Starting phenix.real_space_refine on Sun May 3 08:59:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o6w_70183/05_2026/9o6w_70183.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o6w_70183/05_2026/9o6w_70183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o6w_70183/05_2026/9o6w_70183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o6w_70183/05_2026/9o6w_70183.map" model { file = "/net/cci-nas-00/data/ceres_data/9o6w_70183/05_2026/9o6w_70183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o6w_70183/05_2026/9o6w_70183.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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: "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: "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: "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: "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: "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} Time building chain proxies: 2.46, per 1000 atoms: 0.21 Number of scatterers: 11750 At special positions: 0 Unit cell: (146.634, 95.8318, 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: 1.16 Conformation dependent library (CDL) restraints added in 428.2 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 18 sheets defined 0.0% alpha, 51.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 306 through 310 removed outlier: 6.558A pdb=" N GLN H 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N TYR I 310 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL H 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN F 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR H 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL F 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 313 through 314 removed outlier: 6.820A pdb=" N VAL H 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL F 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 317 through 322 removed outlier: 6.115A pdb=" N LYS H 317 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N SER I 320 " --> pdb=" O LYS H 317 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR H 319 " --> pdb=" O SER I 320 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N CYS I 322 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS H 321 " --> pdb=" O CYS I 322 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LYS F 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N SER H 320 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR F 319 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N CYS H 322 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS F 321 " --> pdb=" O CYS H 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 325 through 330 removed outlier: 6.870A pdb=" N GLY I 326 " --> pdb=" O LEU H 325 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN H 327 " --> pdb=" O GLY I 326 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY H 326 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN F 327 " --> pdb=" O GLY H 326 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY F 326 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N HIS G 329 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE F 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLY G 326 " --> pdb=" O ASN J 327 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N HIS J 329 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE G 328 " --> pdb=" O HIS J 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 336 through 340 removed outlier: 6.550A pdb=" N GLN H 336 " --> pdb=" O VAL I 337 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL I 339 " --> pdb=" O GLN H 336 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLU H 338 " --> pdb=" O VAL I 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 343 through 346 removed outlier: 6.362A pdb=" N LYS H 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE I 346 " --> pdb=" O LYS H 343 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP H 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS F 343 " --> pdb=" O LEU H 344 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE H 346 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP F 345 " --> pdb=" O PHE H 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 351 through 356 removed outlier: 6.654A pdb=" N GLN H 351 " --> pdb=" O SER I 352 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE I 354 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS H 353 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER I 356 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY H 355 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN F 351 " --> pdb=" O SER H 352 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE H 354 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS F 353 " --> pdb=" O ILE H 354 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER H 356 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLY F 355 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER F 356 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER G 356 " --> pdb=" O GLY J 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 359 through 362 removed outlier: 6.543A pdb=" N ASN F 359 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N HIS G 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR F 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN G 359 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N HIS J 362 " --> pdb=" O ASN G 359 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR G 361 " --> pdb=" O HIS J 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 369 through 378 removed outlier: 6.507A pdb=" N LYS H 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU I 372 " --> pdb=" O LYS H 369 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE H 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N HIS I 374 " --> pdb=" O ILE H 371 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR H 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU I 376 " --> pdb=" O THR H 373 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS H 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE I 378 " --> pdb=" O LYS H 375 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR H 377 " --> pdb=" O PHE I 378 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS F 369 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLU H 372 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE F 371 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N HIS H 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR F 373 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU H 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS F 375 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE H 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR F 377 " --> pdb=" O PHE H 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 306 through 310 removed outlier: 6.660A pdb=" N GLN N 307 " --> pdb=" O ILE Q 308 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N TYR Q 310 " --> pdb=" O GLN N 307 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL N 309 " --> pdb=" O TYR Q 310 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN Q 307 " --> pdb=" O ILE R 308 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N TYR R 310 " --> pdb=" O GLN Q 307 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL Q 309 " --> pdb=" O TYR R 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 313 through 314 removed outlier: 6.891A pdb=" N VAL N 313 " --> pdb=" O ASP Q 314 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL Q 313 " --> pdb=" O ASP R 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 317 through 322 removed outlier: 6.122A pdb=" N LYS N 317 " --> pdb=" O VAL Q 318 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N SER Q 320 " --> pdb=" O LYS N 317 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR N 319 " --> pdb=" O SER Q 320 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N CYS Q 322 " --> pdb=" O THR N 319 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS N 321 " --> pdb=" O CYS Q 322 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS Q 317 " --> pdb=" O VAL R 318 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER R 320 " --> pdb=" O LYS Q 317 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR Q 319 " --> pdb=" O SER R 320 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N CYS R 322 " --> pdb=" O THR Q 319 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS Q 321 " --> pdb=" O CYS R 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 325 through 330 removed outlier: 6.006A pdb=" N GLY O 326 " --> pdb=" O ASN P 327 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N HIS P 329 " --> pdb=" O GLY O 326 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE O 328 " --> pdb=" O HIS P 329 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY N 326 " --> pdb=" O ASN O 327 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N HIS O 329 " --> pdb=" O GLY N 326 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE N 328 " --> pdb=" O HIS O 329 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY Q 326 " --> pdb=" O LEU N 325 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN N 327 " --> pdb=" O GLY Q 326 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY R 326 " --> pdb=" O LEU Q 325 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN Q 327 " --> pdb=" O GLY R 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 336 through 340 removed outlier: 6.552A pdb=" N GLN Q 336 " --> pdb=" O VAL R 337 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL R 339 " --> pdb=" O GLN Q 336 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU Q 338 " --> pdb=" O VAL R 339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 343 through 346 removed outlier: 6.437A pdb=" N LYS Q 343 " --> pdb=" O LEU R 344 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE R 346 " --> pdb=" O LYS Q 343 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP Q 345 " --> pdb=" O PHE R 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 351 through 356 removed outlier: 6.815A pdb=" N SER O 356 " --> pdb=" O GLY P 355 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER N 356 " --> pdb=" O GLY O 355 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN N 351 " --> pdb=" O SER Q 352 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE Q 354 " --> pdb=" O GLN N 351 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS N 353 " --> pdb=" O ILE Q 354 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER Q 356 " --> pdb=" O LYS N 353 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLY N 355 " --> pdb=" O SER Q 356 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN Q 351 " --> pdb=" O SER R 352 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE R 354 " --> pdb=" O GLN Q 351 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS Q 353 " --> pdb=" O ILE R 354 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER R 356 " --> pdb=" O LYS Q 353 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLY Q 355 " --> pdb=" O SER R 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 359 through 362 removed outlier: 6.577A pdb=" N ASN O 359 " --> pdb=" O ILE P 360 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N HIS P 362 " --> pdb=" O ASN O 359 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR O 361 " --> pdb=" O HIS P 362 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN N 359 " --> pdb=" O ILE O 360 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N HIS O 362 " --> pdb=" O ASN N 359 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR N 361 " --> pdb=" O HIS O 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 369 through 377 removed outlier: 6.470A pdb=" N LYS N 369 " --> pdb=" O LYS Q 370 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLU Q 372 " --> pdb=" O LYS N 369 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE N 371 " --> pdb=" O GLU Q 372 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N HIS Q 374 " --> pdb=" O ILE N 371 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR N 373 " --> pdb=" O HIS Q 374 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU Q 376 " --> pdb=" O THR N 373 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS N 375 " --> pdb=" O LEU Q 376 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS Q 369 " --> pdb=" O LYS R 370 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU R 372 " --> pdb=" O LYS Q 369 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE Q 371 " --> pdb=" O GLU R 372 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N HIS R 374 " --> pdb=" O ILE Q 371 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR Q 373 " --> pdb=" O HIS R 374 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU R 376 " --> pdb=" O THR Q 373 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS Q 375 " --> pdb=" O LEU R 376 " (cutoff:3.500A) 153 hydrogen bonds defined for protein. 