Starting phenix.real_space_refine on Mon May 4 04:04:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7b_70193/05_2026/9o7b_70193.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7b_70193/05_2026/9o7b_70193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o7b_70193/05_2026/9o7b_70193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7b_70193/05_2026/9o7b_70193.map" model { file = "/net/cci-nas-00/data/ceres_data/9o7b_70193/05_2026/9o7b_70193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7b_70193/05_2026/9o7b_70193.cif" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 15 5.16 5 C 5400 2.51 5 N 1590 2.21 5 O 1620 1.98 5 H 9000 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 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: 17625 Number of models: 1 Model: "" Number of chains: 15 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: "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: "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: "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} Chain: "S" 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: "d" 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: "e" 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: "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: "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: "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: "W" 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: "X" 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: "Y" 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: "Z" 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: "a" 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: 3.79, per 1000 atoms: 0.22 Number of scatterers: 17625 At special positions: 0 Unit cell: (144.325, 133.934, 49.6478, 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 15 16.00 O 1620 8.00 N 1590 7.00 C 5400 6.00 H 9000 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: 1.31 Conformation dependent library (CDL) restraints added in 1.8 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 25 sheets defined 0.0% alpha, 42.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'Q' and resid 306 through 310 removed outlier: 6.464A pdb=" N GLN O 307 " --> pdb=" O ILE R 308 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR R 310 " --> pdb=" O GLN O 307 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL O 309 " --> pdb=" O TYR R 310 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN R 307 " --> pdb=" O ILE S 308 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N TYR S 310 " --> pdb=" O GLN R 307 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL R 309 " --> pdb=" O TYR S 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 317 through 321 removed outlier: 6.281A pdb=" N VAL P 318 " --> pdb=" O THR Q 319 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LYS Q 321 " --> pdb=" O VAL P 318 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER P 320 " --> pdb=" O LYS Q 321 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL O 318 " --> pdb=" O THR P 319 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N LYS P 321 " --> pdb=" O VAL O 318 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER O 320 " --> pdb=" O LYS P 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 325 through 330 removed outlier: 5.759A pdb=" N GLY P 326 " --> pdb=" O ASN Q 327 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N HIS Q 329 " --> pdb=" O GLY P 326 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE P 328 " --> pdb=" O HIS Q 329 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLY O 326 " --> pdb=" O ASN P 327 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N HIS P 329 " --> pdb=" O GLY O 326 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE O 328 " --> pdb=" O HIS P 329 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY R 326 " --> pdb=" O LEU O 325 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN O 327 " --> pdb=" O GLY R 326 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY S 326 " --> pdb=" O LEU R 325 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN R 327 " --> pdb=" O GLY S 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 336 through 340 removed outlier: 6.318A pdb=" N VAL P 337 " --> pdb=" O GLU Q 338 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LYS Q 340 " --> pdb=" O VAL P 337 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL P 339 " --> pdb=" O LYS Q 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Q' and resid 344 through 356 removed outlier: 8.859A pdb=" N ASP P 345 " --> pdb=" O PHE Q 346 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N ASP Q 348 " --> pdb=" O ASP P 345 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS P 347 " --> pdb=" O ASP Q 348 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL Q 350 " --> pdb=" O LYS P 347 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ARG P 349 " --> pdb=" O VAL Q 350 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N SER Q 352 " --> pdb=" O ARG P 349 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N GLN P 351 " --> pdb=" O SER Q 352 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N ILE Q 354 " --> pdb=" O GLN P 351 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N LYS P 353 " --> pdb=" O ILE Q 354 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N SER Q 356 " --> pdb=" O LYS P 353 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY P 355 " --> pdb=" O SER Q 356 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N ASP O 345 " --> pdb=" O PHE P 346 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ASP P 348 " --> pdb=" O ASP O 345 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LYS O 347 " --> pdb=" O ASP P 348 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL P 350 " --> pdb=" O LYS O 347 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ARG O 349 " --> pdb=" O VAL P 350 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N SER P 352 " --> pdb=" O ARG O 349 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N GLN O 351 " --> pdb=" O