Starting phenix.real_space_refine on Mon May 4 04:15:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7c_70194/05_2026/9o7c_70194.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7c_70194/05_2026/9o7c_70194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o7c_70194/05_2026/9o7c_70194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7c_70194/05_2026/9o7c_70194.map" model { file = "/net/cci-nas-00/data/ceres_data/9o7c_70194/05_2026/9o7c_70194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7c_70194/05_2026/9o7c_70194.cif" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 5400 2.51 5 N 1590 2.21 5 O 1620 1.98 5 H 9000 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17625 Number of models: 1 Model: "" Number of chains: 3 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: "i" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "j" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1175 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Restraints were copied for chains: T, U, V, W, k, m, o, q, l, n, p, r Time building chain proxies: 2.11, per 1000 atoms: 0.12 Number of scatterers: 17625 At special positions: 0 Unit cell: (144.325, 133.934, 49.6478, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 1620 8.00 N 1590 7.00 C 5400 6.00 H 9000 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 493.9 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 23 sheets defined 0.0% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'S' and resid 306 through 310 removed outlier: 6.509A pdb=" N GLN S 307 " --> pdb=" O ILE T 308 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR T 310 " --> pdb=" O GLN S 307 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL S 309 " --> pdb=" O TYR T 310 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLN T 307 " --> pdb=" O ILE U 308 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR U 310 " --> pdb=" O GLN T 307 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL T 309 " --> pdb=" O TYR U 310 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN U 307 " --> pdb=" O ILE V 308 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TYR V 310 " --> pdb=" O GLN U 307 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL U 309 " --> pdb=" O TYR V 310 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN V 307 " --> pdb=" O ILE W 308 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TYR W 310 " --> pdb=" O GLN V 307 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL V 309 " --> pdb=" O TYR W 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'S' and resid 313 through 314 removed outlier: 6.691A pdb=" N VAL S 313 " --> pdb=" O ASP T 314 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL T 313 " --> pdb=" O ASP U 314 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL U 313 " --> pdb=" O ASP V 314 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL V 313 " --> pdb=" O ASP W 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'S' and resid 317 through 321 removed outlier: 6.280A pdb=" N LYS S 317 " --> pdb=" O VAL T 318 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N SER T 320 " --> pdb=" O LYS S 317 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR S 319 " --> pdb=" O SER T 320 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS T 317 " --> pdb=" O VAL U 318 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N SER U 320 " --> pdb=" O LYS T 317 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR T 319 " --> pdb=" O SER U 320 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LYS U 317 " --> pdb=" O VAL V 318 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N SER V 320 " --> pdb=" O LYS U 317 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR U 319 " --> pdb=" O SER V 320 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS V 317 " --> pdb=" O VAL W 318 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N SER W 320 " --> pdb=" O LYS V 317 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR V 319 " --> pdb=" O SER W 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'S' and resid 325 through 330 removed outlier: 8.808A pdb=" N LEU S 325 " --> pdb=" O GLY T 326 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N ILE T 328 " --> pdb=" O LEU S 325 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN S 327 " --> pdb=" O ILE T 328 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N HIS T 330 " --> pdb=" O ASN S 327 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS S 329 " --> pdb=" O HIS T 330 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N LEU T 325 " --> pdb=" O GLY U 326 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N ILE U 328 " --> pdb=" O LEU T 325 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN T 327 " --> pdb=" O ILE U 328 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS U 330 " --> pdb=" O ASN T 327 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS T 329 " --> pdb=" O HIS U 330 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N LEU U 325 " --> pdb=" O GLY V 326 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N ILE V 328 " --> pdb=" O LEU U 325 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN U 327 " --> pdb=" O ILE V 328 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS V 330 " --> pdb=" O ASN U 327 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS U 329 " --> pdb=" O HIS V 330 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N LEU V 325 " --> pdb=" O GLY W 326 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N ILE W 328 " --> pdb=" O LEU V 325 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN V 327 " --> pdb=" O ILE W 328 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N HIS W 330 " --> pdb=" O ASN V 327 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N HIS V 329 " --> pdb=" O HIS W 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'S' and resid 336 through 340 Processing sheet with id=AA6, first strand: chain 'S' and resid 344 through 356 removed outlier: 6.935A pdb=" N ASP T 345 " --> pdb=" O LEU S 344 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE S 346 " --> pdb=" O ASP T 345 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS T 347 " --> pdb=" O PHE S 346 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL S 350 " --> pdb=" O ARG T 349 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN T 351 " --> pdb=" O VAL S 350 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER S 352 " --> pdb=" O GLN T 351 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS T 353 " --> pdb=" O SER S 352 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE S 354 " --> pdb=" O LYS T 353 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY T 355 " --> pdb=" O ILE S 354 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP U 345 " --> pdb=" O LEU T 344 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE T 346 " --> pdb=" O ASP U 345 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS U 347 " --> pdb=" O PHE T 346 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL T 350 " --> pdb=" O ARG U 349 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLN U 351 " --> pdb=" O VAL T 350 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER T 352 " --> pdb=" O GLN U 351 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS U 353 " --> pdb=" O SER T 352 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE T 354 " --> pdb=" O LYS U 353 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY U 355 " --> pdb=" O ILE T 354 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP V 345 " --> pdb=" O LEU U 344 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE U 346 " --> pdb=" O ASP V 345 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS V 347 " --> pdb=" O PHE U 346 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL U 350 " --> pdb=" O ARG V 349 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN V 351 " --> pdb=" O VAL U 350 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER U 352 " --> pdb=" O GLN V 351 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS V 353 " --> pdb=" O SER U 352 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE U 354 " --> pdb=" O LYS V 353 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY V 355 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP W 345 " --> pdb=" O LEU V 344 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE V 346 " --> pdb=" O ASP W 345 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS W 347 " --> pdb=" O PHE V 346 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL V 350 " --> pdb=" O ARG W 349 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN W 351 " --> pdb=" O VAL V 350 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N SER V 352 " --> pdb=" O GLN W 351 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS W 353 " --> pdb=" O SER V 352 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE V 354 " --> pdb=" O LYS W 353 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY W 355 " --> pdb=" O ILE V 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 359 through 361 removed outlier: 6.430A pdb=" N ILE S 360 " --> pdb=" O THR T 361 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE T 360 " --> pdb=" O THR U 361 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE U 360 " --> pdb=" O THR V 361 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE V 360 " --> pdb=" O THR W 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'S' and resid 369 through 378 removed outlier: 6.450A pdb=" N LYS S 369 " --> pdb=" O LYS T 370 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLU T 372 " --> pdb=" O LYS S 369 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE S 371 " --> pdb=" O GLU T 372 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N HIS T 374 " --> pdb=" O ILE S 371 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR S 373 " --> pdb=" O HIS T 374 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU T 376 " --> pdb=" O THR S 373 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS S 375 " --> pdb=" O LEU T 376 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N PHE T 378 " --> pdb=" O LYS S 375 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR S 377 " --> pdb=" O PHE T 378 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS T 369 " --> pdb=" O LYS U 370 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLU U 372 " --> pdb=" O LYS T 369 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE T 371 " --> pdb=" O GLU U 372 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N HIS U 374 " --> pdb=" O ILE T 371 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR T 373 " --> pdb=" O HIS U 374 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU U 376 " --> pdb=" O THR T 373 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS T 375 " --> pdb=" O LEU U 376 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE U 378 " --> pdb=" O LYS T 375 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR T 377 " --> pdb=" O PHE U 378 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS U 369 " --> pdb=" O LYS V 370 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLU V 372 " --> pdb=" O LYS U 369 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE U 371 " --> pdb=" O GLU V 372 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N HIS V 374 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR U 373 " --> pdb=" O HIS V 374 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU V 376 " --> pdb=" O THR U 373 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS U 375 " --> pdb=" O LEU V 376 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE V 378 " --> pdb=" O LYS U 375 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR U 377 " --> pdb=" O PHE V 378 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS V 369 " --> pdb=" O LYS W 370 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLU W 372 " --> pdb=" O LYS V 369 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE V 371 " --> pdb=" O GLU W 372 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N HIS W 374 " --> pdb=" O ILE V 371 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR V 373 " --> pdb=" O HIS W 374 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU W 376 " --> pdb=" O THR V 373 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LYS V 375 " --> pdb=" O LEU W 376 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE W 378 " --> pdb=" O LYS V 375 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR V 377 " --> pdb=" O PHE W 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'i' and resid 306 through 310 removed outlier: 6.511A pdb=" N GLN i 307 " --> pdb=" O ILE k 308 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR k 310 " --> pdb=" O GLN i 307 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL i 309 " --> pdb=" O TYR k 310 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLN k 307 " --> pdb=" O ILE m 308 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N TYR m 310 " --> pdb=" O GLN k 307 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL k 309 " --> pdb=" O TYR m 310 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLN m 307 " --> pdb=" O ILE o 308 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR o 310 " --> pdb=" O GLN m 307 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL m 309 " --> pdb=" O TYR o 310 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN o 307 " --> pdb=" O ILE q 308 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N TYR q 310 " --> pdb=" O GLN o 307 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL o 309 " --> pdb=" O TYR q 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'i' and resid 313 through 314 removed outlier: 6.663A pdb=" N VAL i 313 " --> pdb=" O ASP k 314 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL k 313 " --> pdb=" O ASP m 314 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL m 313 " --> pdb=" O ASP o 314 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL o 313 " --> pdb=" O ASP q 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'i' and resid 317 through 321 removed outlier: 6.221A pdb=" N LYS i 317 " --> pdb=" O VAL k 318 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N SER k 320 " --> pdb=" O LYS i 317 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR i 319 " --> pdb=" O SER k 320 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS k 317 " --> pdb=" O VAL m 318 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N SER m 320 " --> pdb=" O LYS k 317 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR k 319 " --> pdb=" O SER m 320 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS m 317 " --> pdb=" O VAL o 318 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N SER o 320 " --> pdb=" O LYS m 317 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR m 319 " --> pdb=" O SER o 320 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS o 317 " --> pdb=" O VAL q 318 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N SER q 320 " --> pdb=" O LYS o 317 