Starting phenix.real_space_refine on Fri Jun 5 05:10:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o6x_70184/06_2026/9o6x_70184.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o6x_70184/06_2026/9o6x_70184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o6x_70184/06_2026/9o6x_70184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o6x_70184/06_2026/9o6x_70184.map" model { file = "/net/cci-nas-00/data/ceres_data/9o6x_70184/06_2026/9o6x_70184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o6x_70184/06_2026/9o6x_70184.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 5400 2.51 5 N 1590 2.21 5 O 1620 1.98 5 H 9000 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17625 Number of models: 1 Model: "" Number of chains: 15 Chain: "R" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "S" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "T" 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: "U" 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: "V" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "W" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "X" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "Y" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "Z" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "a" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "e" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "f" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "g" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "h" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "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} Time building chain proxies: 3.26, per 1000 atoms: 0.18 Number of scatterers: 17625 At special positions: 0 Unit cell: (133.934, 154.716, 50.8024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 1620 8.00 N 1590 7.00 C 5400 6.00 H 9000 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 644.3 milliseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 26 sheets defined 0.0% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'R' and resid 306 through 310 removed outlier: 6.462A pdb=" N GLN S 307 " --> pdb=" O ILE T 308 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N TYR T 310 " --> pdb=" O GLN S 307 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL S 309 " --> pdb=" O TYR T 310 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN T 307 " --> pdb=" O ILE U 308 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TYR U 310 " --> pdb=" O GLN T 307 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL T 309 " --> pdb=" O TYR U 310 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN U 307 " --> pdb=" O ILE V 308 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N TYR V 310 " --> pdb=" O GLN U 307 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL U 309 " --> pdb=" O TYR V 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 313 through 314 removed outlier: 6.570A pdb=" N VAL R 313 " --> pdb=" O ASP S 314 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL S 313 " --> pdb=" O ASP T 314 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL T 313 " --> pdb=" O ASP U 314 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL U 313 " --> pdb=" O ASP V 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'R' and resid 317 through 321 Processing sheet with id=AA4, first strand: chain 'R' and resid 325 through 330 removed outlier: 8.595A pdb=" N LEU R 325 " --> pdb=" O GLY S 326 " (cutoff:3.500A) removed outlier: 9.799A pdb=" N ILE S 328 " --> pdb=" O LEU R 325 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN R 327 " --> pdb=" O ILE S 328 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N HIS S 330 " --> pdb=" O ASN R 327 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS R 329 " --> pdb=" O HIS S 330 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N LEU S 325 " --> pdb=" O GLY T 326 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N ILE T 328 " --> pdb=" O LEU S 325 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN S 327 " --> pdb=" O ILE T 328 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N HIS T 330 " --> pdb=" O ASN S 327 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS S 329 " --> pdb=" O HIS T 330 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N LEU T 325 " --> pdb=" O GLY U 326 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N ILE U 328 " --> pdb=" O LEU T 325 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN T 327 " --> pdb=" O ILE U 328 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N HIS U 330 " --> pdb=" O ASN T 327 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HIS T 329 " --> pdb=" O HIS U 330 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU U 325 " --> pdb=" O GLY V 326 " (cutoff:3.500A) removed outlier: 9.750A pdb=" N ILE V 328 " --> pdb=" O LEU U 325 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN U 327 " --> pdb=" O ILE V 328 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N HIS V 330 " --> pdb=" O ASN U 327 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N HIS U 329 " --> pdb=" O HIS V 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'R' and resid 336 through 339 removed outlier: 6.515A pdb=" N GLN R 336 " --> pdb=" O VAL S 337 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N VAL S 339 " --> pdb=" O GLN R 336 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU R 338 " --> pdb=" O VAL S 339 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN S 336 " --> pdb=" O VAL T 337 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N VAL T 339 " --> pdb=" O GLN S 336 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU S 338 " --> pdb=" O VAL T 339 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN T 336 " --> pdb=" O VAL U 337 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL U 339 " --> pdb=" O GLN T 336 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU T 338 " --> pdb=" O VAL U 339 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN U 336 " --> pdb=" O VAL V 337 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N VAL V 339 " --> pdb=" O GLN U 336 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU U 338 " --> pdb=" O VAL V 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'R' and resid 343 through 346 removed outlier: 6.424A pdb=" N LYS R 343 " --> pdb=" O LEU S 344 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N PHE S 346 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP R 345 " --> pdb=" O PHE S 346 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS S 343 " --> pdb=" O LEU T 344 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N PHE T 346 " --> pdb=" O LYS S 343 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASP S 345 " --> pdb=" O PHE T 346 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS T 343 " --> pdb=" O LEU U 344 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N PHE U 346 " --> pdb=" O LYS T 343 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP T 345 " --> pdb=" O PHE U 346 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS U 343 " --> pdb=" O LEU V 344 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N PHE V 346 " --> pdb=" O LYS U 343 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP U 345 " --> pdb=" O PHE V 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'R' and resid 350 through 356 removed outlier: 6.525A pdb=" N GLN R 351 " --> pdb=" O SER S 352 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE S 354 " --> pdb=" O GLN R 351 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS R 353 " --> pdb=" O ILE S 354 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER S 356 " --> pdb=" O LYS R 353 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N GLY R 355 " --> pdb=" O SER S 356 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLN S 351 " --> pdb=" O SER T 352 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE T 354 " --> pdb=" O GLN S 351 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS S 353 " --> pdb=" O ILE T 354 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER T 356 " --> pdb=" O LYS S 353 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY S 355 " --> pdb=" O SER T 356 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN T 351 " --> pdb=" O SER U 352 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE U 354 " --> pdb=" O GLN T 351 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS T 353 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER U 356 " --> pdb=" O LYS T 353 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLY T 355 " --> pdb=" O SER U 356 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN U 351 " --> pdb=" O SER V 352 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE V 354 " --> pdb=" O GLN U 351 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS U 353 " --> pdb=" O ILE V 354 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER V 356 " --> pdb=" O LYS U 353 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY U 355 " --> pdb=" O SER V 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'R' and resid 359 through 361 removed outlier: 6.383A pdb=" N ILE R 360 " --> pdb=" O THR S 361 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE S 360 " --> pdb=" O THR T 361 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE T 360 " --> pdb=" O THR U 361 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE U 360 " --> pdb=" O THR V 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'R' and resid 369 through 377 removed outlier: 6.485A pdb=" N LYS R 369 " --> pdb=" O LYS S 370 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLU S 372 " --> pdb=" O LYS R 369 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE R 371 " --> pdb=" O GLU S 372 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N HIS S 374 " --> pdb=" O ILE R 371 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR R 373 " --> pdb=" O HIS S 374 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU S 376 " --> pdb=" O THR R 373 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS R 375 " --> pdb=" O LEU S 376 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS S 369 " --> pdb=" O LYS T 370 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLU T 372 " --> pdb=" O LYS S 369 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE S 371 " --> pdb=" O GLU T 372 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N HIS T 374 " --> pdb=" O ILE S 371 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR S 373 " --> pdb=" O HIS T 374 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU T 376 " --> pdb=" O THR S 373 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS S 375 " --> pdb=" O LEU T 376 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS T 369 " --> pdb=" O LYS U 370 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU U 372 " --> pdb=" O LYS T 369 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE T 371 " --> pdb=" O GLU U 372 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N HIS U 374 " --> pdb=" O ILE T 371 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR T 373 " --> pdb=" O HIS U 374 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU U 376 " --> pdb=" O THR T 373 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS T 375 " --> pdb=" O LEU U 376 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS U 369 " --> pdb=" O LYS V 370 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLU V 372 " --> pdb=" O LYS U 369 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE U 371 " --> pdb=" O GLU V 372 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N HIS V 374 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR U 373 " --> pdb=" O HIS V 374 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LEU V 376 " --> pdb=" O THR U 373 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS U 375 " --> pdb=" O LEU V 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'Y' and resid 306 through 310 removed outlier: 6.567A pdb=" N GLN X 307 " --> pdb=" O ILE Y 308 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N TYR Y 310 " --> pdb=" O GLN X 307 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL X 309 " --> pdb=" O TYR Y 310 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN W 307 " --> pdb=" O ILE X 308 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N TYR X 310 " --> pdb=" O GLN W 307 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL W 309 " --> pdb=" O TYR X 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Y' and resid 313 through 314 removed outlier: 6.602A pdb=" N VAL X 313 " --> pdb=" O ASP Y 314 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL W 313 " --> pdb=" O ASP X 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Y' and resid 317 through 321 removed outlier: 6.265A pdb=" N LYS X 317 " --> pdb=" O VAL Y 318 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N SER Y 320 " --> pdb=" O LYS X 317 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR X 319 " --> pdb=" O SER Y 320 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS W 317 " --> pdb=" O VAL X 318 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N SER X 320 " --> pdb=" O LYS W 317 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR W 319 " --> pdb=" O SER X 320 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 325 through 330 removed outlier: 8.890A pdb=" N LEU X 325 " --> pdb=" O GLY Y 326 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N ILE Y 328 " --> pdb=" O LEU X 325 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN X 327 " --> pdb=" O ILE Y 328 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N HIS Y 330 " --> pdb=" O ASN X 327 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N HIS X 329 " --> pdb=" O HIS Y 330 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N LEU W 325 " --> pdb=" O GLY X 326 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N ILE X 328 " --> pdb=" O LEU W 325 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN W 327 " --> pdb=" O ILE X 328 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N HIS X 330 " --> pdb=" O ASN W 327 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N HIS W 329 " --> pdb=" O HIS X 330 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY W 326 " --> pdb=" O LEU Z 325 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN Z 327 " --> pdb=" O GLY W 326 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY Z 326 " --> pdb=" O LEU a 325 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN a 327 " --> pdb=" O GLY Z 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 336 through 340 removed outlier: 6.521A pdb=" N VAL Z 337 " --> pdb=" O GLU a 338 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LYS a 340 " --> pdb=" O VAL Z 337 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL Z 339 " --> pdb=" O LYS a 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 344 through 346 removed outlier: 6.525A pdb=" N ASP X 345 " --> pdb=" O PHE Y 346 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP W 345 " --> pdb=" O PHE X 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Y' and resid 350 through 356 removed outlier: 6.821A pdb=" N SER Y 356 " --> pdb=" O GLY X 355 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER X 356 " --> pdb=" O GLY W 355 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL W 350 " --> pdb=" O GLN Z 351 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LYS Z 353 " --> pdb=" O VAL W 350 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER W 352 " --> pdb=" O LYS Z 353 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N GLY Z 355 " --> pdb=" O SER W 352 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ILE W 354 " --> pdb=" O GLY Z 355 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL Z 350 " --> pdb=" O GLN a 351 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LYS a 353 " --> pdb=" O VAL Z 350 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER Z 352 " --> pdb=" O LYS a 353 