SER P 352 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N ILE P 354 " --> pdb=" O GLN O 351 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N LYS O 353 " --> pdb=" O ILE P 354 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N SER P 356 " --> pdb=" O LYS O 353 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY O 355 " --> pdb=" O SER P 356 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP R 345 " --> pdb=" O LEU O 344 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE O 346 " --> pdb=" O ASP R 345 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS R 347 " --> pdb=" O PHE O 346 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL O 350 " --> pdb=" O ARG R 349 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLN R 351 " --> pdb=" O VAL O 350 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER O 352 " --> pdb=" O GLN R 351 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS R 353 " --> pdb=" O SER O 352 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE O 354 " --> pdb=" O LYS R 353 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY R 355 " --> pdb=" O ILE O 354 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP S 345 " --> pdb=" O LEU R 344 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE R 346 " --> pdb=" O ASP S 345 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS S 347 " --> pdb=" O PHE R 346 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL R 350 " --> pdb=" O ARG S 349 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN S 351 " --> pdb=" O VAL R 350 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER R 352 " --> pdb=" O GLN S 351 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS S 353 " --> pdb=" O SER R 352 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE R 354 " --> pdb=" O LYS S 353 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY S 355 " --> pdb=" O ILE R 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 359 through 361 removed outlier: 6.619A pdb=" N ASN O 359 " --> pdb=" O ILE P 360 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE O 360 " --> pdb=" O THR R 361 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE R 360 " --> pdb=" O THR S 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 369 through 371 removed outlier: 6.399A pdb=" N LYS P 370 " --> pdb=" O ILE Q 371 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS O 370 " --> pdb=" O ILE P 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 374 through 378 removed outlier: 6.562A pdb=" N HIS O 374 " --> pdb=" O LYS P 375 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N THR P 377 " --> pdb=" O HIS O 374 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU O 376 " --> pdb=" O THR P 377 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS O 375 " --> pdb=" O LEU R 376 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE R 378 " --> pdb=" O LYS O 375 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR O 377 " --> pdb=" O PHE R 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 306 through 310 removed outlier: 6.532A pdb=" N GLN d 307 " --> pdb=" O ILE g 308 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR g 310 " --> pdb=" O GLN d 307 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL d 309 " --> pdb=" O TYR g 310 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLN g 307 " --> pdb=" O ILE h 308 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR h 310 " --> pdb=" O GLN g 307 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL g 309 " --> pdb=" O TYR h 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 318 through 321 removed outlier: 6.447A pdb=" N VAL e 318 " --> pdb=" O THR f 319 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N LYS f 321 " --> pdb=" O VAL e 318 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER e 320 " --> pdb=" O LYS f 321 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL d 318 " --> pdb=" O THR e 319 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LYS e 321 " --> pdb=" O VAL d 318 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER d 320 " --> pdb=" O LYS e 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 328 through 330 removed outlier: 6.658A pdb=" N HIS d 329 " --> pdb=" O HIS g 330 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N HIS g 329 " --> pdb=" O HIS h 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 336 through 340 removed outlier: 6.398A pdb=" N VAL e 337 " --> pdb=" O GLU f 338 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LYS f 340 " --> pdb=" O VAL e 337 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL e 339 " --> pdb=" O LYS f 340 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL d 337 " --> pdb=" O GLU e 338 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LYS e 340 " --> pdb=" O VAL d 337 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL d 339 " --> pdb=" O LYS e 340 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 344 through 346 removed outlier: 6.144A pdb=" N ASP d 345 " --> pdb=" O PHE g 346 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASP g 345 " --> pdb=" O PHE h 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 351 through 361 removed outlier: 6.482A pdb=" N SER e 352 " --> pdb=" O LYS f 353 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY f 355 " --> pdb=" O SER e 352 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE e 354 " --> pdb=" O GLY f 355 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU f 357 " --> pdb=" O ILE e 354 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N SER e 356 " --> pdb=" O LEU f 357 " (cutoff:3.500A) removed outlier: 10.450A pdb=" N ASN f 359 " --> pdb=" O SER e 356 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ASP e 358 " --> pdb=" O ASN f 359 " (cutoff:3.500A) removed outlier: 10.404A pdb=" N THR f 361 " --> pdb=" O ASP e 358 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N ILE e 360 " --> pdb=" O THR f 361 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER d 352 " --> pdb=" O LYS e 353 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLY e 355 " --> pdb=" O SER d 