 residues processed: 108 average time/residue: 1.7859 time to fit residues: 199.1183 Evaluate side-chains 104 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 372 GLU Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain P residue 372 GLU Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain Q residue 348 ASP Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN Q 351 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 330 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 = 0.3958 r_free = 0.3958 target = 0.119111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.099061 restraints weight = 20884.691| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.91 r_work: 0.3578 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5840 Z= 0.086 Angle : 0.503 4.944 7820 Z= 0.260 Chirality : 0.050 0.126 880 Planarity : 0.004 0.033 1000 Dihedral : 5.340 14.407 780 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.76 % Allowed : 14.70 % Favored : 84.55 % 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 (0.26), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 349 TYR 0.007 0.001 TYR H 310 PHE 0.003 0.001 PHE O 346 HIS 0.004 0.001 HIS P 330 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 5840) covalent geometry : angle 0.50313 ( 7820) hydrogen bonds : bond 0.01823 ( 138) hydrogen bonds : angle 3.80257 ( 414) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.377 Fit side-chains REVERT: F 340 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8073 (tmtm) REVERT: F 375 LYS cc_start: 0.8852 (ttpt) cc_final: 0.8616 (ttpt) REVERT: N 372 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: G 340 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8268 (tmtm) REVERT: G 342 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: H 340 LYS cc_start: 0.8500 (ttmm) cc_final: 0.7979 (tttm) REVERT: H 347 LYS cc_start: 0.7710 (mttm) cc_final: 0.7467 (mptt) REVERT: P 338 GLU cc_start: 0.8687 (tt0) cc_final: 0.8409 (tm-30) REVERT: P 340 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8064 (tttm) REVERT: P 343 LYS cc_start: 0.8783 (mttp) cc_final: 0.8176 (mtpp) REVERT: P 372 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: I 338 GLU cc_start: 0.8777 (tt0) cc_final: 0.8506 (tm-30) REVERT: I 349 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7101 (mtp85) REVERT: Q 317 LYS cc_start: 0.8345 (mttm) cc_final: 0.7942 (mtpt) REVERT: Q 340 LYS cc_start: 0.8470 (mtpp) cc_final: 0.8227 (ttpp) REVERT: Q 343 LYS cc_start: 0.8769 (mttp) cc_final: 0.7914 (mtpp) REVERT: J 314 ASP cc_start: 0.8743 (t0) cc_final: 0.8501 (t0) REVERT: J 340 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8316 (ttpp) REVERT: J 343 LYS cc_start: 0.8473 (mttp) cc_final: 0.8005 (mtpp) REVERT: R 314 ASP cc_start: 0.8617 (t70) cc_final: 0.8199 (t0) outliers start: 5 outliers final: 1 residues processed: 106 average time/residue: 2.0035 time to fit residues: 218.5836 Evaluate side-chains 105 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 372 GLU Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain O residue 348 ASP Chi-restraints excluded: chain P residue 372 GLU Chi-restraints excluded: chain I residue 349 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 0.0770 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN G 307 GLN Q 351 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 GLN ** R 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.117501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.097373 restraints weight = 20779.549| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.89 r_work: 0.3554 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5840 Z= 0.117 Angle : 0.515 4.657 7820 Z= 0.270 Chirality : 0.050 0.138 880 Planarity : 0.004 0.034 1000 Dihedral : 5.317 14.691 780 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.76 % Allowed : 15.00 % Favored : 84.24 % 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 (0.26), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 349 TYR 0.010 0.002 TYR Q 310 PHE 0.004 0.001 PHE F 378 HIS 0.004 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5840) covalent geometry : angle 0.51472 ( 7820) hydrogen bonds : bond 0.02034 ( 138) hydrogen bonds : angle 3.84580 ( 414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.393 Fit side-chains REVERT: F 340 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8062 (tmtm) REVERT: F 375 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8640 (ttpt) REVERT: N 372 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: G 340 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8254 (tmtm) REVERT: G 342 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: H 340 LYS cc_start: 0.8491 (ttmm) cc_final: 0.7954 (tttm) REVERT: H 347 LYS cc_start: 0.7733 (mttm) cc_final: 0.7267 (mptt) REVERT: H 349 ARG cc_start: 0.7481 (mtp85) cc_final: 0.7230 (mmm-85) REVERT: P 338 GLU cc_start: 0.8687 (tt0) cc_final: 0.8409 (tm-30) REVERT: P 340 LYS cc_start: 0.8434 (mtpp) cc_final: 0.8076 (tttm) REVERT: P 343 LYS cc_start: 0.8764 (mttp) cc_final: 0.8164 (mtpp) REVERT: P 372 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: I 338 GLU cc_start: 0.8776 (tt0) cc_final: 0.8504 (tm-30) REVERT: I 349 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7102 (mtp85) REVERT: Q 311 LYS cc_start: 0.8804 (mtpp) cc_final: 0.7896 (mmtp) REVERT: Q 317 LYS cc_start: 0.8358 (mttm) cc_final: 0.8002 (mtpt) REVERT: Q 340 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8225 (ttpp) REVERT: Q 343 LYS cc_start: 0.8757 (mttp) cc_final: 0.7993 (mtpp) REVERT: J 340 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8310 (ttpp) REVERT: J 343 LYS cc_start: 0.8470 (mttp) cc_final: 0.8003 (mtpp) REVERT: R 314 ASP cc_start: 0.8688 (t70) cc_final: 0.8248 (t0) outliers start: 5 outliers final: 1 residues processed: 101 average time/residue: 1.9558 time to fit residues: 203.4455 Evaluate side-chains 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 372 GLU Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain P residue 372 GLU Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN G 307 GLN Q 351 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.115668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.095357 