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY a 355 " --> pdb=" O SER Z 352 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ILE Z 354 " --> pdb=" O GLY a 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 359 through 361 removed outlier: 6.449A pdb=" N ILE X 360 " --> pdb=" O THR Y 361 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE W 360 " --> pdb=" O THR X 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 369 through 377 removed outlier: 6.412A pdb=" N LYS X 369 " --> pdb=" O LYS Y 370 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLU Y 372 " --> pdb=" O LYS X 369 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE X 371 " --> pdb=" O GLU Y 372 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N HIS Y 374 " --> pdb=" O ILE X 371 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR X 373 " --> pdb=" O HIS Y 374 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU Y 376 " --> pdb=" O THR X 373 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS X 375 " --> pdb=" O LEU Y 376 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS W 369 " --> pdb=" O LYS X 370 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU X 372 " --> pdb=" O LYS W 369 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE W 371 " --> pdb=" O GLU X 372 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N HIS X 374 " --> pdb=" O ILE W 371 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR W 373 " --> pdb=" O HIS X 374 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU X 376 " --> pdb=" O THR W 373 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS W 375 " --> pdb=" O LEU X 376 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'e' and resid 306 through 310 Processing sheet with id=AC2, first strand: chain 'e' and resid 317 through 321 removed outlier: 6.222A pdb=" N LYS e 317 " --> pdb=" O VAL f 318 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N SER f 320 " --> pdb=" O LYS e 317 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR e 319 " --> pdb=" O SER f 320 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS f 317 " --> pdb=" O VAL g 318 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N SER g 320 " --> pdb=" O LYS f 317 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR f 319 " --> pdb=" O SER g 320 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS g 317 " --> pdb=" O VAL h 318 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N SER h 320 " --> pdb=" O LYS g 317 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR g 319 " --> pdb=" O SER h 320 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LYS h 317 " --> pdb=" O VAL i 318 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N SER i 320 " --> pdb=" O LYS h 317 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR h 319 " --> pdb=" O SER i 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'e' and resid 328 through 330 removed outlier: 6.516A pdb=" N HIS e 329 " --> pdb=" O HIS f 330 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS f 329 " --> pdb=" O HIS g 330 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N HIS g 329 " --> pdb=" O HIS h 330 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N HIS h 329 " --> pdb=" O HIS i 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'e' and resid 336 through 340 Processing sheet with id=AC5, first strand: chain 'e' and resid 344 through 348 removed outlier: 6.930A pdb=" N ASP f 345 " --> pdb=" O LEU e 344 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE e 346 " --> pdb=" O ASP f 345 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS f 347 " --> pdb=" O PHE e 346 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP g 345 " --> pdb=" O LEU f 344 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE f 346 " --> pdb=" O ASP g 345 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS g 347 " --> pdb=" O PHE f 346 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP h 345 " --> pdb=" O LEU g 344 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE g 346 " --> pdb=" O ASP h 345 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS h 347 " --> pdb=" O PHE g 346 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP i 345 " --> pdb=" O LEU h 344 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE h 346 " --> pdb=" O ASP i 345 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS i 347 " --> pdb=" O PHE h 346 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 351 through 354 removed outlier: 6.632A pdb=" N GLN e 351 " --> pdb=" O SER f 352 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ILE f 354 " --> pdb=" O GLN e 351 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS e 353 " --> pdb=" O ILE f 354 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN f 351 " --> pdb=" O SER g 352 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE g 354 " --> pdb=" O GLN f 351 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS f 353 " --> pdb=" O ILE g 354 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN g 351 " --> pdb=" O SER h 352 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ILE h 354 " --> pdb=" O GLN g 351 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS g 353 " --> pdb=" O ILE h 354 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN h 351 " --> pdb=" O SER i 352 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE i 354 " --> pdb=" O GLN h 351 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS h 353 " --> pdb=" O ILE i 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'e' and resid 357 through 361 removed outlier: 6.375A pdb=" N ASP e 358 " --> pdb=" O ASN f 359 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N THR f 361 " --> pdb=" O ASP e 358 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE e 360 " --> pdb=" O THR f 361 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP f 358 " --> pdb=" O ASN g 359 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR g 361 " --> pdb=" O ASP f 358 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE f 360 " --> pdb=" O THR g 361 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP g 358 " --> pdb=" O ASN h 359 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR h 361 " --> pdb=" O ASP g 358 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE g 360 " --> pdb=" O THR h 361 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP h 358 " --> pdb=" O ASN i 359 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR i 361 " --> pdb=" O ASP h 358 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE h 360 " --> pdb=" O THR i 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'e' and resid 369 through 377 removed outlier: 6.654A pdb=" N LYS e 369 " --> pdb=" O LYS f 370 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N GLU f 372 " --> pdb=" O LYS e 369 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE e 371 " --> pdb=" O GLU f 372 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N HIS f 374 " --> pdb=" O ILE e 371 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR e 373 " --> pdb=" O HIS f 374 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU f 376 " --> pdb=" O THR e 373 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS e 375 " --> pdb=" O LEU f 376 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS g 369 " --> pdb=" O LYS h 370 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLU h 372 " --> pdb=" O LYS g 369 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE g 371 " --> pdb=" O GLU h 372 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N HIS h 374 " --> pdb=" O ILE g 371 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR g 373 " --> pdb=" O HIS h 374 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LEU h 376 " --> pdb=" O THR g 373 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS g 375 " --> pdb=" O LEU h 376 " (cutoff:3.500A) 142 hydrogen bonds defined for protein. 