352 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ILE d 354 " --> pdb=" O GLY e 355 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU e 357 " --> pdb=" O ILE d 354 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N SER d 356 " --> pdb=" O LEU e 357 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N ASN e 359 " --> pdb=" O SER d 356 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N ASP d 358 " --> pdb=" O ASN e 359 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N THR e 361 " --> pdb=" O ASP d 358 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N ILE d 360 " --> pdb=" O THR e 361 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER g 356 " --> pdb=" O GLY d 355 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU d 357 " --> pdb=" O SER g 356 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP g 358 " --> pdb=" O LEU d 357 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN d 359 " --> pdb=" O ASP g 358 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE g 360 " --> pdb=" O ASN d 359 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR d 361 " --> pdb=" O ILE g 360 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER h 356 " --> pdb=" O GLY g 355 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU g 357 " --> pdb=" O SER h 356 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP h 358 " --> pdb=" O LEU g 357 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN g 359 " --> pdb=" O ASP h 358 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE h 360 " --> pdb=" O ASN g 359 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR g 361 " --> pdb=" O ILE h 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 369 through 377 removed outlier: 6.589A pdb=" N LYS d 369 " --> pdb=" O LYS g 370 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLU g 372 " --> pdb=" O LYS d 369 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE d 371 " --> pdb=" O GLU g 372 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N HIS g 374 " --> pdb=" O ILE d 371 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR d 373 " --> pdb=" O HIS g 374 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU g 376 " --> pdb=" O THR d 373 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS d 375 " --> pdb=" O LEU g 376 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS g 369 " --> pdb=" O LYS h 370 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLU h 372 " --> pdb=" O LYS g 369 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE g 371 " --> pdb=" O GLU h 372 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N HIS h 374 " --> pdb=" O ILE g 371 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR g 373 " --> pdb=" O HIS h 374 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU h 376 " --> pdb=" O THR g 373 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS g 375 " --> pdb=" O LEU h 376 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Y' and resid 306 through 308 removed outlier: 6.431A pdb=" N GLN W 307 " --> pdb=" O ILE Z 308 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN Z 307 " --> pdb=" O ILE a 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 313 through 314 removed outlier: 6.880A pdb=" N VAL W 313 " --> pdb=" O ASP Z 314 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL Z 313 " --> pdb=" O ASP a 314 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 317 through 321 removed outlier: 6.324A pdb=" N VAL X 318 " --> pdb=" O THR Y 319 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS Y 321 " --> pdb=" O VAL X 318 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER X 320 " --> pdb=" O LYS Y 321 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL W 318 " --> pdb=" O THR X 319 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LYS X 321 " --> pdb=" O VAL W 318 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER W 320 " --> pdb=" O LYS X 321 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 328 through 330 removed outlier: 6.267A pdb=" N ILE X 328 " --> pdb=" O HIS Y 329 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE W 328 " --> pdb=" O HIS X 329 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 336 through 340 removed outlier: 6.330A pdb=" N VAL X 337 " --> pdb=" O GLU Y 338 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LYS Y 340 " --> pdb=" O VAL X 337 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL X 339 " --> pdb=" O LYS Y 340 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL W 337 " --> pdb=" O GLU X 338 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LYS X 340 " --> pdb=" O VAL W 337 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL W 339 " --> pdb=" O LYS X 340 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Y' and resid 343 through 346 removed outlier: 6.124A pdb=" N LYS W 343 " --> pdb=" O LEU Z 344 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE Z 346 " --> pdb=" O LYS W 343 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASP W 345 " --> pdb=" O PHE Z 346 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS Z 343 " --> pdb=" O LEU a 344 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N PHE a 346 " --> pdb=" O LYS Z 343 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP Z 345 " --> pdb=" O PHE a 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 350 through 351 removed outlier: 6.340A pdb=" N VAL X 350 " --> pdb=" O GLN Y 351 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL W 350 " --> pdb=" O GLN X 351 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 354 through 357 removed outlier: 6.837A pdb=" N SER Z 356 " --> pdb=" O GLY W 355 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU W 357 " --> pdb=" O SER Z 356 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER a 356 " --> pdb=" O GLY Z 355 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU Z 357 " --> pdb=" O SER a 356 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Y' and resid 372 through 378 removed outlier: 6.177A pdb=" N THR W 373 " --> pdb=" O HIS Z 374 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LEU Z 376 " --> pdb=" O THR W 373 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS W 375 " --> pdb=" O LEU Z 376 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE Z 378 " --> pdb=" O LYS W 375 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR W 377 " --> pdb=" O PHE Z 378 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR Z 373 " --> pdb=" O HIS a 374 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU a 376 " --> pdb=" O THR Z 373 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS Z 375 " --> pdb=" O LEU a 376 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE a 378 " --> pdb=" O LYS Z 375 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR Z 377 " --> pdb=" O PHE a 378 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 354 through 357 removed outlier: 8.438A pdb=" N ILE X 354 " --> pdb=" O GLY Y 355 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU Y 357 " --> pdb=" O ILE X 354 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N SER X 356 " --> pdb=" O LEU Y 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 156 hydrogen bonds defined for protein. 468 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: 3.98 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8985 1.03 - 1.22: 15 1.22 - 1.42: 3401 1.42 - 1.61: 5344 1.61 - 1.80: 15 Bond restraints: 17760 Sorted by residual: bond pdb=" CB ARG e 379 " pdb=" CG ARG e 379 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CB ARG d 379 " pdb=" CG ARG d 379 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB ARG f 379 " pdb=" CG ARG f 379 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.80e+00 bond pdb=" CB ARG h 379 " pdb=" CG ARG h 379 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.78e+00 bond pdb=" CB ARG g 379 " pdb=" CG ARG g 379 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.77e+00 ... (remaining 17755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 31316 1.53 - 3.07: 857 3.07 - 4.60: 182 4.60 - 6.13: 25 6.13 - 7.67: 5 Bond angle restraints: 32385 Sorted by residual: angle pdb=" N LYS Z 370 " pdb=" CA LYS Z 370 " pdb=" C LYS Z 370 " ideal model delta sigma weight residual 110.91 115.46 -4.55 1.17e+00 7.31e-01 1.51e+01 angle pdb=" N LYS Y 370 " pdb=" CA LYS Y 370 " pdb=" C LYS Y 370 " ideal model delta sigma weight residual 110.91 115.44 -4.53 1.17e+00 7.31e-01 1.50e+01 angle pdb=" N LYS W 370 " pdb=" CA LYS W 370 " pdb=" C LYS W 370 " ideal model delta sigma weight residual 110.91 115.42 -4.51 1.17e+00 7.31e-01 1.49e+01 angle pdb=" N LYS X 370 " pdb=" CA LYS X 370 " pdb=" C LYS X 370 " ideal model delta sigma weight residual 110.91 115.42 -4.51 1.17e+00 7.31e-01 1.49e+01 angle pdb=" N LYS a 370 " pdb=" CA LYS a 370 " pdb=" C LYS a 370 " ideal model delta sigma weight residual 110.91 115.42 -4.51 1.17e+00 7.31e-01 1.48e+01 ... (remaining 32380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 6880 15.78 - 31.56: 741 31.56 - 47.34: 354 47.34 - 63.12: 140 63.12 - 78.90: 45 Dihedral angle restraints: 8160 sinusoidal: 4665 harmonic: 3495 Sorted by residual: dihedral pdb=" CA LEU X 357 " pdb=" C LEU X 357 " pdb=" N ASP X 358 " pdb=" CA ASP X 358 " ideal model delta harmonic sigma weight residual -180.00 -153.54 -26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA LEU W 357 " pdb=" C LEU W 357 " pdb=" N ASP W 358 " pdb=" CA ASP W 358 " ideal model delta harmonic sigma weight residual -180.00 -153.57 -26.43 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA LEU Y 357 " pdb=" C LEU Y 357 " pdb=" N ASP Y 358 " pdb=" CA ASP Y 358 " ideal model delta harmonic sigma weight residual -180.00 -153.59 -26.41 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 8157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 787 0.034 - 0.068: 307 0.068 - 0.102: 90 0.102 - 0.135: 131 0.135 - 0.169: 5 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA ILE a 371 " pdb=" N ILE a 371 " pdb=" C ILE a 371 " pdb=" CB ILE a 371 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA ILE Z 371 " pdb=" N ILE Z 371 " pdb=" C ILE Z 371 " pdb=" CB ILE Z 371 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA ILE Y 371 " pdb=" N ILE Y 371 " pdb=" C ILE Y 371 " pdb=" CB ILE Y 371 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 1317 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL Z 363 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO Z 364 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO Z 364 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO Z 364 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL Y 363 " 0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO Y 364 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO Y 364 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO Y 364 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL a 363 " -0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO a 364 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO a 364 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO a 364 " -0.026 5.00e-02 4.00e+02 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1539 2.20 - 2.80: 36148 2.80 - 3.40: 46017 3.40 - 4.00: 66745 4.00 - 4.60: 94985 Nonbonded interactions: 245434 Sorted by model distance: nonbonded pdb=" HD1 HIS d 330 " pdb=" OG1 THR g 361 " model vdw 1.596 2.450 nonbonded pdb=" HD1 HIS g 330 " pdb=" OG1 THR h 361 " model vdw 1.617 2.450 nonbonded pdb=" OG1 THR d 361 " pdb=" HD1 HIS e 330 " model vdw 1.633 2.450 nonbonded pdb=" OG1 THR e 361 " pdb=" HD1 HIS f 330 " model vdw 1.633 2.450 nonbonded pdb=" HB2 LEU W 315 " pdb="HD21 LEU Z 315 " model vdw 1.735 2.440 ... (remaining 245429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.090 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.150 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.004 0.041 8760 Z= 0.187 Angle : 0.834 7.668 11730 Z= 0.464 Chirality : 0.051 0.169 1320 Planarity : 0.005 0.046 1500 Dihedral : 16.207 78.904 3375 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.53 % Favored : 84.47 % Rotamer: Outliers : 0.00 % Allowed : 22.22 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG h 349 TYR 0.009 0.002 TYR Z 310 PHE 