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR o 319 " --> pdb=" O SER q 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'i' and resid 328 through 330 removed outlier: 6.548A pdb=" N HIS i 329 " --> pdb=" O HIS k 330 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS k 329 " --> pdb=" O HIS m 330 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS m 329 " --> pdb=" O HIS o 330 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS o 329 " --> pdb=" O HIS q 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'i' and resid 336 through 346 removed outlier: 6.908A pdb=" N VAL i 337 " --> pdb=" O GLN k 336 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU k 338 " --> pdb=" O VAL i 337 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL i 339 " --> pdb=" O GLU k 338 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS k 340 " --> pdb=" O VAL i 339 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER i 341 " --> pdb=" O LYS k 340 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLU k 342 " --> pdb=" O SER i 341 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL k 337 " --> pdb=" O GLN m 336 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU m 338 " --> pdb=" O VAL k 337 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL k 339 " --> pdb=" O GLU m 338 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS m 340 " --> pdb=" O VAL k 339 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER k 341 " --> pdb=" O LYS m 340 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU m 342 " --> pdb=" O SER k 341 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL m 337 " --> pdb=" O GLN o 336 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU o 338 " --> pdb=" O VAL m 337 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL m 339 " --> pdb=" O GLU o 338 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS o 340 " --> pdb=" O VAL m 339 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER m 341 " --> pdb=" O LYS o 340 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU o 342 " --> pdb=" O SER m 341 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL o 337 " --> pdb=" O GLN q 336 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU q 338 " --> pdb=" O VAL o 337 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL o 339 " --> pdb=" O GLU q 338 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS q 340 " --> pdb=" O VAL o 339 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER o 341 " --> pdb=" O LYS q 340 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU q 342 " --> pdb=" O SER o 341 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'i' and resid 351 through 356 removed outlier: 6.886A pdb=" N SER k 356 " --> pdb=" O GLY i 355 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER m 356 " --> pdb=" O GLY k 355 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N SER o 356 " --> pdb=" O GLY m 355 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER q 356 " --> pdb=" O GLY o 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'i' and resid 359 through 361 Processing sheet with id=AB7, first strand: chain 'i' and resid 369 through 377 removed outlier: 6.538A pdb=" N LYS i 369 " --> pdb=" O LYS k 370 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU k 372 " --> pdb=" O LYS i 369 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE i 371 " --> pdb=" O GLU k 372 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N HIS k 374 " --> pdb=" O ILE i 371 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR i 373 " --> pdb=" O HIS k 374 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU k 376 " --> pdb=" O THR i 373 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS i 375 " --> pdb=" O LEU k 376 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS k 369 " --> pdb=" O LYS m 370 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU m 372 " --> pdb=" O LYS k 369 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE k 371 " --> pdb=" O GLU m 372 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N HIS m 374 " --> pdb=" O ILE k 371 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR k 373 " --> pdb=" O HIS m 374 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU m 376 " --> pdb=" O THR k 373 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS k 375 " --> pdb=" O LEU m 376 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS m 369 " --> pdb=" O LYS o 370 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLU o 372 " --> pdb=" O LYS m 369 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE m 371 " --> pdb=" O GLU o 372 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N HIS o 374 " --> pdb=" O ILE m 371 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR m 373 " --> pdb=" O HIS o 374 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU o 376 " --> pdb=" O THR m 373 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS m 375 " --> pdb=" O LEU o 376 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS o 369 " --> pdb=" O LYS q 370 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLU q 372 " --> pdb=" O LYS o 369 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE o 371 " --> pdb=" O GLU q 372 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N HIS q 374 " --> pdb=" O ILE o 371 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N THR o 373 " --> pdb=" O HIS q 374 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU q 376 " --> pdb=" O THR o 373 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS o 375 " --> pdb=" O LEU q 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'j' and resid 306 through 310 removed outlier: 6.653A pdb=" N GLN j 307 " --> pdb=" O ILE l 308 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR l 310 " --> pdb=" O GLN j 307 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL j 309 " --> pdb=" O TYR l 310 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN l 307 " --> pdb=" O ILE n 308 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N TYR n 310 " --> pdb=" O GLN l 307 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL l 309 " --> pdb=" O TYR n 310 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN n 307 " --> pdb=" O ILE p 308 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N TYR p 310 " --> pdb=" O GLN n 307 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL n 309 " --> pdb=" O TYR p 310 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN p 307 " --> pdb=" O ILE r 308 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N TYR r 310 " --> pdb=" O GLN p 307 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL p 309 " --> pdb=" O TYR r 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'j' and resid 317 through 321 removed outlier: 6.213A pdb=" N LYS j 317 " --> pdb=" O VAL l 318 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N SER l 320 " --> pdb=" O LYS j 317 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR j 319 " --> pdb=" O SER l 320 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS l 317 " --> pdb=" O VAL n 318 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N SER n 320 " --> pdb=" O LYS l 317 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR l 319 " --> pdb=" O SER n 320 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS n 317 " --> pdb=" O VAL p 318 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N SER p 320 " --> pdb=" O LYS n 317 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR n 319 " --> pdb=" O SER p 320 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS p 317 " --> pdb=" O VAL r 318 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N SER r 320 " --> pdb=" O LYS p 317 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR p 319 " --> pdb=" O SER r 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'j' and resid 325 through 330 removed outlier: 8.770A pdb=" N LEU j 325 " --> pdb=" O GLY l 326 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N ILE l 328 " --> pdb=" O LEU j 325 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN j 327 " --> pdb=" O ILE l 328 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N HIS l 330 " --> pdb=" O ASN j 327 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS j 329 " --> pdb=" O HIS l 330 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N LEU l 325 " --> pdb=" O GLY n 326 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N ILE n 328 " --> pdb=" O LEU l 325 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN l 327 " --> pdb=" O ILE n 328 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N HIS n 330 " --> pdb=" O ASN l 327 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N HIS l 329 " --> pdb=" O HIS n 330 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N LEU n 325 " --> pdb=" O GLY p 326 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N ILE p 328 " --> pdb=" O LEU n 325 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN n 327 " --> pdb=" O ILE p 328 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N HIS p 330 " --> pdb=" O ASN n 327 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HIS n 329 " --> pdb=" O HIS p 330 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N LEU p 325 " --> pdb=" O GLY r 326 " (cutoff:3.500A) removed outlier: 9.855A pdb=" N ILE r 328 " --> pdb=" O LEU p 325 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASN p 327 " --> pdb=" O ILE r 328 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N HIS r 330 " --> pdb=" O ASN p 327 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS p 329 " --> pdb=" O HIS r 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'j' and resid 336 through 340 Processing sheet with id=AC3, first strand: chain 'j' and resid 344 through 346 Processing sheet with id=AC4, first strand: chain 'j' and resid 351 through 361 removed outlier: 9.013A pdb=" N SER j 352 " --> pdb=" O LYS l 353 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N GLY l 355 " --> pdb=" O SER j 352 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE j 354 " --> pdb=" O GLY l 355 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N LEU l 357 " --> pdb=" O ILE j 354 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER j 356 " --> pdb=" O LEU l 357 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASN l 359 " --> pdb=" O SER j 356 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP j 358 " --> pdb=" O ASN l 359 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR l 361 " --> pdb=" O ASP j 358 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE j 360 " --> pdb=" O THR l 361 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N SER l 352 " --> pdb=" O LYS n 353 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N GLY n 355 " --> pdb=" O SER l 352 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE l 354 " --> pdb=" O GLY n 355 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU n 357 " --> pdb=" O ILE l 354 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER l 356 " --> pdb=" O LEU n 357 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ASN n 359 " --> pdb=" O SER l 356 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP l 358 " --> pdb=" O ASN n 359 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR n 361 " --> pdb=" O ASP l 358 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE l 360 " --> pdb=" O THR n 361 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N SER n 352 " --> pdb=" O LYS p 353 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N GLY p 355 " --> pdb=" O SER n 352 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE n 354 " --> pdb=" O GLY p 355 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N LEU p 357 " --> pdb=" O ILE n 354 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER n 356 " --> pdb=" O LEU p 357 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ASN p 359 " --> pdb=" O SER n 356 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP n 358 " --> pdb=" O ASN p 359 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N THR p 361 " --> pdb=" O ASP n 358 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE n 360 " --> pdb=" O THR p 361 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N SER p 352 " --> pdb=" O LYS r 353 " (cutoff:3.500A) removed outlier: 10.224A pdb=" N GLY r 355 " --> pdb=" O SER p 352 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE p 354 " --> pdb=" O GLY r 355 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N LEU r 357 " --> pdb=" O ILE p 354 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER p 356 " --> pdb=" O LEU r 357 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ASN r 359 " --> pdb=" O SER p 356 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP p 358 " --> pdb=" O ASN r 359 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR r 361 " --> pdb=" O ASP p 358 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE p 360 " --> pdb=" O THR r 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'j' and resid 369 through 377 removed outlier: 6.524A pdb=" N LYS j 369 " --> pdb=" O LYS l 370 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N GLU l 372 " --> pdb=" O LYS j 369 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE j 371 " --> pdb=" O GLU l 372 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N HIS l 374 " --> pdb=" O ILE j 371 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR j 373 " --> pdb=" O HIS l 374 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU l 376 " --> pdb=" O THR j 373 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LYS j 375 " --> pdb=" O LEU l 376 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS l 369 " --> pdb=" O LYS n 370 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N GLU n 372 " --> pdb=" O LYS l 369 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE l 371 " --> pdb=" O GLU n 372 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N HIS n 374 " --> pdb=" O ILE l 371 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR l 373 " --> pdb=" O HIS n 374 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU n 376 " --> pdb=" O THR l 373 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS l 375 " --> pdb=" O LEU n 376 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS n 369 " --> pdb=" O LYS p 370 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLU p 372 " --> pdb=" O LYS n 369 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE n 371 " --> pdb=" O GLU p 372 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N HIS p 374 " --> pdb=" O ILE n 371 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR n 373 " --> pdb=" O HIS p 374 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU p 376 " --> pdb=" O THR n 373 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS n 375 " --> pdb=" O LEU p 376 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS p 369 " --> pdb=" O LYS r 370 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N GLU r 372 " --> pdb=" O LYS p 369 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE p 371 " --> pdb=" O GLU r 372 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N HIS r 374 " --> pdb=" O ILE p 371 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR p 373 " --> pdb=" O HIS r 374 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU r 376 " --> pdb=" O THR p 373 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS p 375 " --> pdb=" O LEU r 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 92 hydrogen bonds defined for protein. 