459 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: 3.11 Time building geometry restraints manager: 1.62 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: 1609 1.46 - 1.63: 3271 1.63 - 1.80: 10 Bond restraints: 11840 Sorted by residual: bond pdb=" N ASN G 327 " pdb=" H ASN G 327 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" NH1 ARG I 349 " pdb="HH12 ARG I 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ARG G 349 " pdb=" H ARG G 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ARG H 349 " pdb=" H ARG H 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE P 360 " pdb=" H ILE P 360 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 11835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 17665 2.39 - 4.79: 2901 4.79 - 7.18: 958 7.18 - 9.58: 56 9.58 - 11.97: 10 Bond angle restraints: 21590 Sorted by residual: angle pdb=" CA ASP H 348 " pdb=" CB ASP H 348 " pdb=" CG ASP H 348 " ideal model delta sigma weight residual 112.60 118.30 -5.70 1.00e+00 1.00e+00 3.25e+01 angle pdb=" CA ASP G 348 " pdb=" CB ASP G 348 " pdb=" CG ASP G 348 " ideal model delta sigma weight residual 112.60 118.26 -5.66 1.00e+00 1.00e+00 3.20e+01 angle pdb=" CA ASP F 348 " pdb=" CB ASP F 348 " pdb=" CG ASP F 348 " ideal model delta sigma weight residual 112.60 118.24 -5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" CA ASP J 348 " pdb=" CB ASP J 348 " pdb=" CG ASP J 348 " ideal model delta sigma weight residual 112.60 118.23 -5.63 1.00e+00 1.00e+00 3.17e+01 angle pdb=" CA ASP I 348 " pdb=" CB ASP I 348 " pdb=" CG ASP I 348 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.00e+00 1.00e+00 3.16e+01 ... (remaining 21585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 4611 13.97 - 27.94: 451 27.94 - 41.90: 113 41.90 - 55.87: 112 55.87 - 69.84: 153 Dihedral angle restraints: 5440 sinusoidal: 3110 harmonic: 2330 Sorted by residual: dihedral pdb=" CA LYS R 347 " pdb=" C LYS R 347 " pdb=" N ASP R 348 " pdb=" CA ASP R 348 " ideal model delta harmonic sigma weight residual -180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA LYS O 347 " pdb=" C LYS O 347 " pdb=" N ASP O 348 " pdb=" CA ASP O 348 " ideal model delta harmonic sigma weight residual 180.00 -155.51 -24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA LYS Q 347 " pdb=" C LYS Q 347 " pdb=" N ASP Q 348 " pdb=" CA ASP Q 348 " ideal model delta harmonic sigma weight residual -180.00 -155.54 -24.46 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 591 0.079 - 0.157: 234 0.157 - 0.236: 44 0.236 - 0.314: 1 0.314 - 0.392: 10 Chirality restraints: 880 Sorted by residual: chirality pdb=" CA ASP P 348 " pdb=" N ASP P 348 " pdb=" C ASP P 348 " pdb=" CB ASP P 348 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA ASP N 348 " pdb=" N ASP N 348 " pdb=" C ASP N 348 " pdb=" CB ASP N 348 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA ASP R 348 " pdb=" N ASP R 348 " pdb=" C ASP R 348 " pdb=" CB ASP R 348 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 877 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN J 336 " -0.049 2.00e-02 2.50e+03 4.74e-02 3.37e+01 pdb=" CD GLN J 336 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN J 336 " 0.024 2.00e-02 2.50e+03 pdb=" NE2 GLN J 336 " 0.055 2.00e-02 2.50e+03 pdb="HE21 GLN J 336 " 0.023 2.00e-02 2.50e+03 pdb="HE22 GLN J 336 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN I 336 " -0.049 2.00e-02 2.50e+03 4.72e-02 3.35e+01 pdb=" CD GLN I 336 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN I 336 " 0.024 2.00e-02 2.50e+03 pdb=" NE2 GLN I 336 " 0.054 2.00e-02 2.50e+03 pdb="HE21 GLN I 336 " 0.024 2.00e-02 2.50e+03 pdb="HE22 GLN I 336 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 336 " -0.049 2.00e-02 2.50e+03 4.71e-02 3.33e+01 pdb=" CD GLN G 336 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN G 336 " 0.024 2.00e-02 2.50e+03 pdb=" NE2 GLN G 336 " 0.054 2.00e-02 2.50e+03 pdb="HE21 GLN G 336 " 0.023 2.00e-02 2.50e+03 pdb="HE22 GLN G 336 " -0.078 2.00e-02 2.50e+03 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 789 2.15 - 2.76: 19396 2.76 - 3.38: 31803 3.38 - 3.99: 45805 3.99 - 4.60: 61912 Nonbonded interactions: 159705 Sorted by model distance: nonbonded pdb=" OD1 ASP P 314 " pdb=" HG SER P 316 " model vdw 1.538 2.450 nonbonded pdb=" OD1 ASP N 314 " pdb=" HG SER N 316 " model vdw 1.538 2.450 nonbonded pdb=" OD1 ASP Q 314 " pdb=" HG SER Q 316 " model vdw 1.538 2.450 nonbonded pdb=" OD1 ASP O 314 " pdb=" HG SER O 316 " model vdw 1.538 2.450 nonbonded pdb=" OD1 ASP R 314 " pdb=" HG SER R 316 " model vdw 1.538 2.450 ... (remaining 159700 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 '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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 14.060 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 0.036 5840 Z= 0.702 Angle : 1.963 7.074 7820 Z= 1.304 Chirality : 0.090 0.392 880 Planarity : 0.010 0.038 1000 Dihedral : 11.131 60.840 2250 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.15 % 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: -1.25 (0.27), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 349 TYR 0.066 0.022 TYR I 310 PHE 0.029 0.009 PHE N 346 HIS 0.005 0.002 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.01095 ( 5840) covalent geometry : angle 1.96341 ( 7820) hydrogen bonds : bond 0.10266 ( 153) hydrogen bonds : angle 7.47944 ( 459) *********************** 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 234 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 343 LYS cc_start: 0.8670 (mttp) cc_final: 0.8214 (mtpp) REVERT: F 348 ASP cc_start: 0.8311 (p0) cc_final: 0.8108 (p0) REVERT: F 369 LYS cc_start: 0.8747 (mttm) cc_final: 0.8501 (mtmt) REVERT: G 317 LYS cc_start: 0.8116 (mttm) cc_final: 0.7882 (mtpt) REVERT: G 340 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8449 (mtpp) REVERT: G 343 LYS cc_start: 0.8697 (mttp) cc_final: 0.8158 (mtpp) REVERT: G 373 THR cc_start: 0.9213 (m) cc_final: 0.8706 (p) REVERT: G 375 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8463 (tttt) REVERT: H 317 LYS cc_start: 0.8271 (mttm) cc_final: 0.7866 (mtmt) REVERT: H 340 LYS cc_start: 0.8525 (ttmm) cc_final: 0.8261 (mttp) REVERT: H 343 LYS cc_start: 0.8635 (mttp) cc_final: 0.8243 (mtpm) REVERT: H 344 LEU cc_start: 0.9346 (mp) cc_final: 0.9105 (mt) REVERT: H 369 LYS cc_start: 0.8865 (mttm) cc_final: 0.8565 (mtmt) REVERT: H 375 LYS cc_start: 0.8706 (ttpt) cc_final: 0.8489 (tttm) REVERT: I 317 LYS cc_start: 0.8506 (mttm) cc_final: 0.8277 (mtmt) REVERT: I 340 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8614 (mttp) REVERT: I 343 LYS cc_start: 0.8713 (mttp) cc_final: 0.8343 (mtpp) REVERT: I 344 LEU cc_start: 0.9391 (mp) cc_final: 0.9049 (mp) REVERT: I 369 LYS cc_start: 0.9006 (mttm) cc_final: 0.8764 (mtpp) REVERT: I 379 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7267 (mpp-170) REVERT: J 311 LYS cc_start: 0.8828 (mttt) cc_final: 0.7920 (mmpt) REVERT: J 317 LYS cc_start: 0.8316 (mttm) cc_final: 0.8087 (mtmt) REVERT: J 343 LYS cc_start: 0.8500 (mttp) cc_final: 0.7938 (mtpp) REVERT: J 369 LYS cc_start: 0.8822 (mttm) cc_final: 0.8561 (mtpt) REVERT: J 371 ILE cc_start: 0.9124 (mt) cc_final: 0.8881 (mp) REVERT: N 317 LYS cc_start: 0.8196 (mttm) cc_final: 0.7877 (mtmt) REVERT: N 331 LYS cc_start: 0.9091 (mtmt) cc_final: 0.8876 (mtpm) REVERT: N 340 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8274 (mtpp) REVERT: N 343 LYS cc_start: 0.8746 (mttp) cc_final: 0.8109 (mtpp) REVERT: N 369 LYS cc_start: 0.8815 (mttp) cc_final: 0.8521 (mtmt) REVERT: N 375 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8489 (tttt) REVERT: O 317 LYS cc_start: 0.8326 (mttm) cc_final: 0.8119 (mtpt) REVERT: O 343 LYS cc_start: 0.8746 (mttp) cc_final: 0.8223 (mtpp) REVERT: O 369 LYS cc_start: 0.8756 (mttp) cc_final: 0.8505 (mtpt) REVERT: O 375 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8424 (tttt) REVERT: P 311 LYS cc_start: 0.8835 (mttt) cc_final: 0.8069 (mmpt) REVERT: P 317 LYS cc_start: 0.8362 (mttm) cc_final: 0.8042 (mtmt) REVERT: P 331 LYS cc_start: 0.9198 (mtmt) cc_final: 0.8105 (tmtt) REVERT: P 343 LYS cc_start: 0.8555 (mttp) cc_final: 0.8058 (mtpp) REVERT: P 371 ILE cc_start: 0.9132 (mt) cc_final: 0.8921 (mp) REVERT: Q 317 LYS cc_start: 0.8194 (mttm) cc_final: 0.7944 (mtmt) REVERT: Q 331 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8668 (mtmt) REVERT: Q 343 LYS cc_start: 0.8798 (mttp) cc_final: 0.8211 (mtpp) REVERT: Q 375 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8469 (tttt) REVERT: R 317 LYS cc_start: 0.8389 (mttm) cc_final: 0.8143 (mtmt) REVERT: R 343 LYS cc_start: 0.8763 (mttp) cc_final: 0.8432 (mtpm) REVERT: R 344 LEU cc_start: 0.9404 (mp) cc_final: 0.9190 (mt) REVERT: R 379 ARG cc_start: 0.8002 (mtt-85) cc_final: 0.6947 (mpp-170) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 1.9959 time to fit residues: 479.4352 Evaluate side-chains 177 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN N 307 GLN Q 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.110394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.094795 restraints weight = 24196.975| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.84 r_work: 0.3504 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5840 Z= 0.155 Angle : 0.673 4.674 7820 Z= 0.357 Chirality : 0.051 0.135 880 Planarity : 0.004 0.049 1000 Dihedral : 7.478 22.713 780 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.76 % Allowed : 13.03 % Favored : 86.21 % 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 0.006 0.001 ARG G 379 TYR 0.014 0.003 TYR O 310 PHE 0.005 0.001 PHE H 346 HIS 0.008 0.002 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5840) covalent geometry : angle 0.67340 ( 7820) hydrogen bonds : bond 0.02882 ( 153) hydrogen bonds : angle 5.09406 ( 459) *********************** 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 189 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 340 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8389 (mttp) REVERT: F 342 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7434 (mm-30) REVERT: F 343 LYS cc_start: 0.8879 (mttp) cc_final: 0.8345 (mtpp) REVERT: F 369 LYS cc_start: 0.8858 (mttm) cc_final: 0.8654 (mtmt) REVERT: F 375 LYS cc_start: 0.8827 (ttpt) cc_final: 0.8608 (tttt) REVERT: G 317 LYS cc_start: 0.8356 (mttm) cc_final: 0.8129 (mtpt) REVERT: G 340 LYS cc_start: 0.8608 (ttmm) cc_final: 0.8196 (mtpp) REVERT: G 342 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7558 (tp30) REVERT: G 343 LYS cc_start: 0.8886 (mttp) cc_final: 0.8320 (mtpp) REVERT: H 343 LYS cc_start: 0.8805 (mttp) cc_final: 0.8401 (mtpm) REVERT: H 369 LYS cc_start: 0.9077 (mttm) cc_final: 0.8835 (mtmt) REVERT: H 375 LYS cc_start: 0.8903 (ttpt) cc_final: 0.8680 (tttt) REVERT: I 343 LYS cc_start: 0.8795 (mttp) cc_final: 0.8426 (mtpp) REVERT: I 344 LEU cc_start: 0.9288 (mp) cc_final: 0.9085 (mt) REVERT: I 379 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7269 (mpp-170) REVERT: J 342 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: J 343 LYS cc_start: 0.8769 (mttp) cc_final: 0.8096 (mtpp) REVERT: N 340 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8336 (mtpp) REVERT: N 342 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7636 (mm-30) REVERT: N 343 LYS cc_start: 0.8870 (mttp) cc_final: 0.8200 (mtpp) REVERT: N 369 LYS cc_start: 0.8873 (mttp) cc_final: 0.8586 (mtmt) REVERT: N 375 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8620 (tttt) REVERT: O 317 LYS cc_start: 0.8497 (mttm) cc_final: 0.8297 (mtpt) REVERT: O 321 LYS cc_start: 0.8890 (mttm) cc_final: 0.8674 (mppt) REVERT: O 342 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7796 (tp30) REVERT: O 343 LYS cc_start: 0.8896 (mttp) cc_final: 0.8252 (mtpp) REVERT: O 369 LYS cc_start: 0.8886 (mttp) cc_final: 0.8607 (mtpt) REVERT: O 375 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8603 (tttt) REVERT: P 311 LYS cc_start: 0.8892 (mttt) cc_final: 0.8241 (mmpt) REVERT: P 317 LYS cc_start: 0.8490 (mttm) cc_final: 0.8188 (mtmt) REVERT: P 331 LYS cc_start: 0.9094 (mtmt) cc_final: 0.7993 (tmtt) REVERT: P 342 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7170 (mm-30) REVERT: P 343 LYS cc_start: 0.8721 (mttp) cc_final: 0.8228 (mtpp) REVERT: P 375 LYS cc_start: 0.9009 (tttt) cc_final: 0.8788 (tppp) REVERT: Q 343 LYS cc_start: 0.8931 (mttp) cc_final: 0.8372 (mtpp) REVERT: Q 375 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8675 (tttt) REVERT: R 379 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.6875 (mpp-170) outliers start: 5 outliers final: 1 residues processed: 186 average time/residue: 1.7468 time to fit residues: 335.0479 Evaluate side-chains 165 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain P residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Q 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.091795 restraints weight = 24129.465| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.86 r_work: 0.3461 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5840 Z= 0.251 Angle : 0.660 4.753 7820 Z= 0.350 Chirality : 0.051 0.126 880 Planarity : 0.005 0.034 1000 Dihedral : 7.185 23.549 780 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.42 % Allowed : 16.36 % Favored : 81.21 % 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: -1.75 (0.26), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 349 TYR 0.016 0.003 TYR G 310 PHE 0.007 0.002 PHE I 378 HIS 0.008 0.003 HIS P 330 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 5840) covalent geometry : angle 0.65962 ( 7820) hydrogen bonds : bond 0.02687 ( 153) hydrogen bonds : angle 4.97167 ( 459) *********************** 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 187 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 342 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7578 (mm-30) REVERT: F 343 LYS cc_start: 0.8931 (mttp) cc_final: 0.8410 (mtpp) REVERT: F 372 GLU cc_start: 0.8477 (tt0) cc_final: 0.8207 (mt-10) REVERT: F 375 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8584 (tttt) REVERT: G 340 LYS cc_start: 0.8610 (ttmm) cc_final: 0.8123 (mtpp) REVERT: G 342 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7735 (tp30) REVERT: G 343 LYS cc_start: 0.8937 (mttp) cc_final: 0.8282 (mtpp) REVERT: H 343 LYS cc_start: 0.8738 (mttp) cc_final: 0.8439 (mtpm) REVERT: H 369 LYS cc_start: 0.9094 (mttm) cc_final: 0.8873 (mtmt) REVERT: H 375 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8566 (tttt) REVERT: I 379 ARG cc_start: 0.8079 (mtt-85) cc_final: 0.7153 (mpp-170) REVERT: J 342 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7050 (mm-30) REVERT: J 343 LYS cc_start: 0.8753 (mttp) cc_final: 0.8017 (mtpp) REVERT: J 369 LYS cc_start: 0.8936 (mttm) cc_final: 0.8733 (mtpt) REVERT: N 340 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8384 (mtpp) REVERT: N 342 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7870 (mm-30) REVERT: N 343 LYS cc_start: 0.8875 (mttp) cc_final: 0.8176 (mtpp) REVERT: N 369 LYS cc_start: 0.8895 (mttp) cc_final: 0.8621 (mtmt) REVERT: N 375 LYS cc_start: 0.8845 (ttpt) cc_final: 0.8612 (tttt) REVERT: O 317 LYS cc_start: 0.8568 (mttm) cc_final: 0.8319 (mtmt) REVERT: O 342 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7916 (tp30) REVERT: O 343 LYS cc_start: 0.8866 (mttp) cc_final: 0.8253 (mtpp) REVERT: O 369 LYS cc_start: 0.9048 (mttp) cc_final: 0.8752 (mtpt) REVERT: O 375 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8484 (tttt) REVERT: P 311 LYS cc_start: 0.8916 (mttt) cc_final: 0.8221 (mmpt) REVERT: P 317 LYS cc_start: 0.8491 (mttm) cc_final: 0.8187 (mtmt) REVERT: P 342 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: P 343 LYS cc_start: 0.8712 (mttp) cc_final: 0.8242 (mtpp) REVERT: P 375 LYS cc_start: 0.8975 (tttt) cc_final: 0.8729 (tppp) REVERT: Q 343 LYS cc_start: 0.8937 (mttp) cc_final: 0.8344 (mtpp) REVERT: Q 375 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8570 (tttt) REVERT: R 342 GLU cc_start: 0.5776 (mp0) cc_final: 0.5412 (pm20) REVERT: R 379 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.6901 (mpp-170) outliers start: 16 outliers final: 7 residues processed: 175 average time/residue: 1.7387 time to fit residues: 313.7719 Evaluate side-chains 171 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 325 LEU Chi-restraints excluded: chain O residue 347 LYS Chi-restraints excluded: chain P residue 342 GLU Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 373 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN N 307 GLN Q 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.111573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.095556 restraints weight = 23834.328| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.88 r_work: 0.3508 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5840 Z= 0.149 Angle : 0.566 3.767 7820 Z= 0.296 Chirality : 0.050 0.124 880 Planarity : 0.004 0.033 1000 Dihedral : 6.488 19.381 780 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.06 % Allowed : 18.64 % Favored : 80.30 % 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: -1.64 (0.27), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 379 TYR 0.011 0.002 TYR G 310 PHE 0.003 0.001 PHE N 378 HIS 0.006 0.002 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5840) covalent geometry : angle 0.56621 ( 7820) hydrogen bonds : bond 0.02147 ( 153) hydrogen bonds : angle 4.59476 ( 459) *********************** 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 178 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 171 time to evaluate : 0.338 Fit side-chains REVERT: F 342 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7513 (mm-30) REVERT: F 343 LYS cc_start: 0.8910 (mttp) cc_final: 0.8340 (mtpp) REVERT: F 372 GLU cc_start: 0.8448 (tt0) cc_final: 0.8245 (mt-10) REVERT: F 375 LYS cc_start: 0.8774 (ttpt) cc_final: 0.8545 (tttt) REVERT: G 340 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8086 (mtpp) REVERT: G 342 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7745 (tp30) REVERT: G 343 LYS cc_start: 0.8909 (mttp) cc_final: 0.8186 (mtpp) REVERT: H 340 LYS cc_start: 0.8748 (mttp) cc_final: 0.8544 (mttp) REVERT: H 343 LYS cc_start: 0.8774 (mttp) cc_final: 0.8471 (mtpm) REVERT: H 375 LYS cc_start: 0.8895 (ttpt) cc_final: 0.8555 (tttt) REVERT: I 369 LYS cc_start: 0.9141 (mttm) cc_final: 0.8903 (mtpp) REVERT: I 379 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7114 (mpp-170) REVERT: J 342 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6986 (mm-30) REVERT: J 343 LYS cc_start: 0.8747 (mttp) cc_final: 0.8011 (mtpp) REVERT: N 340 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8406 (mtpp) REVERT: N 342 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7738 (mm-30) REVERT: N 343 LYS cc_start: 0.8879 (mttp) cc_final: 0.8164 (mtpp) REVERT: N 369 LYS cc_start: 0.8894 (mttp) cc_final: 0.8655 (mtmt) REVERT: N 372 GLU cc_start: 0.8557 (tt0) cc_final: 0.8157 (mt-10) REVERT: N 375 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8609 (tttt) REVERT: O 342 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7878 (tp30) REVERT: O 343 LYS cc_start: 0.8893 (mttp) cc_final: 0.8279 (mtpp) REVERT: O 369 LYS cc_start: 0.9012 (mttp) cc_final: 0.8729 (mtpt) REVERT: O 375 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8535 (tttt) REVERT: P 311 LYS cc_start: 0.8900 (mttt) cc_final: 0.8167 (mmpt) REVERT: P 317 LYS cc_start: 0.8422 (mttm) cc_final: 0.8148 (mtmt) REVERT: P 342 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7245 (mm-30) REVERT: P 343 LYS cc_start: 0.8705 (mttp) cc_final: 0.8232 (mtpp) REVERT: P 375 LYS cc_start: 0.8981 (tttt) cc_final: 0.8738 (tppp) REVERT: Q 340 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8341 (mttp) REVERT: Q 343 LYS cc_start: 0.8968 (mttp) cc_final: 0.8353 (mtpp) REVERT: Q 372 GLU cc_start: 0.8752 (tt0) cc_final: 0.8538 (tt0) REVERT: Q 375 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8520 (tttt) REVERT: R 379 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.6915 (mpp-170) outliers start: 7 outliers final: 2 residues processed: 175 average time/residue: 1.6410 time to fit residues: 296.4751 Evaluate side-chains 158 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain N residue 370 LYS Chi-restraints excluded: chain O residue 347 LYS Chi-restraints excluded: chain P residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN N 307 GLN Q 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.110432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.094763 