0.005 0.001 PHE X 346 HIS 0.004 0.001 HIS P 330 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8760) covalent geometry : angle 0.83381 (11730) hydrogen bonds : bond 0.13802 ( 156) hydrogen bonds : angle 7.57937 ( 468) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: P 375 LYS cc_start: 0.8656 (tttt) cc_final: 0.8440 (tttt) REVERT: Q 321 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8269 (mtmt) REVERT: Q 369 LYS cc_start: 0.8851 (mttt) cc_final: 0.8569 (mttm) REVERT: R 319 THR cc_start: 0.9031 (m) cc_final: 0.8777 (m) REVERT: R 379 ARG cc_start: 0.7019 (mtt-85) cc_final: 0.6807 (mtt-85) REVERT: h 317 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8319 (ttmt) REVERT: W 340 LYS cc_start: 0.8625 (mtpm) cc_final: 0.8361 (mmtm) REVERT: W 343 LYS cc_start: 0.8764 (mttp) cc_final: 0.8380 (mtpm) REVERT: X 338 GLU cc_start: 0.8830 (tt0) cc_final: 0.8623 (tt0) REVERT: X 343 LYS cc_start: 0.8718 (mttp) cc_final: 0.8424 (mtpp) REVERT: Y 321 LYS cc_start: 0.8987 (tttp) cc_final: 0.8756 (tmtm) REVERT: Y 338 GLU cc_start: 0.8678 (tt0) cc_final: 0.8450 (tm-30) REVERT: Y 343 LYS cc_start: 0.8734 (mttp) cc_final: 0.8405 (mtpm) REVERT: Y 348 ASP cc_start: 0.7898 (t0) cc_final: 0.7676 (t70) REVERT: Y 372 GLU cc_start: 0.7984 (pt0) cc_final: 0.7646 (tt0) REVERT: Z 321 LYS cc_start: 0.8831 (tttp) cc_final: 0.8544 (tptt) REVERT: Z 345 ASP cc_start: 0.7972 (p0) cc_final: 0.7476 (p0) REVERT: Z 351 GLN cc_start: 0.8504 (mt0) cc_final: 0.8297 (mt0) REVERT: a 343 LYS cc_start: 0.8847 (mttp) cc_final: 0.8540 (mtpt) REVERT: a 345 ASP cc_start: 0.8022 (p0) cc_final: 0.7670 (t70) REVERT: a 348 ASP cc_start: 0.7766 (t0) cc_final: 0.7198 (t70) outliers start: 0 outliers final: 1 residues processed: 284 average time/residue: 1.6492 time to fit residues: 489.9119 Evaluate side-chains 223 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 371 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 330 HIS d 327 ASN e 327 ASN f 327 ASN g 327 ASN h 307 GLN h 327 ASN W 307 GLN W 374 HIS X 307 GLN Y 307 GLN Z 307 GLN a 374 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.123828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.107129 restraints weight = 28979.417| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.34 r_work: 0.3582 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8760 Z= 0.210 Angle : 0.781 6.478 11730 Z= 0.417 Chirality : 0.052 0.139 1320 Planarity : 0.006 0.046 1500 Dihedral : 8.683 71.220 1172 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 1.82 % Allowed : 20.30 % Favored : 77.88 % 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: -2.96 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 349 TYR 0.015 0.003 TYR g 310 PHE 0.010 0.002 PHE d 378 HIS 0.005 0.001 HIS P 330 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 8760) covalent geometry : angle 0.78096 (11730) hydrogen bonds : bond 0.03507 ( 156) hydrogen bonds : angle 5.47574 ( 468) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.504 Fit side-chains REVERT: P 307 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: R 340 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8621 (tttt) REVERT: R 379 ARG cc_start: 0.7133 (mtt-85) cc_final: 0.6854 (mtt-85) REVERT: S 379 ARG cc_start: 0.7142 (mmm-85) cc_final: 0.6803 (mmt-90) REVERT: h 315 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8186 (mp) REVERT: W 321 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8340 (tmtt) REVERT: W 343 LYS cc_start: 0.8889 (mttm) cc_final: 0.8488 (mtpm) REVERT: W 345 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7419 (p0) REVERT: X 343 LYS cc_start: 0.8776 (mttm) cc_final: 0.8458 (mtpp) REVERT: Y 342 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: Y 343 LYS cc_start: 0.8768 (mttm) cc_final: 0.8400 (mtpm) REVERT: Z 345 ASP cc_start: 0.8217 (p0) cc_final: 0.7589 (p0) REVERT: a 343 LYS cc_start: 0.8749 (mttm) cc_final: 0.8441 (mtpt) outliers start: 18 outliers final: 7 residues processed: 226 average time/residue: 1.7064 time to fit residues: 403.5014 Evaluate side-chains 222 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 307 GLN Chi-restraints excluded: chain P residue 341 SER Chi-restraints excluded: chain d residue 321 LYS Chi-restraints excluded: chain d residue 327 ASN Chi-restraints excluded: chain e residue 327 ASN Chi-restraints excluded: chain f residue 327 ASN Chi-restraints excluded: chain g residue 327 ASN Chi-restraints excluded: chain h residue 315 LEU Chi-restraints excluded: chain h residue 327 ASN Chi-restraints excluded: chain W residue 345 ASP Chi-restraints excluded: chain Y residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 307 GLN X 374 HIS Y 307 GLN Y 374 HIS Z 307 GLN Z 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.123149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.106327 restraints weight = 29134.952| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.35 r_work: 0.3574 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8760 Z= 0.223 Angle : 0.781 6.609 11730 Z= 0.420 Chirality : 0.053 0.155 1320 Planarity : 0.006 0.045 1500 Dihedral : 8.628 72.809 1170 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.25 % Favored : 84.75 % Rotamer: Outliers : 1.41 % Allowed : 21.01 % Favored : 77.58 % 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: -2.89 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Z 379 TYR 0.014 0.003 TYR g 310 PHE 0.008 0.001 PHE e 378 HIS 0.005 0.001 HIS X 329 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 8760) covalent geometry : angle 0.78107 (11730) hydrogen bonds : bond 0.03307 ( 156) hydrogen bonds : angle 5.32317 ( 468) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 307 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: R 379 ARG cc_start: 0.7202 (mtt-85) cc_final: 0.6693 (mpt90) REVERT: e 315 LEU cc_start: 0.8622 (mp) cc_final: 0.8408 (mp) REVERT: h 315 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8158 (mp) REVERT: W 343 LYS cc_start: 0.8909 (mttm) cc_final: 0.8498 (mtpm) REVERT: W 345 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7476 (p0) REVERT: X 343 LYS cc_start: 