276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 1.87 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 - 1.47: 2715 1.47 - 1.64: 4605 1.64 - 1.81: 15 Bond restraints: 17760 Sorted by residual: bond pdb=" N ASP p 358 " pdb=" H ASP p 358 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD1 PHE m 346 " pdb=" HD1 PHE m 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS o 353 " pdb=" H LYS o 353 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE2 PHE r 346 " pdb=" HE2 PHE r 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N GLY k 335 " pdb=" H GLY k 335 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 17755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 26093 2.40 - 4.80: 4790 4.80 - 7.20: 1397 7.20 - 9.60: 90 9.60 - 12.00: 15 Bond angle restraints: 32385 Sorted by residual: angle pdb=" OE1 GLN p 307 " pdb=" CD GLN p 307 " pdb=" NE2 GLN p 307 " ideal model delta sigma weight residual 122.60 117.26 5.34 1.00e+00 1.00e+00 2.85e+01 angle pdb=" OE1 GLN l 307 " pdb=" CD GLN l 307 " pdb=" NE2 GLN l 307 " ideal model delta sigma weight residual 122.60 117.28 5.32 1.00e+00 1.00e+00 2.83e+01 angle pdb=" OE1 GLN j 307 " pdb=" CD GLN j 307 " pdb=" NE2 GLN j 307 " ideal model delta sigma weight residual 122.60 117.28 5.32 1.00e+00 1.00e+00 2.83e+01 angle pdb=" OE1 GLN n 307 " pdb=" CD GLN n 307 " pdb=" NE2 GLN n 307 " ideal model delta sigma weight residual 122.60 117.29 5.31 1.00e+00 1.00e+00 2.82e+01 angle pdb=" OE1 GLN r 307 " pdb=" CD GLN r 307 " pdb=" NE2 GLN r 307 " ideal model delta sigma weight residual 122.60 117.30 5.30 1.00e+00 1.00e+00 2.81e+01 ... (remaining 32380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 7181 16.44 - 32.87: 529 32.87 - 49.30: 225 49.30 - 65.74: 205 65.74 - 82.17: 20 Dihedral angle restraints: 8160 sinusoidal: 4665 harmonic: 3495 Sorted by residual: dihedral pdb=" C VAL p 363 " pdb=" N VAL p 363 " pdb=" CA VAL p 363 " pdb=" CB VAL p 363 " ideal model delta harmonic sigma weight residual -122.00 -136.64 14.64 0 2.50e+00 1.60e-01 3.43e+01 dihedral pdb=" C VAL j 363 " pdb=" N VAL j 363 " pdb=" CA VAL j 363 " pdb=" CB VAL j 363 " ideal model delta harmonic sigma weight residual -122.00 -136.60 14.60 0 2.50e+00 1.60e-01 3.41e+01 dihedral pdb=" C VAL n 363 " pdb=" N VAL n 363 " pdb=" CA VAL n 363 " pdb=" CB VAL n 363 " ideal model delta harmonic sigma weight residual -122.00 -136.57 14.57 0 2.50e+00 1.60e-01 3.40e+01 ... (remaining 8157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 814 0.087 - 0.175: 360 0.175 - 0.262: 95 0.262 - 0.349: 26 0.349 - 0.437: 25 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA VAL p 363 " pdb=" N VAL p 363 " pdb=" C VAL p 363 " pdb=" CB VAL p 363 " both_signs ideal model delta sigma weight residual False 2.44 2.00 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA VAL j 363 " pdb=" N VAL j 363 " pdb=" C VAL j 363 " pdb=" CB VAL j 363 " both_signs ideal model delta sigma weight residual False 2.44 2.01 0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA VAL l 363 " pdb=" N VAL l 363 " pdb=" C VAL l 363 " pdb=" CB VAL l 363 " both_signs ideal model delta sigma weight residual False 2.44 2.01 0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 1317 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG j 349 " 0.457 9.50e-02 1.11e+02 1.56e-01 4.99e+01 pdb=" NE ARG j 349 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG j 349 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG j 349 " 0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG j 349 " -0.062 2.00e-02 2.50e+03 pdb="HH11 ARG j 349 " 0.023 2.00e-02 2.50e+03 pdb="HH12 ARG j 349 " -0.017 2.00e-02 2.50e+03 pdb="HH21 ARG j 349 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG j 349 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG n 349 " 0.457 9.50e-02 1.11e+02 1.56e-01 4.99e+01 pdb=" NE ARG n 349 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG n 349 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG n 349 " 0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG n 349 " -0.062 2.00e-02 2.50e+03 pdb="HH11 ARG n 349 " 0.023 2.00e-02 2.50e+03 pdb="HH12 ARG n 349 " -0.017 2.00e-02 2.50e+03 pdb="HH21 ARG n 349 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG n 349 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG l 349 " 0.457 9.50e-02 1.11e+02 1.56e-01 4.99e+01 pdb=" NE ARG l 349 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG l 349 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG l 349 " 0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG l 349 " -0.062 2.00e-02 2.50e+03 pdb="HH11 ARG l 349 " 0.023 2.00e-02 2.50e+03 pdb="HH12 ARG l 349 " -0.017 2.00e-02 2.50e+03 pdb="HH21 ARG l 349 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG l 349 " 0.061 2.00e-02 2.50e+03 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 1.28 - 1.94: 477 1.94 - 2.61: 18348 2.61 - 3.27: 52505 3.27 - 3.94: 69586 3.94 - 4.60: 101448 Nonbonded interactions: 242364 Sorted by model distance: nonbonded pdb=" HD1 HIS p 330 " pdb=" HG1 THR r 361 " model vdw 1.280 2.100 nonbonded pdb=" HD1 HIS n 330 " pdb=" HG1 THR p 361 " model vdw 1.288 2.100 nonbonded pdb=" HD1 HIS l 330 " pdb=" HG1 THR n 361 " model vdw 1.308 2.100 nonbonded pdb=" HD1 HIS j 330 " pdb=" HG1 THR l 361 " model vdw 1.313 2.100 nonbonded pdb="HG23 THR o 377 " pdb=" HG1 THR q 377 " model vdw 1.518 2.270 ... (remaining 242359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.980 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: 0.080 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.370 Find NCS groups from input model: 0.160 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:8.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 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 0.038 8760 Z= 0.697 Angle : 2.011 9.461 11730 Z= 1.306 Chirality : 0.118 0.437 1320 Planarity : 0.014 0.179 1500 Dihedral : 11.940 82.175 3375 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 1.52 % 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: -1.92 (0.22), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 349 TYR 0.068 0.028 TYR r 310 PHE 0.023 0.007 PHE n 346 HIS 0.014 0.003 HIS k 330 Details of bonding type rmsd covalent geometry : bond 0.01091 ( 8760) covalent geometry : angle 2.01127 (11730) hydrogen bonds : bond 0.13421 ( 92) hydrogen bonds : angle 9.02598 ( 276) *********************** 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 355 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.514 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: S 311 LYS cc_start: 0.7163 (mttt) cc_final: 0.6739 (tptt) REVERT: S 331 LYS cc_start: 0.7134 (tttt) cc_final: 0.6383 (tptt) REVERT: S 338 GLU cc_start: 0.7419 (tt0) cc_final: 0.6283 (tm-30) REVERT: i 324 SER cc_start: 0.8345 (m) cc_final: 0.7621 (p) REVERT: i 369 LYS cc_start: 0.7500 (pttt) cc_final: 0.7175 (ptpt) REVERT: j 338 GLU cc_start: 0.7614 (tt0) cc_final: 0.7233 (tt0) REVERT: j 375 LYS cc_start: 0.8179 (tttt) cc_final: 0.7929 (tttm) REVERT: T 351 GLN cc_start: 0.6570 (mt0) cc_final: 0.6324 (mt0) REVERT: k 338 GLU cc_start: 0.7357 (tt0) cc_final: 0.7132 (tt0) REVERT: l 338 GLU cc_start: 0.7591 (tt0) cc_final: 0.7134 (tt0) REVERT: l 369 LYS cc_start: 0.7823 (mttt) cc_final: 0.7484 (mttt) REVERT: U 369 LYS cc_start: 0.7398 (mttt) cc_final: 0.6732 (mtpp) REVERT: m 369 LYS cc_start: 0.7418 (pttt) cc_final: 0.7040 (ptpt) REVERT: n 338 GLU cc_start: 0.7530 (tt0) cc_final: 0.7063 (tt0) REVERT: V 338 GLU cc_start: 0.7240 (tt0) cc_final: 0.6981 (tt0) REVERT: o 375 LYS cc_start: 0.6981 (pttt) cc_final: 0.6758 (ptmt) REVERT: p 338 GLU cc_start: 0.7587 (tt0) cc_final: 0.7148 (tt0) REVERT: p 375 LYS cc_start: 0.8014 (tttt) cc_final: 0.7718 (tttm) REVERT: q 324 SER cc_start: 0.8643 (m) cc_final: 0.8360 (p) REVERT: q 345 ASP cc_start: 0.6473 (p0) cc_final: 0.6032 (t70) REVERT: q 369 LYS cc_start: 0.8124 (pttt) cc_final: 0.7877 (ptpt) REVERT: r 338 GLU cc_start: 0.7959 (tt0) cc_final: 0.7700 (tt0) REVERT: r 340 LYS cc_start: 0.6845 (mttp) cc_final: 0.6564 (ttpp) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 1.5848 time to fit residues: 589.6984 Evaluate side-chains 218 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 374 HIS j 336 GLN k 307 GLN k 374 HIS m 374 HIS o 374 HIS p 374 HIS q 307 GLN r 336 GLN r 374 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.118599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.100702 restraints weight = 29969.154| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.60 r_work: 0.3544 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8760 Z= 0.253 Angle : 0.919 6.451 11730 Z= 0.476 Chirality : 0.059 0.217 1320 Planarity : 0.006 0.080 1500 Dihedral : 8.421 56.574 1170 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 1.82 % Allowed : 15.66 % Favored : 82.53 % 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: -2.59 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG k 349 TYR 0.012 0.003 TYR r 310 PHE 0.009 0.001 PHE S 378 HIS 0.008 0.002 HIS V 330 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 8760) covalent geometry : angle 0.91940 (11730) hydrogen bonds : bond 0.06638 ( 92) hydrogen bonds : angle 7.71107 ( 276) *********************** 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 233 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 324 SER cc_start: 0.8849 (m) cc_final: 0.8627 (p) REVERT: j 307 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: j 321 LYS cc_start: 0.8713 (mttt) cc_final: 0.8404 (mtpp) REVERT: j 338 GLU cc_start: 0.8729 (tt0) cc_final: 0.8523 (tt0) REVERT: U 321 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8304 (mtmm) REVERT: U 369 LYS cc_start: 0.8787 (mttt) cc_final: 0.8489 (mtpp) REVERT: m 314 ASP cc_start: 0.8970 (t0) cc_final: 0.8335 (t0) REVERT: n 315 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8547 (mt) REVERT: n 317 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7714 (ttpt) REVERT: V 338 GLU cc_start: 0.8884 (tt0) cc_final: 0.8545 (tm-30) REVERT: p 315 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8522 (mt) REVERT: W 338 GLU cc_start: 0.8877 (tt0) cc_final: 0.8672 (tm-30) REVERT: q 345 ASP cc_start: 0.8299 (p0) cc_final: 0.7821 (p0) outliers start: 18 outliers final: 8 residues processed: 225 average time/residue: 1.7472 time to fit residues: 410.5609 Evaluate side-chains 177 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 307 GLN Chi-restraints excluded: chain T residue 340 LYS Chi-restraints excluded: chain l residue 315 LEU Chi-restraints excluded: chain l residue 341 SER Chi-restraints excluded: chain m residue 317 LYS Chi-restraints excluded: chain n residue 315 LEU Chi-restraints excluded: chain n residue 341 SER Chi-restraints excluded: chain V residue 307 GLN Chi-restraints excluded: chain o residue 324 SER Chi-restraints excluded: chain p residue 315 LEU Chi-restraints excluded: chain q residue 340 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 330 HIS S 374 HIS j 374 HIS T 374 HIS l 374 HIS U 374 HIS m 307 GLN n 374 HIS V 374 HIS o 307 GLN W 374 HIS q 307 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.118803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.101164 restraints weight = 30285.374| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.59 r_work: 0.3560 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8760 Z= 0.230 Angle : 0.770 6.042 11730 Z= 0.406 Chirality : 0.055 0.183 1320 Planarity : 0.005 0.046 1500 Dihedral : 7.711 55.125 1170 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 2.02 % Allowed : 16.87 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.20), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG n 379 TYR 0.012 0.002 TYR S 310 PHE 0.007 0.001 PHE T 378 HIS 0.008 0.002 HIS T 330 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 8760) covalent geometry : angle 0.77016 (11730) hydrogen bonds : bond 0.05402 ( 92) hydrogen bonds : angle 7.47058 ( 276) *********************** 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 206 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 349 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7951 (mtp180) REVERT: i 372 GLU cc_start: 0.8075 (pt0) cc_final: 0.7858 (pt0) REVERT: j 307 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: j 317 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7601 (ttpt) REVERT: j 321 LYS cc_start: 0.8725 (mttt) cc_final: 0.8486 (mtpp) REVERT: T 340 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8543 (tttp) REVERT: T 342 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8017 (mt-10) REVERT: k 314 ASP cc_start: 0.9055 (t0) cc_final: 0.8789 (t0) REVERT: l 341 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8679 (t) REVERT: U 321 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8360 (mtmm) REVERT: U 369 LYS cc_start: 0.8820 (mttt) cc_final: 0.8514 (mtpp) REVERT: m 314 ASP cc_start: 0.8954 (t70) cc_final: 0.8300 (t0) REVERT: V 307 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: V 338 GLU cc_start: 0.8899 (tt0) cc_final: 0.8579 (tm-30) REVERT: V 340 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8548 (tttp) REVERT: o 345 ASP cc_start: 0.7803 (p0) cc_final: 0.7406 (t70) REVERT: p 341 SER cc_start: 0.8904 (m) cc_final: 0.8674 (t) REVERT: W 338 GLU cc_start: 0.8888 (tt0) cc_final: 0.8684 (tm-30) REVERT: q 345 ASP cc_start: 0.8162 (p0) cc_final: 0.7939 (t70) outliers start: 20 outliers final: 7 residues processed: 197 average time/residue: 1.5772 time to fit residues: 325.8559 Evaluate side-chains 183 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 345 ASP Chi-restraints excluded: chain j residue 307 GLN Chi-restraints excluded: chain j residue 317 LYS Chi-restraints excluded: chain T residue 340 LYS Chi-restraints excluded: chain l residue 315 LEU Chi-restraints excluded: chain l residue 341 SER Chi-restraints excluded: chain m residue 324 SER Chi-restraints excluded: chain m residue 369 LYS Chi-restraints excluded: chain V residue 307 GLN Chi-restraints excluded: chain V residue 340 LYS Chi-restraints excluded: chain o residue 324 SER Chi-restraints excluded: chain o residue 363 VAL Chi-restraints excluded: chain q residue 340 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 307 GLN m 307 GLN o 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.118826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.101293 restraints weight = 30190.420| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.57 r_work: 0.3565 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8760 Z= 0.215 Angle : 0.733 6.117 11730 Z= 0.385 Chirality : 0.054 0.178 1320 Planarity : 0.006 0.077 1500 Dihedral : 7.406 50.047 1170 