426 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: 4.43 Time building geometry restraints manager: 2.12 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: 8985 1.12 - 1.29: 1440 1.29 - 1.46: 2610 1.46 - 1.64: 4710 1.64 - 1.81: 15 Bond restraints: 17760 Sorted by residual: bond pdb=" N ASP g 345 " pdb=" H ASP g 345 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL i 363 " pdb=" H VAL i 363 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLU X 342 " pdb=" H GLU X 342 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ASN S 359 " pdb=" H ASN S 359 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 PHE Z 346 " pdb=" HE1 PHE Z 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 17755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 26549 2.48 - 4.97: 4491 4.97 - 7.45: 1284 7.45 - 9.94: 46 9.94 - 12.42: 15 Bond angle restraints: 32385 Sorted by residual: angle pdb=" N GLY a 326 " pdb=" CA GLY a 326 " pdb=" C GLY a 326 " ideal model delta sigma weight residual 110.69 117.97 -7.28 1.33e+00 5.65e-01 2.99e+01 angle pdb=" N GLY W 326 " pdb=" CA GLY W 326 " pdb=" C GLY W 326 " ideal model delta sigma weight residual 110.69 117.94 -7.25 1.33e+00 5.65e-01 2.97e+01 angle pdb=" N GLY Z 326 " pdb=" CA GLY Z 326 " pdb=" C GLY Z 326 " ideal model delta sigma weight residual 110.69 117.94 -7.25 1.33e+00 5.65e-01 2.97e+01 angle pdb=" N GLY Y 326 " pdb=" CA GLY Y 326 " pdb=" C GLY Y 326 " ideal model delta sigma weight residual 110.69 117.91 -7.22 1.33e+00 5.65e-01 2.95e+01 angle pdb=" N GLY X 326 " pdb=" CA GLY X 326 " pdb=" C GLY X 326 " ideal model delta sigma weight residual 110.69 117.90 -7.21 1.33e+00 5.65e-01 2.94e+01 ... (remaining 32380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.37: 7042 14.37 - 28.74: 578 28.74 - 43.11: 240 43.11 - 57.47: 165 57.47 - 71.84: 135 Dihedral angle restraints: 8160 sinusoidal: 4665 harmonic: 3495 Sorted by residual: dihedral pdb=" C VAL Z 363 " pdb=" N VAL Z 363 " pdb=" CA VAL Z 363 " pdb=" CB VAL Z 363 " ideal model delta harmonic sigma weight residual -122.00 -137.15 15.15 0 2.50e+00 1.60e-01 3.67e+01 dihedral pdb=" C VAL W 363 " pdb=" N VAL W 363 " pdb=" CA VAL W 363 " pdb=" CB VAL W 363 " ideal model delta harmonic sigma weight residual -122.00 -137.10 15.10 0 2.50e+00 1.60e-01 3.65e+01 dihedral pdb=" C VAL X 363 " pdb=" N VAL X 363 " pdb=" CA VAL X 363 " pdb=" CB VAL X 363 " ideal model delta harmonic sigma weight residual -122.00 -137.10 15.10 0 2.50e+00 1.60e-01 3.65e+01 ... (remaining 8157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 919 0.089 - 0.178: 278 0.178 - 0.267: 70 0.267 - 0.356: 38 0.356 - 0.445: 15 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA VAL a 363 " pdb=" N VAL a 363 " pdb=" C VAL a 363 " pdb=" CB VAL a 363 " both_signs ideal model delta sigma weight residual False 2.44 2.00 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CA VAL Z 363 " pdb=" N VAL Z 363 " pdb=" C VAL Z 363 " pdb=" CB VAL Z 363 " both_signs ideal model delta sigma weight residual False 2.44 2.00 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CA VAL W 363 " pdb=" N VAL W 363 " pdb=" C VAL W 363 " pdb=" CB VAL W 363 " both_signs ideal model delta sigma weight residual False 2.44 2.00 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 1317 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR a 310 " 0.089 2.00e-02 2.50e+03 4.03e-02 4.87e+01 pdb=" CG TYR a 310 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR a 310 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR a 310 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR a 310 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR a 310 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR a 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR a 310 " 0.084 2.00e-02 2.50e+03 pdb=" HD1 TYR a 310 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR a 310 " -0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR a 310 " -0.020 2.00e-02 2.50e+03 pdb=" HE2 TYR a 310 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR X 310 " 0.089 2.00e-02 2.50e+03 4.03e-02 4.86e+01 pdb=" CG TYR X 310 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR X 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR X 310 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR X 310 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR X 310 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR X 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR X 310 " 0.084 2.00e-02 2.50e+03 pdb=" HD1 TYR X 310 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR X 310 " -0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR X 310 " -0.020 2.00e-02 2.50e+03 pdb=" HE2 TYR X 310 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Y 310 " 0.089 2.00e-02 2.50e+03 4.02e-02 4.86e+01 pdb=" CG TYR Y 310 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR Y 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR Y 310 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR Y 310 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR Y 310 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR Y 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR Y 310 " 0.084 2.00e-02 2.50e+03 pdb=" HD1 TYR Y 310 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR Y 310 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 TYR Y 310 " -0.020 2.00e-02 2.50e+03 pdb=" HE2 TYR Y 310 " -0.010 2.00e-02 2.50e+03 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.90: 338 1.90 - 2.57: 16286 2.57 - 3.25: 53437 3.25 - 3.92: 69365 3.92 - 4.60: 102720 Nonbonded interactions: 242146 Sorted by model distance: nonbonded pdb="HD13 LEU U 315 " pdb="HD22 LEU V 315 " model vdw 1.219 2.440 nonbonded pdb="HD13 LEU S 315 " pdb="HD22 LEU T 315 " model vdw 1.253 2.440 nonbonded pdb="HD13 LEU T 315 " pdb="HD22 LEU U 315 " model vdw 1.257 2.440 nonbonded pdb=" HB2 LEU U 315 " pdb="HD23 LEU V 315 " model vdw 1.268 2.440 nonbonded pdb="HD13 LEU R 315 " pdb="HD22 LEU S 315 " model vdw 1.274 2.440 ... (remaining 242141 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 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } 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: 0.940 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.340 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 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 0.035 8760 Z= 0.703 Angle : 2.009 9.521 11730 Z= 1.310 Chirality : 0.107 0.445 1320 Planarity : 0.010 0.047 1500 Dihedral : 12.111 71.842 3375 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Cbeta Deviations : 1.01 % 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: -1.81 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG Z 349 TYR 0.080 0.028 TYR Z 310 PHE 0.027 0.009 PHE g 346 HIS 0.016 0.004 HIS S 330 Details of bonding type rmsd/Z covalent geometry : bond 0.01088 / 0.70 ( 8760) covalent geometry : angle 2.00931 / 1.31 (11730) hydrogen bonds : bond 0.13283 / 8.63 ( 142) hydrogen bonds : angle 8.33962 / 5.56 ( 426) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 311 LYS cc_start: 0.7358 (ttmt) cc_final: 0.6908 (mmtm) REVERT: S 338 GLU cc_start: 0.7738 (tt0) cc_final: 0.7347 (tt0) REVERT: T 338 GLU cc_start: 0.8123 (tt0) cc_final: 0.7864 (tt0) REVERT: U 358 ASP cc_start: 0.6824 (m-30) cc_final: 0.6303 (m-30) REVERT: V 338 GLU cc_start: 0.8079 (tt0) cc_final: 0.7825 (tt0) REVERT: W 369 LYS cc_start: 0.7622 (mttt) cc_final: 0.7373 (mttt) REVERT: W 375 LYS cc_start: 0.7478 (tttt) cc_final: 0.7118 (ttpt) REVERT: X 369 LYS cc_start: 0.7578 (mttt) cc_final: 0.7299 (mttt) REVERT: Y 338 GLU cc_start: 0.7860 (tt0) cc_final: 0.7620 (tt0) REVERT: Y 348 ASP cc_start: 0.6766 (t0) cc_final: 0.6547 (t0) REVERT: Y 369 LYS cc_start: 0.8255 (mttt) cc_final: 0.7892 (mttp) REVERT: Y 379 ARG cc_start: 0.6334 (mtt-85) cc_final: 0.6099 (mtm-85) REVERT: Z 369 LYS cc_start: 0.7415 (mttt) cc_final: 0.7163 (mttt) REVERT: a 311 LYS cc_start: 0.7446 (mttt) cc_final: 0.6975 (mmtt) REVERT: a 317 LYS cc_start: 0.6129 (mttm) cc_final: 0.5773 (mmtm) REVERT: a 331 LYS cc_start: 0.7734 (tttt) cc_final: 0.6665 (tptp) REVERT: a 369 LYS cc_start: 0.7546 (mttt) cc_final: 0.7341 (mttp) REVERT: e 307 GLN cc_start: 0.7770 (pt0) cc_final: 0.7324 (pt0) REVERT: e 311 LYS cc_start: 0.7300 (mttt) cc_final: 0.6821 (mmtm) REVERT: e 369 LYS cc_start: 0.7571 (mttt) cc_final: 0.7349 (mttt) REVERT: f 375 LYS cc_start: 0.7721 (tttt) cc_final: 0.7497 (tttp) REVERT: g 338 GLU cc_start: 0.7380 (tt0) cc_final: 0.7149 (tt0) REVERT: h 307 GLN cc_start: 0.7537 (pt0) cc_final: 0.7107 (pt0) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 1.6173 time to fit residues: 648.0264 Evaluate side-chains 250 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 374 HIS W 307 GLN W 374 HIS X 307 GLN X 374 HIS Y 374 HIS ** Z 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 351 GLN Z 374 HIS ** a 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 374 HIS e 351 GLN f 351 GLN ** f 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 374 HIS ** h 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 368 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.115621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100076 restraints weight = 30639.503| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.59 r_work: 0.3477 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8760 Z= 0.174 Angle : 0.826 6.329 11730 Z= 0.426 Chirality : 0.053 0.142 1320 Planarity : 0.005 0.052 1500 Dihedral : 8.167 70.047 1170 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 1.82 % Allowed : 18.18 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z 379 TYR 0.010 0.002 TYR S 310 PHE 0.007 0.001 PHE T 378 HIS 0.007 0.002 HIS W 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 8760) covalent geometry : angle 0.82604 / 0.43 (11730) hydrogen bonds : bond 0.04331 / 2.95 ( 142) hydrogen bonds : angle 6.47438 / 4.32 ( 426) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 311 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8201 (mmtm) REVERT: R 372 GLU cc_start: 0.8430 (tt0) cc_final: 0.8227 (tt0) REVERT: S 371 ILE cc_start: 0.8581 (tt) cc_final: 0.8325 (mt) REVERT: U 340 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8089 (mptm) REVERT: V 321 LYS cc_start: 0.8659 (tttt) cc_final: 0.8424 (tptp) REVERT: X 340 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8125 (tttp) REVERT: Y 369 LYS cc_start: 0.8940 (mttt) cc_final: 0.8642 (mttp) REVERT: Y 379 ARG cc_start: 0.7609 (mtt-85) cc_final: 0.6593 (mtm-85) REVERT: Z 340 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8203 (tmtp) REVERT: e 307 GLN cc_start: 0.8010 (pt0) cc_final: 0.7710 (pt0) REVERT: h 307 GLN cc_start: 0.8007 (pt0) cc_final: 0.7727 (pt0) REVERT: i 379 ARG cc_start: 0.5328 (tmm160) cc_final: 0.5087 (ptt-90) outliers start: 18 outliers final: 3 residues processed: 256 average time/residue: 1.6380 time to fit residues: 439.7012 Evaluate side-chains 218 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 214 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 369 LYS Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain g residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 374 HIS S 374 HIS T 374 HIS U 374 HIS W 307 GLN X 307 GLN a 307 GLN e 374 HIS f 374 HIS h 374 HIS i 374 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.112077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.097374 restraints weight = 33642.494| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.62 r_work: 0.3479 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8760 Z= 0.235 Angle : 0.775 7.266 11730 Z= 0.408 Chirality : 0.052 0.141 1320 Planarity : 0.005 0.044 1500 Dihedral : 7.619 64.652 1170 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 1.82 % Allowed : 21.11 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG h 379 TYR 0.013 0.003 TYR g 310 PHE 0.011 0.002 PHE g 378 HIS 0.007 0.002 HIS V 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 ( 8760) covalent geometry : angle 0.77484 / 0.41 (11730) hydrogen bonds : bond 0.03611 / 2.48 ( 142) hydrogen bonds : angle 6.06890 / 4.12 ( 426) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 311 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8186 (mmtm) REVERT: R 348 ASP cc_start: 0.7833 (t0) cc_final: 0.7625 (t70) REVERT: R 372 GLU cc_start: 0.8590 (tt0) cc_final: 0.8304 (tt0) REVERT: S 338 GLU cc_start: 0.8670 (tt0) cc_final: 0.8452 (tt0) REVERT: S 340 LYS cc_start: 0.8487 (mptp) cc_final: 0.8254 (mptm) REVERT: U 345 ASP cc_start: 0.8112 (p0) cc_final: 0.7755 (p0) REVERT: U 347 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7718 (mtmt) REVERT: U 349 ARG cc_start: 0.8605 (mtm180) cc_final: 0.8405 (mtm180) REVERT: V 317 LYS cc_start: 0.8944 (pttp) cc_final: 0.8596 (ptpp) REVERT: V 321 LYS cc_start: 0.8737 (tttt) cc_final: 0.8493 (tptp) REVERT: X 340 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8279 (tttp) REVERT: X 348 ASP cc_start: 0.7780 (t0) cc_final: 0.7559 (t70) REVERT: Y 369 LYS cc_start: 0.8937 (mttt) cc_final: 0.8626 (mttp) REVERT: Y 379 ARG cc_start: 0.7553 (mtt-85) cc_final: 0.6544 (mtm-85) REVERT: Z 340 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8432 (tmtp) REVERT: e 340 LYS cc_start: 0.8722 (mtpp) cc_final: 0.8254 (mptt) REVERT: f 317 LYS cc_start: 0.8039 (mtpm) cc_final: 0.7386 (mttt) REVERT: g 379 ARG cc_start: 0.7731 (ttm110) cc_final: 0.7201 (tpm170) REVERT: h 307 GLN cc_start: 0.7956 (pt0) cc_final: 0.7695 (pt0) REVERT: h 321 LYS cc_start: 0.8781 (mttt) cc_final: 0.8349 (ttmm) REVERT: h 379 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7237 (tpm170) REVERT: i 340 LYS cc_start: 0.9016 (mttp) cc_final: 0.8781 (mtpp) outliers start: 18 outliers final: 9 residues processed: 224 average time/residue: 1.6068 time to fit residues: 377.8557 Evaluate side-chains 201 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain U residue 347 LYS Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain g residue 320 SER Chi-restraints excluded: chain g residue 327 ASN Chi-restraints excluded: chain g residue 356 SER Chi-restraints excluded: chain h residue 305 SER Chi-restraints excluded: chain i residue 305 SER Chi-restraints excluded: chain i residue 307 GLN Chi-restraints excluded: chain i residue 327 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 307 GLN Y 307 GLN a 307 GLN g 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.112135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.097441 restraints weight = 33572.601| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.62 r_work: 0.3477 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8760 Z= 0.224 Angle : 0.716 5.778 11730 Z= 0.375 Chirality : 0.051 0.135 1320 Planarity : 0.005 0.046 1500 Dihedral : 7.485 59.940 1170 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.42 % Allowed : 21.52 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 379 TYR 0.011 0.002 TYR g 310 PHE 0.011 0.001 PHE S 378 HIS 0.006 0.002 HIS V 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 ( 8760) covalent geometry : angle 0.71579 / 0.38 (11730) hydrogen bonds : bond 0.03229 / 2.19 ( 142) hydrogen bonds : angle 5.83262 / 3.99 ( 426) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 348 ASP cc_start: 0.7820 (t0) cc_final: 0.7568 (t70) REVERT: R 349 ARG cc_start: 0.9005 (mtm180) cc_final: 0.8715 (mtm180) REVERT: R 372 GLU cc_start: 0.8564 (tt0) cc_final: 0.8279 (tt0) REVERT: S 317 LYS cc_start: 0.8539 (ptpp) cc_final: 0.8086 (pttp) REVERT: S 369 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8731 (mttm) REVERT: T 340 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8025 (mptp) REVERT: T 342 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: T 345 ASP cc_start: 0.8249 (p0) cc_final: 0.7658 (p0) REVERT: U 342 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7554 (mm-30) REVERT: V 317 LYS cc_start: 0.8936 (pttp) cc_final: 0.8625 (ptpp) REVERT: V 321 LYS cc_start: 0.8732 (tttt) cc_final: 0.8476 (tptp) REVERT: V 342 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: V 345 ASP cc_start: 0.8264 (p0) cc_final: 0.7954 (t70) REVERT: X 321 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8236 (mtpt) REVERT: X 340 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8335 (tttp) REVERT: X 348 ASP cc_start: 0.7721 (t0) cc_final: 0.7442 (t70) REVERT: Y 369 LYS cc_start: 0.8941 (mttt) cc_final: 0.8625 (mttp) REVERT: Y 379 ARG cc_start: 0.7574 (mtt-85) cc_final: 0.6370 (ttp-110) REVERT: Z 340 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8472 (tmtp) REVERT: a 345 ASP cc_start: 0.8903 (t0) cc_final: 0.8579 (t0) REVERT: e 340 LYS cc_start: 0.8784 (mtpp) cc_final: 0.8105 (mptt) REVERT: f 317 LYS cc_start: 0.8014 (mtpm) cc_final: 0.7370 (mttt) REVERT: f 340 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8229 (mmtm) REVERT: f 348 ASP cc_start: 0.7759 (t0) cc_final: 0.7466 (t0) REVERT: g 379 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7593 (ttm110) REVERT: h 307 GLN cc_start: 0.7908 (pt0) cc_final: 0.7673 (pt0) REVERT: h 321 LYS cc_start: 0.8774 (mttt) cc_final: 0.8360 (ttmm) REVERT: i 340 LYS cc_start: 0.8993 (mttp) cc_final: 0.8754 (mtpp) REVERT: i 342 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8090 (mt-10) outliers start: 24 outliers final: 13 residues processed: 211 average time/residue: 1.6563 time to fit residues: 366.1765 Evaluate side-chains 205 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain T residue 315 LEU Chi-restraints excluded: chain T residue 340 LYS Chi-restraints excluded: chain T residue 342 GLU Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain U residue 342 GLU Chi-restraints excluded: chain V residue 342 GLU Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain X residue 321 LYS Chi-restraints excluded: chain e residue 327 ASN Chi-restraints excluded: chain e residue 356 SER Chi-restraints excluded: chain f residue 307 GLN Chi-restraints excluded: chain g residue 320 SER Chi-restraints excluded: chain g residue 327 ASN Chi-restraints excluded: chain g residue 356 SER Chi-restraints excluded: chain h residue 305 SER Chi-restraints excluded: chain i residue 305 SER Chi-restraints excluded: chain i residue 307 GLN Chi-restraints excluded: chain i residue 327 ASN Chi-restraints excluded: chain i residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 61 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 307 GLN X 307 GLN Y 307 GLN ** Y 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 307 GLN g 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.116874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.102592 restraints weight = 33122.069| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.64 r_work: 0.3559 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8760 Z= 0.096 Angle : 0.596 4.884 11730 Z= 0.308 Chirality : 0.051 0.133 1320 Planarity : 0.004 0.049 1500 Dihedral : 6.768 55.639 1170 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.31 % Allowed : 22.93 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 379 TYR 0.009 0.001 TYR g 310 PHE 0.004 0.001 PHE U 378 HIS 0.006 0.001 HIS W 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 8760) covalent geometry : angle 0.59639 / 0.31 (11730) hydrogen bonds : bond 0.02220 / 1.54 ( 142) hydrogen bonds : angle 5.42611 / 3.71 ( 426) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.515 Fit side-chains REVERT: R 311 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8014 (mmtm) REVERT: R 349 ARG cc_start: 0.8913 (mtm180) cc_final: 0.8554 (mtm180) REVERT: T 340 LYS cc_start: 0.8266 (mptp) cc_final: 0.8061 (mptm) REVERT: T 342 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: T 345 ASP cc_start: 0.7879 (p0) cc_final: 0.7151 (p0) REVERT: U 342 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: U 345 ASP cc_start: 0.7781 (p0) cc_final: 0.7043 (t70) REVERT: V 317 LYS cc_start: 0.8934 (pttp) cc_final: 0.8599 (ptpp) REVERT: V 321 LYS cc_start: 0.8712 (tttt) cc_final: 0.8454 (tptp) REVERT: V 342 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: X 319 THR cc_start: 0.8967 (m) cc_final: 0.8482 (p) REVERT: X 340 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8254 (tttp) REVERT: Y 379 ARG cc_start: 0.7460 (mtt-85) cc_final: 0.6410 (ttp-110) REVERT: Z 340 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8396 (tmtp) REVERT: Z 342 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7609 (mt-10) REVERT: e 340 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8159 (mptt) REVERT: f 317 LYS cc_start: 0.7966 (mtpm) cc_final: 0.7332 (mttt) REVERT: f 340 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8321 (mttp) REVERT: h 321 LYS cc_start: 0.8647 (mttt) cc_final: 0.8289 (ttmm) REVERT: i 342 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7866 (mt-10) outliers start: 13 outliers final: 2 residues processed: 217 average time/residue: 1.5668 time to fit residues: 357.5061 Evaluate side-chains 201 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 342 GLU Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain U residue 342 GLU Chi-restraints excluded: chain V residue 342 GLU Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain i residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 28 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 307 GLN Y 307 GLN a 307 GLN e 307 GLN f 307 GLN g 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.114639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.100166 restraints weight = 33037.095| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.60 r_work: 0.3519 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8760 Z= 0.150 Angle : 0.622 5.827 11730 Z= 0.323 Chirality : 0.050 0.132 1320 Planarity : 0.005 0.056 1500 Dihedral : 6.689 54.375 1170 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 1.62 % Allowed : 23.84 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG h 379 TYR 0.009 0.002 TYR g 310 PHE 0.009 0.001 PHE T 378 HIS 0.005 0.001 HIS W 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 8760) covalent geometry : angle 0.62220 / 0.32 (11730) hydrogen bonds : bond 0.02504 / 1.70 ( 142) hydrogen bonds : angle 5.38837 / 3.70 ( 426) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 311 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8112 (mmtm) REVERT: T 342 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: T 345 ASP cc_start: 0.8016 (p0) cc_final: 0.7338 (p0) REVERT: U 342 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7543 (mm-30) REVERT: U 345 ASP cc_start: 0.7816 (p0) cc_final: 0.7110 (t70) REVERT: V 317 LYS cc_start: 0.8962 (pttp) cc_final: 0.8621 (ptpp) REVERT: V 321 LYS cc_start: 0.8712 (tttt) cc_final: 0.8439 (tptp) REVERT: V 342 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: X 319 THR cc_start: 0.8981 (m) cc_final: 0.8481 (p) REVERT: X 340 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8277 (tttp) REVERT: X 379 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7556 (mmt-90) REVERT: Y 379 ARG cc_start: 0.7516 (mtt-85) cc_final: 0.6421 (ttp-110) REVERT: Z 340 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8459 (tmtp) REVERT: Z 342 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7743 (mt-10) REVERT: e 340 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8141 (mptt) REVERT: f 317 LYS cc_start: 0.8046 (mtpm) cc_final: 0.7408 (mttt) REVERT: f 340 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8289 (mttm) REVERT: f 342 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: h 321 LYS cc_start: 0.8697 (mttt) cc_final: 0.8352 (ttmm) REVERT: i 342 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8059 (mt-10) outliers start: 16 outliers final: 9 residues processed: 205 average time/residue: 1.6799 time to fit residues: 361.1261 Evaluate side-chains 205 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 341 SER Chi-restraints excluded: chain T residue 342 GLU Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain U residue 342 GLU Chi-restraints excluded: chain V residue 342 GLU Chi-restraints excluded: chain W residue 348 ASP Chi-restraints excluded: chain W residue 363 VAL Chi-restraints excluded: chain e residue 373 THR Chi-restraints