restraints weight = 24054.434| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.81 r_work: 0.3511 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4738 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= 0.145 Angle : 0.557 3.757 7820 Z= 0.290 Chirality : 0.050 0.122 880 Planarity : 0.004 0.032 1000 Dihedral : 6.156 18.667 780 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.21 % Allowed : 19.09 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.28), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 379 TYR 0.011 0.002 TYR G 310 PHE 0.004 0.001 PHE N 378 HIS 0.006 0.002 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5840) covalent geometry : angle 0.55672 ( 7820) hydrogen bonds : bond 0.02072 ( 153) hydrogen bonds : angle 4.48439 ( 459) *********************** 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 171 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.341 Fit side-chains REVERT: F 342 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7558 (mm-30) REVERT: F 343 LYS cc_start: 0.8907 (mttp) cc_final: 0.8384 (mtpp) REVERT: F 349 ARG cc_start: 0.7844 (mtm180) cc_final: 0.7585 (mtm180) REVERT: F 375 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8590 (tttt) REVERT: G 340 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8126 (mtpp) REVERT: G 342 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7747 (tp30) REVERT: G 343 LYS cc_start: 0.8871 (mttp) cc_final: 0.8217 (mtpp) REVERT: H 343 LYS cc_start: 0.8726 (mttp) cc_final: 0.8453 (mtpm) REVERT: H 375 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8625 (tttt) REVERT: I 369 LYS cc_start: 0.9167 (mttm) cc_final: 0.8950 (mtmt) REVERT: I 379 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7150 (mpp-170) REVERT: J 342 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6977 (mm-30) REVERT: J 343 LYS cc_start: 0.8759 (mttp) cc_final: 0.8082 (mtpp) REVERT: N 342 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7746 (mm-30) REVERT: N 343 LYS cc_start: 0.8870 (mttp) cc_final: 0.8219 (mtpp) REVERT: N 349 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7124 (mtt180) REVERT: N 372 GLU cc_start: 0.8506 (tt0) cc_final: 0.8130 (mt-10) REVERT: O 342 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7925 (tp30) REVERT: O 343 LYS cc_start: 0.8889 (mttp) cc_final: 0.8277 (mtpp) REVERT: O 369 LYS cc_start: 0.8986 (mttp) cc_final: 0.8725 (mtpt) REVERT: O 375 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8552 (tttt) REVERT: P 342 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7294 (mm-30) REVERT: P 343 LYS cc_start: 0.8681 (mttp) cc_final: 0.8244 (mtpp) REVERT: Q 340 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8423 (mttp) REVERT: Q 343 LYS cc_start: 0.8969 (mttp) cc_final: 0.8392 (mtpp) REVERT: Q 372 GLU cc_start: 0.8689 (tt0) cc_final: 0.8474 (tt0) REVERT: Q 375 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8566 (tttt) REVERT: R 379 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.6885 (mpp-170) outliers start: 8 outliers final: 3 residues processed: 168 average time/residue: 1.6665 time to fit residues: 289.0763 Evaluate side-chains 156 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain N residue 325 LEU Chi-restraints excluded: chain N residue 349 ARG Chi-restraints excluded: chain O residue 347 LYS Chi-restraints excluded: chain P residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Q 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.107999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.091782 restraints weight = 24381.072| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.85 r_work: 0.3460 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5840 Z= 0.245 Angle : 0.620 4.163 7820 Z= 0.326 Chirality : 0.050 0.125 880 Planarity : 0.004 0.035 1000 Dihedral : 6.545 23.657 780 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.82 % Allowed : 19.70 % Favored : 78.48 % 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: -1.53 (0.28), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 379 TYR 0.013 0.003 TYR G 310 PHE 0.007 0.001 PHE R 346 HIS 0.007 0.002 HIS P 330 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 5840) covalent geometry : angle 0.61957 ( 7820) hydrogen bonds : bond 0.02482 ( 153) hydrogen bonds : angle 4.71550 ( 459) *********************** 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 165 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.409 Fit side-chains REVERT: F 342 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7566 (mm-30) REVERT: F 343 LYS cc_start: 0.8928 (mttp) cc_final: 0.8404 (mtpp) REVERT: F 375 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8519 (tttt) REVERT: G 342 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7686 (tp30) REVERT: G 343 LYS cc_start: 0.8887 (mttp) cc_final: 0.8178 (mtpp) REVERT: H 343 LYS cc_start: 0.8752 (mttp) cc_final: 0.8451 (mtpm) REVERT: H 375 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8623 (tttt) REVERT: I 369 LYS cc_start: 0.9215 (mttm) cc_final: 0.8975 (mtpp) REVERT: I 379 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7221 (mpp-170) REVERT: J 342 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: J 343 LYS cc_start: 0.8799 (mttp) cc_final: 0.8052 (mtpp) REVERT: N 342 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7866 (mm-30) REVERT: N 343 LYS cc_start: 0.8877 (mttp) cc_final: 0.8184 (mtpp) REVERT: N 349 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7133 (mtt180) REVERT: N 372 GLU cc_start: 0.8558 (tt0) cc_final: 0.8151 (mt-10) REVERT: O 342 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7928 (tp30) REVERT: O 343 LYS cc_start: 0.8887 (mttp) cc_final: 0.8295 (mtpp) REVERT: O 369 LYS cc_start: 0.8972 (mttp) cc_final: 0.8706 (mtpt) REVERT: O 375 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8475 (tttt) REVERT: P 342 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: P 343 LYS cc_start: 0.8697 (mttp) cc_final: 0.8233 (mtpp) REVERT: Q 343 LYS cc_start: 0.8956 (mttp) cc_final: 0.8350 (mtpp) REVERT: Q 372 GLU cc_start: 0.8699 (tt0) cc_final: 0.8482 (tt0) REVERT: Q 375 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8544 (tttt) REVERT: R 379 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.6911 (mpp-170) outliers start: 12 outliers final: 5 residues processed: 157 average time/residue: 1.5967 time to fit residues: 259.2637 Evaluate side-chains 157 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain N residue 325 LEU Chi-restraints excluded: chain N residue 349 ARG Chi-restraints excluded: chain O residue 347 LYS Chi-restraints excluded: chain P residue 342 GLU Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain R residue 373 THR 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: 6.9990 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 307 GLN N 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.111637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.095925 restraints weight = 23990.925| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.82 r_work: 0.3532 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.5000 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= 0.118 Angle : 0.548 5.101 7820 Z= 0.282 Chirality : 0.050 0.127 880 Planarity : 0.004 0.028 1000 Dihedral : 5.901 18.018 780 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.21 % Allowed : 20.61 % Favored : 78.18 % 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: -1.50 (0.28), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 379 TYR 0.009 0.002 TYR G 310 PHE 0.003 0.001 PHE J 378 HIS 0.005 0.001 HIS H 330 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5840) covalent geometry : angle 0.54807 ( 7820) hydrogen bonds : bond 0.01934 ( 153) hydrogen bonds : angle 4.33194 ( 459) *********************** 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 165 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.353 Fit side-chains REVERT: F 342 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7569 (mm-30) REVERT: F 343 LYS cc_start: 0.8885 (mttp) cc_final: 0.8368 (mtpp) REVERT: F 375 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8561 (tttt) REVERT: G 342 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7742 (tp30) REVERT: G 343 LYS cc_start: 0.8900 (mttp) cc_final: 0.8246 (mtpp) REVERT: H 343 LYS cc_start: 0.8722 (mttp) cc_final: 0.8450 (mtpm) REVERT: H 375 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8609 (tttt) REVERT: I 369 LYS cc_start: 0.9160 (mttm) cc_final: 0.8939 (mtmt) REVERT: I 379 ARG cc_start: 0.8068 (mtt-85) cc_final: 0.7215 (mpp-170) REVERT: J 342 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7011 (mm-30) REVERT: J 343 LYS cc_start: 0.8753 (mttp) cc_final: 0.8096 (mtpp) REVERT: N 342 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7814 (mm-30) REVERT: N 343 LYS cc_start: 0.8867 (mttp) cc_final: 0.8230 (mtpp) REVERT: N 372 GLU cc_start: 0.8509 (tt0) cc_final: 0.8152 (mt-10) REVERT: O 342 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7911 (tp30) REVERT: O 343 LYS cc_start: 0.8879 (mttp) cc_final: 0.8343 (mtpp) REVERT: O 369 LYS cc_start: 0.8929 (mttp) cc_final: 0.8718 (mtpt) REVERT: O 375 LYS cc_start: 0.8834 (ttpt) cc_final: 0.8576 (tttt) REVERT: P 342 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7253 (mm-30) REVERT: P 343 LYS cc_start: 0.8665 (mttp) cc_final: 0.8253 (mtpp) REVERT: Q 343 LYS cc_start: 0.8950 (mttp) cc_final: 0.8384 (mtpp) REVERT: Q 372 GLU cc_start: 0.8668 (tt0) cc_final: 0.8460 (tt0) REVERT: Q 375 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8538 (tttt) REVERT: R 379 ARG cc_start: 0.8106 (mtt-85) cc_final: 0.6896 (mpp-170) outliers start: 8 outliers final: 3 residues processed: 162 average time/residue: 1.5201 time to fit residues: 255.0893 Evaluate side-chains 156 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain N residue 325 LEU Chi-restraints excluded: chain O residue 347 LYS Chi-restraints excluded: chain P residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 0.0060 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 307 GLN Q 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.115460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.099934 restraints weight = 23705.507| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.90 r_work: 0.3593 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5840 Z= 0.083 Angle : 0.522 5.294 7820 Z= 0.266 Chirality : 0.051 0.129 880 Planarity : 0.003 0.026 1000 Dihedral : 5.308 14.678 780 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.91 % Allowed : 21.97 % Favored : 77.12 % 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: -1.51 (0.28), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 379 TYR 0.006 0.001 TYR G 310 PHE 0.004 0.001 PHE Q 346 HIS 0.006 0.001 HIS H 330 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 5840) covalent geometry : angle 0.52205 ( 7820) hydrogen bonds : bond 0.01677 ( 153) hydrogen bonds : angle 4.04187 ( 459) *********************** 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 166 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: F 342 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7463 (mm-30) REVERT: F 343 LYS cc_start: 0.8854 (mttp) cc_final: 0.8332 (mtpp) REVERT: G 342 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7488 (tp30) REVERT: G 343 LYS cc_start: 0.8848 (mttp) cc_final: 0.8207 (mtpp) REVERT: H 343 LYS cc_start: 0.8689 (mttp) cc_final: 0.8397 (mtpm) REVERT: H 375 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8582 (tttt) REVERT: I 369 LYS cc_start: 0.9075 (mttm) cc_final: 0.8844 (mtmt) REVERT: I 379 ARG cc_start: 0.8048 (mtt-85) cc_final: 0.7111 (mpp-170) REVERT: J 343 LYS cc_start: 0.8762 (mttp) cc_final: 0.8105 (mtpp) REVERT: N 342 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7808 (mm-30) REVERT: N 343 LYS cc_start: 0.8812 (mttp) cc_final: 0.8207 (mtpp) REVERT: N 372 GLU cc_start: 0.8492 (tt0) cc_final: 0.8155 (mt-10) REVERT: O 342 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7882 (tp30) REVERT: O 343 LYS cc_start: 0.8854 (mttp) cc_final: 0.8344 (mtpp) REVERT: O 375 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8616 (tttt) REVERT: P 342 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: P 343 LYS cc_start: 0.8615 (mttp) cc_final: 0.8199 (mtpp) REVERT: Q 343 LYS cc_start: 0.8939 (mttp) cc_final: 0.8368 (mtpp) REVERT: Q 372 GLU cc_start: 0.8663 (tt0) cc_final: 0.8449 (tt0) REVERT: Q 375 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8518 (tttt) REVERT: R 379 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.6885 (mpp-170) outliers start: 6 outliers final: 1 residues processed: 164 average time/residue: 1.5693 time to fit residues: 266.3845 Evaluate side-chains 148 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain P residue 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 0.3980 chunk 56 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN N 307 GLN Q 307 GLN R 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.112003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096365 restraints weight = 23905.546| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.84 r_work: 0.3541 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.5280 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= 0.131 Angle : 0.556 5.918 7820 Z= 0.282 Chirality : 0.050 0.123 880 Planarity : 0.003 0.025 