0.8794 (mttm) cc_final: 0.8468 (mtpp) REVERT: Y 338 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: Y 342 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: Y 343 LYS cc_start: 0.8792 (mttm) cc_final: 0.8412 (mtpm) REVERT: Z 340 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8319 (mtmp) REVERT: Z 345 ASP cc_start: 0.8129 (p0) cc_final: 0.7558 (p0) REVERT: a 343 LYS cc_start: 0.8781 (mttm) cc_final: 0.8465 (mtpt) outliers start: 14 outliers final: 5 residues processed: 215 average time/residue: 1.6223 time to fit residues: 365.1086 Evaluate side-chains 207 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 307 GLN Chi-restraints excluded: chain P residue 341 SER Chi-restraints excluded: chain d residue 327 ASN Chi-restraints excluded: chain e residue 327 ASN Chi-restraints excluded: chain g residue 327 ASN Chi-restraints excluded: chain h residue 315 LEU Chi-restraints excluded: chain W residue 345 ASP Chi-restraints excluded: chain Y residue 338 GLU Chi-restraints excluded: chain Y residue 342 GLU Chi-restraints excluded: chain a residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 307 GLN g 336 GLN W 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.122964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.106210 restraints weight = 29055.161| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.34 r_work: 0.3579 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8760 Z= 0.220 Angle : 0.763 6.445 11730 Z= 0.412 Chirality : 0.053 0.146 1320 Planarity : 0.006 0.046 1500 Dihedral : 8.590 71.968 1170 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.34 % Favored : 85.66 % Rotamer: Outliers : 1.72 % Allowed : 21.82 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 379 TYR 0.014 0.003 TYR g 310 PHE 0.011 0.002 PHE e 378 HIS 0.005 0.001 HIS X 329 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 8760) covalent geometry : angle 0.76318 (11730) hydrogen bonds : bond 0.03064 ( 156) hydrogen bonds : angle 5.18620 ( 468) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: P 375 LYS cc_start: 0.8635 (tttt) cc_final: 0.8431 (tppp) REVERT: R 379 ARG cc_start: 0.7195 (mtt-85) cc_final: 0.6643 (mpt90) REVERT: S 307 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7616 (tp40) REVERT: e 315 LEU cc_start: 0.8554 (mp) cc_final: 0.8345 (mp) REVERT: f 319 THR cc_start: 0.9028 (m) cc_final: 0.8749 (p) REVERT: h 315 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8105 (mp) REVERT: W 343 LYS cc_start: 0.8918 (mttm) cc_final: 0.8505 (mtpm) REVERT: X 343 LYS cc_start: 0.8818 (mttm) cc_final: 0.8472 (mtpp) REVERT: Y 321 LYS cc_start: 0.8950 (tttp) cc_final: 0.8715 (ttmt) REVERT: Y 338 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8317 (tm-30) REVERT: Y 343 LYS cc_start: 0.8813 (mttm) cc_final: 0.8418 (mtpm) REVERT: Z 345 ASP cc_start: 0.8125 (p0) cc_final: 0.7801 (p0) REVERT: a 343 LYS cc_start: 0.8738 (mttm) cc_final: 0.8440 (mtpt) outliers start: 17 outliers final: 9 residues processed: 217 average time/residue: 1.6295 time to fit residues: 370.2762 Evaluate side-chains 206 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 341 SER Chi-restraints excluded: chain S residue 307 GLN Chi-restraints excluded: chain d residue 321 LYS Chi-restraints excluded: chain d residue 327 ASN Chi-restraints excluded: chain f residue 315 LEU Chi-restraints excluded: chain g residue 327 ASN Chi-restraints excluded: chain h residue 315 LEU Chi-restraints excluded: chain h residue 317 LYS Chi-restraints excluded: chain h residue 327 ASN Chi-restraints excluded: chain X residue 321 LYS Chi-restraints excluded: chain Y residue 338 GLU Chi-restraints excluded: chain a residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 61 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 307 GLN W 307 GLN Y 307 GLN Z 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.121817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105096 restraints weight = 29087.843| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.33 r_work: 0.3562 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8760 Z= 0.248 Angle : 0.799 6.921 11730 Z= 0.432 Chirality : 0.053 0.145 1320 Planarity : 0.006 0.052 1500 Dihedral : 8.681 70.725 1170 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.98 % Favored : 85.02 % Rotamer: Outliers : 1.62 % Allowed : 21.82 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z 379 TYR 0.013 0.003 TYR a 310 PHE 0.010 0.002 PHE f 378 HIS 0.006 0.001 HIS X 329 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 8760) covalent geometry : angle 0.79930 (11730) hydrogen bonds : bond 0.03185 ( 156) hydrogen bonds : angle 5.23331 ( 468) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: P 375 LYS cc_start: 0.8623 (tttt) cc_final: 0.8419 (tppp) REVERT: R 379 ARG cc_start: 0.7187 (mtt-85) cc_final: 0.6621 (mpt90) REVERT: S 307 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7699 (tp40) REVERT: e 315 LEU cc_start: 0.8596 (mp) cc_final: 0.8383 (mp) REVERT: f 319 THR cc_start: 0.9046 (m) cc_final: 0.8766 (p) REVERT: h 315 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8113 (mp) REVERT: W 340 LYS cc_start: 0.8545 (mtpm) cc_final: 0.8180 (mmtm) REVERT: W 343 LYS cc_start: 0.8914 (mttm) cc_final: 0.8491 (mtpm) REVERT: X 343 LYS cc_start: 0.8811 (mttm) cc_final: 0.8472 (mtpt) REVERT: Y 343 LYS cc_start: 0.8819 (mttm) cc_final: 0.8424 (mtpm) REVERT: a 343 LYS cc_start: 0.8743 (mttm) cc_final: 0.8444 (mtpt) outliers start: 16 outliers final: 6 residues processed: 210 average time/residue: 1.6598 time to fit residues: 365.1897 Evaluate side-chains 201 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 341 SER Chi-restraints excluded: chain S residue 307 GLN Chi-restraints excluded: chain d residue 327 ASN Chi-restraints excluded: chain f residue 315 LEU Chi-restraints excluded: chain h residue 315 LEU Chi-restraints excluded: chain h residue 327 ASN Chi-restraints excluded: chain X residue 321 LYS Chi-restraints excluded: chain a residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 307 GLN Y 