restraints weight = 20720.759| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.87 r_work: 0.3520 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5840 Z= 0.159 Angle : 0.543 4.673 7820 Z= 0.286 Chirality : 0.050 0.132 880 Planarity : 0.004 0.036 1000 Dihedral : 5.561 15.503 780 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.76 % Allowed : 15.30 % Favored : 83.94 % 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: -2.05 (0.26), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 349 TYR 0.011 0.002 TYR Q 310 PHE 0.005 0.001 PHE O 346 HIS 0.005 0.001 HIS Q 330 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5840) covalent geometry : angle 0.54321 ( 7820) hydrogen bonds : bond 0.02314 ( 138) hydrogen bonds : angle 4.01934 ( 414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.342 Fit side-chains REVERT: F 340 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8060 (tmtm) REVERT: F 375 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8658 (ttpt) REVERT: N 372 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: G 340 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8273 (tmtm) REVERT: H 340 LYS cc_start: 0.8505 (ttmm) cc_final: 0.7958 (tttm) REVERT: H 347 LYS cc_start: 0.7779 (mttm) cc_final: 0.7557 (mptt) REVERT: H 349 ARG cc_start: 0.7456 (mtp85) cc_final: 0.7220 (mmm-85) REVERT: P 338 GLU cc_start: 0.8702 (tt0) cc_final: 0.8407 (tm-30) REVERT: P 340 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8060 (tttm) REVERT: P 343 LYS cc_start: 0.8769 (mttp) cc_final: 0.8139 (mtpp) REVERT: P 372 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8560 (mt-10) REVERT: I 338 GLU cc_start: 0.8710 (tt0) cc_final: 0.8420 (tm-30) REVERT: I 349 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7135 (mtp85) REVERT: Q 311 LYS cc_start: 0.8812 (mtpp) cc_final: 0.7884 (mmtp) REVERT: Q 340 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8229 (ttpp) REVERT: Q 343 LYS cc_start: 0.8730 (mttp) cc_final: 0.7938 (mtpp) REVERT: J 340 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8325 (ttpp) outliers start: 5 outliers final: 2 residues processed: 102 average time/residue: 2.0029 time to fit residues: 210.2858 Evaluate side-chains 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 372 GLU Chi-restraints excluded: chain O residue 348 ASP Chi-restraints excluded: chain P residue 372 GLU Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN Q 351 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 GLN ** R 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.116276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.095822 restraints weight = 20814.975| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.89 r_work: 0.3530 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5840 Z= 0.148 Angle : 0.539 4.570 7820 Z= 0.282 Chirality : 0.050 0.133 880 Planarity : 0.004 0.037 1000 Dihedral : 5.533 15.395 780 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.91 % Allowed : 15.76 % Favored : 83.33 % 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 (0.26), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 349 TYR 0.010 0.002 TYR H 310 PHE 0.004 0.001 PHE H 378 HIS 0.005 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 5840) covalent geometry : angle 0.53870 ( 7820) hydrogen bonds : bond 0.02276 ( 138) hydrogen bonds : angle 4.03284 ( 414) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.364 Fit side-chains REVERT: F 340 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8076 (tmtm) REVERT: F 375 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8664 (ttpt) REVERT: N 372 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: G 340 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8282 (tmtm) REVERT: H 340 LYS cc_start: 0.8524 (ttmm) cc_final: 0.7971 (tttm) REVERT: H 347 LYS cc_start: 0.7769 (mttm) cc_final: 0.7323 (mptt) REVERT: H 349 ARG cc_start: 0.7488 (mtp85) cc_final: 0.7264 (mmm-85) REVERT: P 338 GLU cc_start: 0.8709 (tt0) cc_final: 0.8422 (tm-30) REVERT: P 340 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8127 (tptt) REVERT: P 343 LYS cc_start: 0.8769 (mttp) cc_final: 0.8146 (mtpp) REVERT: P 372 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: I 338 GLU cc_start: 0.8711 (tt0) cc_final: 0.8424 (tm-30) REVERT: I 349 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7186 (mtp85) REVERT: Q 311 LYS cc_start: 0.8800 (mtpp) cc_final: 0.7876 (mmtp) REVERT: Q 340 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8250 (ttpp) REVERT: Q 343 LYS cc_start: 0.8743 (mttp) cc_final: 0.7950 (mtpp) REVERT: J 340 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8332 (ttpp) REVERT: R 379 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7821 (mpt-90) outliers start: 6 outliers final: 2 residues processed: 99 average time/residue: 2.0260 time to fit residues: 206.3934 Evaluate side-chains 101 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 372 GLU Chi-restraints excluded: chain O residue 348 ASP Chi-restraints excluded: chain P residue 372 GLU Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN Q 351 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 330 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 = 0.3929 r_free = 0.3929 target = 0.116647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096290 restraints weight = 20807.766| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.89 r_work: 0.3538 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5840 Z= 0.129 Angle : 0.523 4.552 7820 Z= 0.274 Chirality : 0.050 0.136 880 Planarity : 0.004 0.037 1000 Dihedral : 5.472 14.952 780 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.61 % Allowed : 16.06 % Favored : 83.33 % 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 (0.26), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 349 TYR 0.009 0.002 TYR H 310 PHE 0.004 0.001 PHE H 378 HIS 0.005 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5840) covalent geometry : angle 0.52331 ( 7820) hydrogen bonds : bond 0.02161 ( 138) hydrogen bonds : angle 3.98026 ( 414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5532.18 seconds wall clock time: 94 minutes 28.64 seconds (5668.64 seconds total)