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 2.42 % Allowed : 16.67 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG n 349 TYR 0.011 0.002 TYR W 310 PHE 0.006 0.001 PHE k 378 HIS 0.006 0.001 HIS T 330 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 8760) covalent geometry : angle 0.73299 (11730) hydrogen bonds : bond 0.04715 ( 92) hydrogen bonds : angle 7.30139 ( 276) *********************** 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 206 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 349 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7900 (mtp180) REVERT: j 307 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: j 321 LYS cc_start: 0.8717 (mttt) cc_final: 0.8503 (mtpp) REVERT: k 314 ASP cc_start: 0.9067 (t0) cc_final: 0.8805 (t0) REVERT: U 321 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8373 (mtmm) REVERT: U 340 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8623 (tttp) REVERT: U 342 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8105 (mt-10) REVERT: U 369 LYS cc_start: 0.8824 (mttt) cc_final: 0.8522 (mtpp) REVERT: m 314 ASP cc_start: 0.8949 (t70) cc_final: 0.8281 (t0) REVERT: n 349 ARG cc_start: 0.7850 (mtm-85) cc_final: 0.7590 (mtm180) REVERT: V 307 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: V 338 GLU cc_start: 0.8879 (tt0) cc_final: 0.8565 (tm-30) REVERT: r 321 LYS cc_start: 0.8729 (mttp) cc_final: 0.8490 (mtpm) outliers start: 24 outliers final: 10 residues processed: 194 average time/residue: 1.6422 time to fit residues: 333.9469 Evaluate side-chains 180 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 345 ASP Chi-restraints excluded: chain j residue 307 GLN Chi-restraints excluded: chain j residue 356 SER Chi-restraints excluded: chain k residue 369 LYS Chi-restraints excluded: chain l residue 315 LEU Chi-restraints excluded: chain l residue 341 SER Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain m residue 324 SER Chi-restraints excluded: chain m residue 369 LYS Chi-restraints excluded: chain V residue 307 GLN Chi-restraints excluded: chain o residue 324 SER Chi-restraints excluded: chain p residue 307 GLN Chi-restraints excluded: chain q residue 340 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 61 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 91 optimal weight: 0.0070 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 307 GLN m 307 GLN o 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.121002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.103737 restraints weight = 30274.446| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.59 r_work: 0.3602 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8760 Z= 0.135 Angle : 0.647 5.376 11730 Z= 0.337 Chirality : 0.052 0.155 1320 Planarity : 0.005 0.047 1500 Dihedral : 6.954 50.112 1170 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 1.82 % Allowed : 17.88 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG l 349 TYR 0.007 0.001 TYR r 310 PHE 0.004 0.001 PHE S 378 HIS 0.003 0.001 HIS T 330 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8760) covalent geometry : angle 0.64733 (11730) hydrogen bonds : bond 0.03656 ( 92) hydrogen bonds : angle 6.96894 ( 276) *********************** 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 190 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 349 ARG cc_start: 0.8069 (mtm180) cc_final: 0.7868 (mtp180) REVERT: T 307 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: k 314 ASP cc_start: 0.9091 (t0) cc_final: 0.8833 (t0) REVERT: U 321 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8350 (mtmm) REVERT: U 340 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8559 (tttp) REVERT: U 369 LYS cc_start: 0.8815 (mttt) cc_final: 0.8518 (mtpp) REVERT: m 314 ASP cc_start: 0.8928 (t70) cc_final: 0.8315 (t0) REVERT: V 338 GLU cc_start: 0.8861 (tt0) cc_final: 0.8553 (tm-30) REVERT: V 340 LYS cc_start: 0.8824 (mtpt) cc_final: 0.8584 (tttp) REVERT: r 321 LYS cc_start: 0.8661 (mttp) cc_final: 0.8444 (mtpm) REVERT: r 342 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: r 379 ARG cc_start: 0.6926 (ttp80) cc_final: 0.6353 (tmm-80) outliers start: 18 outliers final: 4 residues processed: 179 average time/residue: 1.6555 time to fit residues: 311.1457 Evaluate side-chains 164 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 356 SER Chi-restraints excluded: chain T residue 307 GLN Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain m residue 324 SER Chi-restraints excluded: chain n residue 315 LEU Chi-restraints excluded: chain o residue 324 SER Chi-restraints excluded: chain r 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: 5.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 307 GLN m 307 GLN o 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.120095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.102859 restraints weight = 30108.170| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.58 r_work: 0.3591 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8760 Z= 0.168 Angle : 0.664 6.045 11730 Z= 0.346 Chirality : 0.052 0.153 1320 Planarity : 0.005 0.055 1500 Dihedral : 6.919 51.493 1170 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.41 % Allowed : 18.69 % Favored : 79.90 % 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: -2.74 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG l 379 TYR 0.008 0.002 TYR S 310 PHE 0.004 0.001 PHE W 378 HIS 0.003 0.001 HIS V 330 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8760) covalent geometry : angle 0.66441 (11730) hydrogen bonds : bond 0.03780 ( 92) hydrogen bonds : angle 6.93890 ( 276) *********************** 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 188 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 349 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7793 (mtp180) REVERT: T 342 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: k 314 ASP cc_start: 0.9077 (t0) cc_final: 0.8818 (t0) REVERT: U 319 THR cc_start: 0.8858 (m) cc_final: 0.8507 (p) REVERT: U 321 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8378 (mtmm) REVERT: U 340 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8553 (tttp) REVERT: U 369 LYS cc_start: 0.8830 (mttt) cc_final: 0.8525 (mtpp) REVERT: m 314 ASP cc_start: 0.8925 (t70) cc_final: 0.8322 (t0) REVERT: n 321 LYS cc_start: 0.8473 (mtpp) cc_final: 0.7935 (mttp) REVERT: V 338 GLU cc_start: 0.8867 (tt0) cc_final: 0.8552 (tm-30) REVERT: V 340 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8607 (tttp) REVERT: W 342 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7379 (mp0) REVERT: r 321 LYS cc_start: 0.8669 (mttp) cc_final: 0.8467 (mtpm) REVERT: r 342 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: r 379 ARG cc_start: 0.6961 (ttp80) cc_final: 0.6297 (tmm-80) outliers start: 14 outliers final: 7 residues processed: 181 average time/residue: 1.6572 time to fit residues: 314.0373 Evaluate side-chains 177 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 342 GLU Chi-restraints excluded: chain k residue 369 LYS Chi-restraints excluded: chain l residue 315 LEU Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain m residue 324 SER Chi-restraints excluded: chain m residue 369 LYS Chi-restraints excluded: chain V residue 307 GLN Chi-restraints excluded: chain o residue 324 SER Chi-restraints excluded: chain p residue 307 GLN Chi-restraints excluded: chain r 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: 4.9990 chunk 15 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 307 GLN m 307 GLN o 