excluded: chain f residue 342 GLU Chi-restraints excluded: chain g residue 320 SER Chi-restraints excluded: chain g residue 327 ASN Chi-restraints excluded: chain g residue 356 SER Chi-restraints excluded: chain i residue 307 GLN Chi-restraints excluded: chain i residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 307 GLN X 307 GLN Y 307 GLN a 307 GLN e 307 GLN g 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.114493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.099922 restraints weight = 33329.856| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.61 r_work: 0.3517 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8760 Z= 0.150 Angle : 0.627 4.826 11730 Z= 0.327 Chirality : 0.050 0.148 1320 Planarity : 0.005 0.061 1500 Dihedral : 6.711 57.628 1170 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.02 % Allowed : 23.13 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 379 TYR 0.010 0.002 TYR g 310 PHE 0.007 0.001 PHE S 378 HIS 0.006 0.001 HIS a 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 8760) covalent geometry : angle 0.62669 / 0.33 (11730) hydrogen bonds : bond 0.02451 / 1.65 ( 142) hydrogen bonds : angle 5.35197 / 3.67 ( 426) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: R 311 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8211 (mmtm) REVERT: T 342 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: T 345 ASP cc_start: 0.8027 (p0) cc_final: 0.7271 (p0) REVERT: U 342 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7568 (mm-30) REVERT: U 345 ASP cc_start: 0.7799 (p0) cc_final: 0.7305 (t70) REVERT: V 317 LYS cc_start: 0.8955 (pttp) cc_final: 0.8632 (ptpp) REVERT: V 321 LYS cc_start: 0.8749 (tttt) cc_final: 0.8452 (tptp) REVERT: V 342 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: X 319 THR cc_start: 0.8979 (m) cc_final: 0.8495 (p) REVERT: X 340 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8274 (tttp) REVERT: X 379 ARG cc_start: 0.7830 (mtt90) cc_final: 0.7539 (mmt-90) REVERT: Y 379 ARG cc_start: 0.7501 (mtt-85) cc_final: 0.6386 (ttp-110) REVERT: Z 340 LYS cc_start: 0.8735 (ttmm) cc_final: 0.8464 (tmtp) REVERT: Z 342 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7734 (mt-10) REVERT: e 340 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8150 (mptt) REVERT: f 317 LYS cc_start: 0.8057 (mtpm) cc_final: 0.7426 (mttt) REVERT: f 340 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8341 (mttm) REVERT: f 342 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: h 321 LYS cc_start: 0.8704 (mttt) cc_final: 0.8366 (ttmm) REVERT: i 342 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7936 (mt-10) outliers start: 20 outliers final: 12 residues processed: 211 average time/residue: 1.6643 time to fit residues: 368.5384 Evaluate side-chains 209 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 315 LEU Chi-restraints excluded: chain T residue 341 SER Chi-restraints excluded: chain T residue 342 GLU Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain U residue 342 GLU Chi-restraints excluded: chain V residue 342 GLU Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain W residue 348 ASP Chi-restraints excluded: chain W residue 363 VAL Chi-restraints excluded: chain e residue 327 ASN Chi-restraints excluded: chain e residue 356 SER Chi-restraints excluded: chain f residue 342 GLU Chi-restraints excluded: chain g residue 320 SER Chi-restraints excluded: chain g residue 327 ASN Chi-restraints excluded: chain g residue 356 SER Chi-restraints excluded: chain h residue 305 SER Chi-restraints excluded: chain i residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 307 GLN X 307 GLN Y 307 GLN a 307 GLN e 307 GLN g 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.113270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.098664 restraints weight = 33126.384| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.59 r_work: 0.3496 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8760 Z= 0.176 Angle : 0.643 5.146 11730 Z= 0.336 Chirality : 0.050 0.152 1320 Planarity : 0.005 0.061 1500 Dihedral : 6.784 59.086 1170 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 2.02 % Allowed : 23.33 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG f 379 TYR 0.010 0.002 TYR g 310 PHE 0.006 0.001 PHE T 378 HIS 0.006 0.001 HIS a 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 8760) covalent geometry : angle 0.64340 / 0.34 (11730) hydrogen bonds : bond 0.02584 / 1.75 ( 142) hydrogen bonds : angle 5.40000 / 3.71 ( 426) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.546 Fit side-chains REVERT: R 311 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8183 (mmtm) REVERT: R 349 ARG cc_start: 0.8779 (mtm180) cc_final: 0.8479 (mtm180) REVERT: T 342 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: T 345 ASP cc_start: 0.8067 (p0) cc_final: 0.7302 (p0) REVERT: U 342 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7607 (mm-30) REVERT: U 345 ASP cc_start: 0.7835 (p0) cc_final: 0.7378 (t70) REVERT: V 317 LYS cc_start: 0.8956 (pttp) cc_final: 0.8645 (ptpp) REVERT: V 321 LYS cc_start: 0.8755 (tttt) cc_final: 0.8459 (tptp) REVERT: V 342 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: X 319 THR cc_start: 0.8996 (m) cc_final: 0.8500 (p) REVERT: X 340 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8294 (tttp) REVERT: X 348 ASP cc_start: 0.7648 (t0) cc_final: 0.7416 (t70) REVERT: X 379 ARG cc_start: 0.7838 (mtt90) cc_final: 0.7545 (mmt-90) REVERT: Y 369 LYS cc_start: 0.8959 (mttt) cc_final: 0.8707 (mttt) REVERT: Y 379 ARG cc_start: 0.7425 (mtt-85) cc_final: 0.6148 (ttp-110) REVERT: Z 340 LYS cc_start: 0.8735 (ttmm) cc_final: 0.8483 (tmtp) REVERT: Z 342 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7750 (mt-10) REVERT: a 345 ASP cc_start: 0.8753 (t0) cc_final: 0.8369 (t0) REVERT: e 340 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8205 (mptt) REVERT: f 317 LYS cc_start: 0.8078 (mtpm) cc_final: 0.7427 (mttt) REVERT: f 340 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8302 (mttm) REVERT: f 342 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: h 321 LYS cc_start: 0.8707 (mttt) cc_final: 0.8387 (ttmm) REVERT: i 342 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8109 (mt-10) outliers start: 20 outliers final: 16 residues processed: 205 average time/residue: 1.6185 time to fit residues: 348.1805 Evaluate side-chains 215 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 315 LEU Chi-restraints excluded: chain T residue 341 SER Chi-restraints excluded: chain T residue 342 GLU Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain U residue 342 GLU Chi-restraints excluded: chain V residue 342 GLU Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain W residue 348 ASP Chi-restraints excluded: chain W residue 363 VAL Chi-restraints excluded: chain e residue 327 ASN Chi-restraints excluded: chain e residue 356 SER Chi-restraints excluded: chain e residue 373 THR Chi-restraints excluded: chain f residue 327 ASN Chi-restraints excluded: chain f residue 342 GLU Chi-restraints excluded: chain g residue 320 SER Chi-restraints excluded: chain g residue 327 ASN Chi-restraints excluded: chain g residue 356 SER Chi-restraints excluded: chain h residue 305 SER Chi-restraints excluded: chain h residue 373 THR Chi-restraints excluded: chain i residue 305 SER Chi-restraints excluded: chain i residue 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 307 GLN V 307 GLN Y 307 GLN g 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.113699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099108 restraints weight = 33083.383| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.60 r_work: 0.3512 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8760 Z= 0.165 Angle : 0.642 5.993 11730 Z= 0.334 Chirality : 0.050 0.157 1320 Planarity : 0.005 0.063 1500 Dihedral : 6.846 60.188 1170 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 1.82 % Allowed : 23.94 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG f 379 TYR 0.010 0.002 TYR V 310 PHE 0.006 0.001 PHE T 378 HIS 0.005 0.001 HIS W 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 8760) covalent geometry : angle 0.64240 / 0.33 (11730) hydrogen bonds : bond 0.02475 / 1.66 ( 142) hydrogen bonds : angle 5.33740 / 3.64 ( 426) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.438 Fit side-chains REVERT: R 311 LYS cc_start: 0.8846 (ttmt) cc_final: 0.8213 (mmtm) REVERT: S 345 ASP cc_start: 0.7880 (p0) cc_final: 0.7499 (t70) REVERT: T 342 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: T 345 ASP cc_start: 0.7991 (p0) cc_final: 0.7441 (p0) REVERT: U 342 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: U 345 ASP cc_start: 0.7802 (p0) cc_final: 0.7391 (t70) REVERT: V 307 GLN cc_start: 0.8477 (tt0) cc_final: 0.8241 (tt0) REVERT: V 317 LYS cc_start: 0.8958 (pttp) cc_final: 0.8648 (ptpp) REVERT: V 321 LYS cc_start: 0.8760 (tttt) cc_final: 0.8461 (tptp) REVERT: V 342 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: X 319 THR cc_start: 0.8996 (m) cc_final: 0.8508 (p) REVERT: X 340 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8327 (tttp) REVERT: X 348 ASP cc_start: 0.7635 (t0) cc_final: 0.7410 (t70) REVERT: X 379 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7539 (mmt-90) REVERT: Y 369 LYS cc_start: 0.8969 (mttt) cc_final: 0.8717 (mttt) REVERT: Y 379 ARG cc_start: 0.7431 (mtt-85) cc_final: 0.6126 (ttp-110) REVERT: Z 340 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8485 (tmtp) REVERT: Z 342 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7760 (mt-10) REVERT: a 345 ASP cc_start: 0.8724 (t0) cc_final: 0.8360 (t0) REVERT: e 340 LYS cc_start: 0.8799 (mtpp) cc_final: 0.8196 (mptt) REVERT: f 317 LYS cc_start: 0.8049 (mtpm) cc_final: 0.7410 (mttt) REVERT: f 342 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: g 379 ARG cc_start: 0.7503 (ttm110) cc_final: 0.6850 (tpm170) REVERT: h 321 LYS cc_start: 0.8725 (mttt) cc_final: 0.8406 (ttmm) REVERT: h 379 ARG cc_start: 0.7805 (ttm110) cc_final: 0.7361 (tmt-80) REVERT: i 342 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7955 (mt-10) outliers start: 18 outliers final: 14 residues processed: 206 average time/residue: 1.7096 time to fit residues: 370.1664 Evaluate side-chains 212 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 315 LEU Chi-restraints excluded: chain T residue 341 SER Chi-restraints excluded: chain T residue 342 GLU Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain U residue 342 GLU Chi-restraints excluded: chain V residue 342 GLU Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain W residue 348 ASP Chi-restraints excluded: chain W residue 363 VAL Chi-restraints excluded: chain e residue 327 ASN Chi-restraints excluded: chain e residue 356 SER Chi-restraints excluded: chain e residue 373 THR Chi-restraints excluded: chain f residue 327 ASN Chi-restraints excluded: chain f residue 342 GLU Chi-restraints excluded: chain g residue 320 SER Chi-restraints excluded: chain g residue 327 ASN Chi-restraints excluded: chain g residue 356 SER Chi-restraints excluded: chain h residue 305 SER Chi-restraints excluded: chain i residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 36 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 307 GLN g 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.111190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096518 restraints weight = 33340.902| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.60 r_work: 0.3465 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8760 Z= 0.240 Angle : 0.701 6.662 11730 Z= 0.366 Chirality : 0.051 0.160 1320 Planarity : 0.006 0.067 1500 Dihedral : 7.043 60.913 1170 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 1.92 % Allowed : 23.84 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG f 379 TYR 0.011 0.002 TYR V 310 PHE 0.011 0.002 PHE T 378 HIS 0.006 0.001 HIS a 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 ( 8760) covalent geometry : angle 0.70113 / 0.37 (11730) hydrogen bonds : bond 0.02884 / 1.92 ( 142) hydrogen bonds : angle 5.45086 / 3.70 ( 426) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.530 Fit side-chains REVERT: R 311 LYS cc_start: 0.8823 (ttmt) cc_final: 0.8216 (mmtm) REVERT: R 349 ARG cc_start: 0.8795 (mtm180) cc_final: 0.8568 (mtm180) REVERT: T 342 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: T 345 ASP cc_start: 0.8045 (p0) cc_final: 0.7464 (p0) REVERT: U 342 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: U 345 ASP cc_start: 0.7907 (p0) cc_final: 0.7457 (t70) REVERT: V 317 LYS cc_start: 0.8967 (pttp) cc_final: 0.8655 (ptpp) REVERT: V 321 LYS cc_start: 0.8753 (tttt) cc_final: 0.8438 (tptp) REVERT: V 342 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: X 319 THR cc_start: 0.8954 (m) cc_final: 0.8466 (p) REVERT: X 340 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8314 (tttp) REVERT: X 348 ASP cc_start: 0.7699 (t0) cc_final: 0.7397 (t70) REVERT: X 379 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7554 (mmt-90) REVERT: Y 369 LYS cc_start: 0.8964 (mttt) cc_final: 0.8763 (mttt) REVERT: Y 379 ARG cc_start: 0.7432 (mtt-85) cc_final: 0.6127 (ttp-110) REVERT: Z 340 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8474 (tmtp) REVERT: Z 342 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7761 (mt-10) REVERT: a 345 ASP cc_start: 0.8890 (t0) cc_final: 0.8554 (t0) REVERT: a 379 ARG cc_start: 0.5702 (mmp-170) cc_final: 0.4928 (tpp-160) REVERT: e 340 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8140 (mptt) REVERT: f 317 LYS cc_start: 0.8068 (mtpm) cc_final: 0.7427 (mttt) REVERT: f 340 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8392 (mttm) REVERT: g 379 ARG cc_start: 0.7539 (ttm110) cc_final: 0.6845 (tpm170) REVERT: h 321 LYS cc_start: 0.8740 (mttt) cc_final: 0.8398 (ttmm) REVERT: i 342 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8153 (mt-10) outliers start: 19 outliers final: 14 residues processed: 199 average time/residue: 1.6685 time to fit residues: 348.4231 Evaluate side-chains 206 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 315 LEU Chi-restraints excluded: chain T residue 341 SER Chi-restraints excluded: chain T residue 342 GLU Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain U residue 342 GLU Chi-restraints excluded: chain V residue 342 GLU Chi-restraints excluded: chain W residue 363 VAL Chi-restraints excluded: chain e residue 327 ASN Chi-restraints excluded: chain e residue 356 SER Chi-restraints excluded: chain e residue 373 THR Chi-restraints excluded: chain f residue 327 ASN Chi-restraints excluded: chain g residue 320 SER Chi-restraints excluded: chain g residue 327 ASN Chi-restraints excluded: chain g residue 356 SER Chi-restraints excluded: chain h residue 305 SER Chi-restraints excluded: chain h residue 373 THR Chi-restraints excluded: chain i residue 305 SER Chi-restraints excluded: chain i residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 89 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 307 GLN Y 307 GLN g 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.113335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.098813 restraints weight = 33337.277| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.62 r_work: 0.3516 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8760 Z= 0.139 Angle : 0.632 6.289 11730 Z= 0.328 Chirality : 0.050 0.146 1320 Planarity : 0.005 0.063 1500 Dihedral : 6.864 58.935 1170 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 1.62 % Allowed : 24.34 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG f 379 TYR 0.009 0.002 TYR f 310 PHE 0.004 0.001 PHE W 378 HIS 0.005 0.001 HIS W 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 8760) covalent geometry : angle 0.63216 / 0.33 (11730) hydrogen bonds : bond 0.02331 / 1.57 ( 142) hydrogen bonds : angle 5.30756 / 3.60 ( 426) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8234.30 seconds wall clock time: 140 minutes 4.72 seconds (8404.72 seconds total)