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.123394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106776 restraints weight = 28897.435| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.33 r_work: 0.3588 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8760 Z= 0.199 Angle : 0.746 6.684 11730 Z= 0.398 Chirality : 0.052 0.138 1320 Planarity : 0.006 0.051 1500 Dihedral : 8.519 70.637 1170 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.34 % Favored : 85.66 % Rotamer: Outliers : 1.11 % Allowed : 22.12 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Z 379 TYR 0.011 0.002 TYR d 310 PHE 0.007 0.001 PHE f 378 HIS 0.004 0.001 HIS X 329 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 8760) covalent geometry : angle 0.74601 (11730) hydrogen bonds : bond 0.02827 ( 156) hydrogen bonds : angle 5.07397 ( 468) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 0.431 Fit side-chains REVERT: P 375 LYS cc_start: 0.8570 (tttt) cc_final: 0.8365 (tppp) REVERT: R 379 ARG cc_start: 0.7163 (mtt-85) cc_final: 0.6599 (mpt90) REVERT: S 319 THR cc_start: 0.9107 (m) cc_final: 0.8854 (p) REVERT: e 315 LEU cc_start: 0.8565 (mp) cc_final: 0.8345 (mp) REVERT: f 319 THR cc_start: 0.9037 (m) cc_final: 0.8795 (p) REVERT: h 315 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8064 (mp) REVERT: W 343 LYS cc_start: 0.8898 (mttm) cc_final: 0.8493 (mtpm) REVERT: X 343 LYS cc_start: 0.8773 (mttm) cc_final: 0.8423 (mtpp) REVERT: Y 338 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: Y 343 LYS cc_start: 0.8817 (mttm) cc_final: 0.8419 (mtpm) REVERT: a 343 LYS cc_start: 0.8744 (mttm) cc_final: 0.8433 (mtpt) outliers start: 11 outliers final: 7 residues processed: 213 average time/residue: 1.5994 time to fit residues: 356.8624 Evaluate side-chains 207 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 341 SER Chi-restraints excluded: chain d residue 327 ASN Chi-restraints excluded: chain e residue 327 ASN Chi-restraints excluded: chain f residue 315 LEU Chi-restraints excluded: chain h residue 315 LEU Chi-restraints excluded: chain h residue 327 ASN Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain Y residue 338 GLU Chi-restraints excluded: chain a residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 95 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 54 optimal weight: 0.0670 overall best weight: 3.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.123460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.107095 restraints weight = 29464.113| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.33 r_work: 0.3595 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8760 Z= 0.190 Angle : 0.743 7.072 11730 Z= 0.394 Chirality : 0.052 0.139 1320 Planarity : 0.005 0.057 1500 Dihedral : 8.434 69.830 1170 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.89 % Favored : 85.11 % Rotamer: Outliers : 1.31 % Allowed : 22.53 % Favored : 76.16 % 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: -2.84 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Z 379 TYR 0.011 0.002 TYR d 310 PHE 0.008 0.001 PHE d 378 HIS 0.004 0.001 HIS X 329 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 8760) covalent geometry : angle 0.74262 (11730) hydrogen bonds : bond 0.02730 ( 156) hydrogen bonds : angle 5.00601 ( 468) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: R 379 ARG cc_start: 0.7171 (mtt-85) cc_final: 0.6602 (mpt90) REVERT: S 319 THR cc_start: 0.9101 (m) cc_final: 0.8849 (p) REVERT: e 315 LEU cc_start: 0.8558 (mp) cc_final: 0.8345 (mp) REVERT: f 319 THR cc_start: 0.9036 (m) cc_final: 0.8799 (p) REVERT: h 315 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8064 (mp) REVERT: W 343 LYS cc_start: 0.8901 (mttm) cc_final: 0.8497 (mtpm) REVERT: X 314 ASP cc_start: 0.8790 (t70) cc_final: 0.8289 (t0) REVERT: Y 338 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8321 (tm-30) REVERT: Y 343 LYS cc_start: 0.8814 (mttm) cc_final: 0.8423 (mtpm) REVERT: a 343 LYS cc_start: 0.8751 (mttm) cc_final: 0.8444 (mtpt) outliers start: 13 outliers final: 9 residues processed: 209 average time/residue: 1.5983 time to fit residues: 349.8030 Evaluate side-chains 206 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 341 SER Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain d residue 327 ASN Chi-restraints excluded: chain f residue 315 LEU Chi-restraints excluded: chain h residue 315 LEU Chi-restraints excluded: chain h residue 327 ASN Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain Y residue 338 GLU Chi-restraints excluded: chain Y residue 340 LYS Chi-restraints excluded: chain a residue 325 LEU Chi-restraints excluded: chain a residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 3 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 307 GLN X 307 GLN Y 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.124760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.108513 restraints weight = 29414.522| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.32 r_work: 0.3620 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8760 Z= 0.169 Angle : 0.716 6.934 11730 Z= 0.376 Chirality : 0.051 0.134 1320 Planarity : 0.005 0.059 1500 Dihedral : 8.313 70.067 1170 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.97 % Favored : 86.03 % Rotamer: Outliers : 1.11 % Allowed : 22.83 % Favored : 76.06 % 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: -2.85 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 379 TYR 0.010 0.002 TYR d 310 PHE 0.006 0.001 PHE e 378 HIS 0.004 0.001 HIS f 330 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8760) covalent geometry : angle 0.71563 (11730) hydrogen bonds : bond 0.02557 ( 156) hydrogen bonds : angle 4.91170 ( 468) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 0.453 Fit side-chains REVERT: R 379 ARG cc_start: 0.7243 (mtt-85) cc_final: 0.6656 (mpt90) REVERT: S 319 THR cc_start: 0.9057 (m) cc_final: 0.8815 (p) REVERT: f 319 THR cc_start: 0.9028 (m) cc_final: 0.8800 (p) REVERT: g 320 SER cc_start: 0.8910 (p) cc_final: 0.8644 (t) REVERT: W 343 LYS cc_start: 0.8905 (mttm) cc_final: 0.8500 (mtpm) REVERT: Y 338 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: Y 343 LYS cc_start: 0.8809 (mttm) cc_final: 0.8415 (mtpm) REVERT: a 343 LYS cc_start: 0.8760 (mttm) cc_final: 0.8425 (mtpt) outliers start: 11 outliers final: 8 residues processed: 211 average time/residue: 1.6654 time to fit residues: 367.7769 Evaluate side-chains 209 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 200 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 341 SER Chi-restraints excluded: chain d residue 327 ASN Chi-restraints excluded: chain f residue 315 LEU Chi-restraints excluded: chain h residue 327 ASN Chi-restraints excluded: chain W residue 357 LEU Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain Y residue 338 GLU Chi-restraints excluded: chain a residue 325 LEU Chi-restraints excluded: chain a residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 307 GLN P 307 GLN W 307 GLN X 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.128436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.112406 restraints weight = 29417.787| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.32 r_work: 0.3685 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8760 Z= 0.127 Angle : 0.662 7.315 11730 Z= 0.342 Chirality : 0.051 0.137 1320 Planarity : 0.005 0.062 1500 Dihedral : 8.055 74.040 1170 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.42 % Favored : 86.58 % Rotamer: Outliers : 1.11 % Allowed : 22.63 % Favored : 76.26 % 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: -2.82 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Z 379 TYR 0.009 0.002 TYR d 310 PHE 0.004 0.001 PHE e 378 HIS 0.004 0.001 HIS f 330 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8760) covalent geometry : angle 0.66231 (11730) hydrogen bonds : bond 0.02147 ( 156) hydrogen bonds : angle 4.68739 ( 468) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 0.520 Fit side-chains REVERT: S 319 THR cc_start: 0.8972 (m) cc_final: 0.8760 (p) REVERT: S 342 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7281 (mp0) REVERT: W 343 LYS cc_start: 0.8886 (mttm) cc_final: 0.8494 (mtpm) REVERT: X 314 ASP cc_start: 0.8764 (t70) cc_final: 0.8300 (t0) REVERT: a 342 GLU cc_start: 0.5514 (OUTLIER) cc_final: 0.4849 (mp0) REVERT: a 343 LYS cc_start: 0.8688 (mttm) cc_final: 0.8397 (mtpt) outliers start: 11 outliers final: 6 residues processed: 220 average time/residue: 1.6131 time to fit residues: 372.7068 Evaluate side-chains 207 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 200 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 327 ASN Chi-restraints excluded: chain f residue 315 LEU Chi-restraints excluded: chain W residue 357 LEU Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain a residue 325 LEU Chi-restraints excluded: chain a residue 342 GLU Chi-restraints excluded: chain a residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 36 optimal weight: 9.9990 chunk 78 optimal weight: 0.0570 chunk 58 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 307 GLN P 307 GLN W 307 GLN X 307 GLN ** X 362 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 = 0.3937 r_free = 0.3937 target = 0.124640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.107911 restraints weight = 28927.082| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.34 r_work: 0.3611 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8760 Z= 0.190 Angle : 0.759 8.038 11730 Z= 0.397 Chirality : 0.052 0.135 1320 Planarity : 0.005 0.062 1500 Dihedral : 8.307 71.354 1170 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.88 % Favored : 86.12 % Rotamer: Outliers : 0.81 % Allowed : 22.93 % Favored : 76.26 % 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: -2.82 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Z 379 TYR 0.011 0.002 TYR d 310 PHE 0.008 0.001 PHE e 378 HIS 0.004 0.001 HIS e 330 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8760) covalent geometry : angle 0.75905 (11730) hydrogen bonds : bond 0.02645 ( 156) hydrogen bonds : angle 4.87813 ( 468) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.482 Fit side-chains REVERT: S 319 THR cc_start: 0.9059 (m) cc_final: 0.8812 (p) REVERT: W 343 LYS cc_start: 0.8908 (mttm) cc_final: 0.8506 (mtpm) REVERT: Y 338 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: Y 343 LYS cc_start: 0.8809 (mttm) cc_final: 0.8402 (mtpm) REVERT: a 342 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5024 (pm20) REVERT: a 343 LYS cc_start: 0.8675 (mttm) cc_final: 0.8292 (mtpt) outliers start: 8 outliers final: 6 residues processed: 202 average time/residue: 1.7645 time to fit residues: 372.8187 Evaluate side-chains 205 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 327 ASN Chi-restraints excluded: chain f residue 315 LEU Chi-restraints excluded: chain h residue 327 ASN Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain Y residue 338 GLU Chi-restraints excluded: chain a residue 325 LEU Chi-restraints excluded: chain a residue 342 GLU Chi-restraints excluded: chain a residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 89 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 307 GLN P 307 GLN X 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.127864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.111321 restraints weight = 28944.272| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.35 r_work: 0.3661 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8760 Z= 0.139 Angle : 0.682 7.648 11730 Z= 0.353 Chirality : 0.051 0.136 1320 Planarity : 0.005 0.065 1500 Dihedral : 8.099 72.914 1170 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Rotamer: Outliers : 0.91 % Allowed : 23.03 % Favored : 76.06 % 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: -2.83 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Z 379 TYR 0.010 0.002 TYR d 310 PHE 0.004 0.001 PHE d 378 HIS 0.004 0.001 HIS f 330 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8760) covalent geometry : angle 0.68227 (11730) hydrogen bonds : bond 0.02216 ( 156) hydrogen bonds : angle 4.69707 ( 468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8225.48 seconds wall clock time: 139 minutes 54.82 seconds (8394.82 seconds total)