1000 Dihedral : 5.500 15.421 780 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.45 % Allowed : 23.64 % Favored : 75.91 % 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: -1.47 (0.28), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 379 TYR 0.009 0.002 TYR G 310 PHE 0.004 0.001 PHE N 378 HIS 0.005 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5840) covalent geometry : angle 0.55624 ( 7820) hydrogen bonds : bond 0.01929 ( 153) hydrogen bonds : angle 4.18375 ( 459) *********************** 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 152 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.368 Fit side-chains REVERT: F 342 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7498 (mm-30) REVERT: F 349 ARG cc_start: 0.7837 (mtm180) cc_final: 0.7614 (mtm180) REVERT: G 342 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7011 (tp30) REVERT: G 343 LYS cc_start: 0.8860 (mttp) cc_final: 0.8239 (mtpp) REVERT: H 343 LYS cc_start: 0.8734 (mttp) cc_final: 0.8439 (mtpm) REVERT: H 375 LYS cc_start: 0.8864 (ttpt) cc_final: 0.8561 (tttt) REVERT: I 369 LYS cc_start: 0.9151 (mttm) cc_final: 0.8907 (mtmt) REVERT: I 379 ARG cc_start: 0.8063 (mtt-85) cc_final: 0.7109 (mpp-170) REVERT: J 342 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6664 (mt-10) REVERT: J 343 LYS cc_start: 0.8754 (mttp) cc_final: 0.8116 (mtpp) REVERT: N 342 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7883 (mm-30) REVERT: N 343 LYS cc_start: 0.8838 (mttp) cc_final: 0.8190 (mtpp) REVERT: N 372 GLU cc_start: 0.8518 (tt0) cc_final: 0.8157 (mt-10) REVERT: O 342 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7937 (tp30) REVERT: O 343 LYS cc_start: 0.8859 (mttp) cc_final: 0.8320 (mtpp) REVERT: O 375 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8550 (tttt) REVERT: P 342 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: P 343 LYS cc_start: 0.8646 (mttp) cc_final: 0.8225 (mtpp) REVERT: Q 343 LYS cc_start: 0.8943 (mttp) cc_final: 0.8369 (mtpp) REVERT: Q 372 GLU cc_start: 0.8699 (tt0) cc_final: 0.8479 (tt0) REVERT: Q 375 LYS cc_start: 0.8818 (ttpt) cc_final: 0.8512 (tttt) REVERT: R 379 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.6911 (mpp-170) outliers start: 3 outliers final: 0 residues processed: 149 average time/residue: 1.5418 time to fit residues: 237.9539 Evaluate side-chains 149 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain P residue 342 GLU 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: 3.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Q 307 GLN R 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.111971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096134 restraints weight = 23965.181| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.84 r_work: 0.3534 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.5302 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= 0.135 Angle : 0.562 6.021 7820 Z= 0.285 Chirality : 0.050 0.124 880 Planarity : 0.004 0.042 1000 Dihedral : 5.583 15.533 780 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.30 % Allowed : 24.39 % Favored : 75.30 % 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: -1.47 (0.28), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 379 TYR 0.009 0.002 TYR G 310 PHE 0.005 0.001 PHE Q 378 HIS 0.005 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5840) covalent geometry : angle 0.56209 ( 7820) hydrogen bonds : bond 0.01950 ( 153) hydrogen bonds : angle 4.22153 ( 459) ********************** 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 152 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.354 Fit side-chains REVERT: F 342 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7500 (mm-30) REVERT: F 349 ARG cc_start: 0.7842 (mtm180) cc_final: 0.7615 (mtm180) REVERT: G 340 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8102 (mtpp) REVERT: G 342 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7773 (tp30) REVERT: G 343 LYS cc_start: 0.8858 (mttp) cc_final: 0.8223 (mtpp) REVERT: H 343 LYS cc_start: 0.8749 (mttp) cc_final: 0.8456 (mtpm) REVERT: H 375 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8584 (tttt) REVERT: I 369 LYS cc_start: 0.9159 (mttm) cc_final: 0.8900 (mtmt) REVERT: I 379 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7113 (mpp-170) REVERT: J 342 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6997 (mm-30) REVERT: J 343 LYS cc_start: 0.8765 (mttp) cc_final: 0.8103 (mtpp) REVERT: N 342 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7774 (mm-30) REVERT: N 343 LYS cc_start: 0.8841 (mttp) cc_final: 0.8174 (mtpp) REVERT: N 372 GLU cc_start: 0.8533 (tt0) cc_final: 0.8170 (mt-10) REVERT: O 342 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7909 (tp30) REVERT: O 343 LYS cc_start: 0.8866 (mttp) cc_final: 0.8306 (mtpp) REVERT: O 375 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8551 (tttt) REVERT: P 342 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7275 (mm-30) REVERT: P 343 LYS cc_start: 0.8655 (mttp) cc_final: 0.8215 (mtpp) REVERT: Q 343 LYS cc_start: 0.8958 (mttp) cc_final: 0.8357 (mtpp) REVERT: Q 372 GLU cc_start: 0.8718 (tt0) cc_final: 0.8495 (tt0) REVERT: Q 375 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8485 (tttt) REVERT: R 379 ARG cc_start: 0.8134 (mtt-85) cc_final: 0.6896 (mpp-170) outliers start: 2 outliers final: 0 residues processed: 150 average time/residue: 1.5555 time to fit residues: 241.5641 Evaluate side-chains 150 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain P residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 34 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Q 307 GLN R 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.112330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.096493 restraints weight = 23958.838| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.85 r_work: 0.3540 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.5298 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= 0.128 Angle : 0.560 5.448 7820 Z= 0.284 Chirality : 0.050 0.123 880 Planarity : 0.003 0.024 1000 Dihedral : 5.534 15.495 780 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.45 % Allowed : 24.24 % Favored : 75.30 % 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: -1.47 (0.28), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 349 TYR 0.009 0.002 TYR G 310 PHE 0.003 0.001 PHE R 346 HIS 0.005 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 5840) covalent geometry : angle 0.56050 ( 7820) hydrogen bonds : bond 0.01900 ( 153) hydrogen bonds : angle 4.20328 ( 459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5990.33 seconds wall clock time: 102 minutes 4.13 seconds (6124.13 seconds total)