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.118312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.101041 restraints weight = 30511.241| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.58 r_work: 0.3565 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.5311 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= 0.234 Angle : 0.719 6.783 11730 Z= 0.379 Chirality : 0.054 0.170 1320 Planarity : 0.006 0.069 1500 Dihedral : 7.145 52.686 1170 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 1.62 % Allowed : 18.48 % Favored : 79.90 % 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: -2.80 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG l 379 TYR 0.011 0.002 TYR S 310 PHE 0.010 0.001 PHE i 346 HIS 0.004 0.001 HIS S 329 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 8760) covalent geometry : angle 0.71915 (11730) hydrogen bonds : bond 0.04109 ( 92) hydrogen bonds : angle 7.06410 ( 276) *********************** 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 183 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: j 317 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7596 (ttpt) REVERT: T 307 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: T 342 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: k 314 ASP cc_start: 0.9049 (t0) cc_final: 0.8796 (t0) REVERT: U 319 THR cc_start: 0.8899 (m) cc_final: 0.8552 (p) REVERT: U 321 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8402 (mtmm) REVERT: U 340 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8548 (tttp) REVERT: U 369 LYS cc_start: 0.8838 (mttt) cc_final: 0.8524 (mtpp) REVERT: m 314 ASP cc_start: 0.8983 (t70) cc_final: 0.8332 (t0) REVERT: n 321 LYS cc_start: 0.8610 (mtpp) cc_final: 0.7993 (mttp) REVERT: n 340 LYS cc_start: 0.8966 (mtpm) cc_final: 0.8393 (ttpt) REVERT: V 307 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: V 338 GLU cc_start: 0.8889 (tt0) cc_final: 0.8562 (tm-30) REVERT: V 340 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8621 (tttp) REVERT: r 342 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8178 (mt-10) outliers start: 16 outliers final: 7 residues processed: 178 average time/residue: 1.6651 time to fit residues: 310.5497 Evaluate side-chains 177 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 317 LYS Chi-restraints excluded: chain T residue 307 GLN Chi-restraints excluded: chain T residue 342 GLU Chi-restraints excluded: chain k residue 369 LYS Chi-restraints excluded: chain l residue 315 LEU Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain m residue 324 SER Chi-restraints excluded: chain m residue 369 LYS Chi-restraints excluded: chain n residue 315 LEU Chi-restraints excluded: chain V residue 307 GLN Chi-restraints excluded: chain o residue 324 SER Chi-restraints excluded: chain p residue 307 GLN Chi-restraints excluded: chain r 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: 3.9990 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 307 GLN m 307 GLN o 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.117734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.100617 restraints weight = 30449.354| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.57 r_work: 0.3561 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8760 Z= 0.209 Angle : 0.708 7.516 11730 Z= 0.370 Chirality : 0.053 0.163 1320 Planarity : 0.005 0.050 1500 Dihedral : 6.972 47.724 1170 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 1.41 % Allowed : 19.19 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG n 379 TYR 0.009 0.002 TYR S 310 PHE 0.007 0.001 PHE i 346 HIS 0.003 0.001 HIS T 330 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 8760) covalent geometry : angle 0.70801 (11730) hydrogen bonds : bond 0.03923 ( 92) hydrogen bonds : angle 7.03588 ( 276) *********************** 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 181 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: j 317 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7585 (ttpt) REVERT: T 307 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: k 314 ASP cc_start: 0.9022 (t0) cc_final: 0.8766 (t0) REVERT: l 340 LYS cc_start: 0.8823 (mtpm) cc_final: 0.8358 (ttpt) REVERT: U 319 THR cc_start: 0.8877 (m) cc_final: 0.8535 (p) REVERT: U 321 LYS cc_start: 0.8591 (mtpp) cc_final: 0.8375 (mtmm) REVERT: U 340 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8556 (tttp) REVERT: U 369 LYS cc_start: 0.8813 (mttt) cc_final: 0.8494 (mtpp) REVERT: m 314 ASP cc_start: 0.8961 (t70) cc_final: 0.8292 (t0) REVERT: n 340 LYS cc_start: 0.8968 (mtpm) cc_final: 0.8368 (ttpt) REVERT: n 379 ARG cc_start: 0.7721 (ttm110) cc_final: 0.7409 (ttm-80) REVERT: V 338 GLU cc_start: 0.8882 (tt0) cc_final: 0.8538 (tm-30) REVERT: V 340 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8554 (tttp) REVERT: o 324 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8301 (p) REVERT: p 379 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.7361 (ttm110) REVERT: r 342 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8233 (mt-10) outliers start: 14 outliers final: 8 residues processed: 174 average time/residue: 1.7105 time to fit residues: 311.3928 Evaluate side-chains 176 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 317 LYS Chi-restraints excluded: chain T residue 307 GLN Chi-restraints excluded: chain k residue 369 LYS Chi-restraints excluded: chain l residue 315 LEU Chi-restraints excluded: chain U residue 340 LYS Chi-restraints excluded: chain U residue 342 GLU Chi-restraints excluded: chain m residue 324 SER Chi-restraints excluded: chain m residue 369 LYS Chi-restraints excluded: chain n residue 315 LEU Chi-restraints excluded: chain V residue 307 GLN Chi-restraints excluded: chain o residue 324 SER Chi-restraints excluded: chain p residue 307 GLN Chi-restraints excluded: chain r 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: 10.0000 chunk 41 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 307 GLN m 307 GLN o 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.119101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.102162 restraints weight = 30407.518| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.57 r_work: 0.3587 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8760 Z= 0.145 Angle : 0.665 7.701 11730 Z= 0.344 Chirality : 0.052 0.144 1320 Planarity : 0.005 0.070 1500 Dihedral : 6.667 44.895 1170 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 1.31 % Allowed : 19.70 % Favored : 78.99 % 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: -2.81 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG l 379 TYR 0.007 0.001 TYR r 310 PHE 0.004 0.001 PHE m 378 HIS 0.004 0.001 HIS l 330 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8760) covalent geometry : angle 0.66541 (11730) hydrogen bonds : bond 0.03424 ( 92) hydrogen bonds : angle 6.89635 ( 276) *********************** 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 180 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 307 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: T 342 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7873 (mt-10) REVERT: k 314 ASP cc_start: 0.9014 (t0) cc_final: 0.8728 (t0) REVERT: l 340 LYS cc_start: 0.8796 (mtpm) cc_final: 0.8356 (ttpt) REVERT: U 319 THR cc_start: 0.8856 (m) cc_final: 0.8551 (p) REVERT: U 321 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8349 (mtmm) REVERT: U 369 LYS cc_start: 0.8792 (mttt) cc_final: 0.8488 (mtpp) REVERT: m 314 ASP cc_start: 0.8897 (t70) cc_final: 0.8234 (t0) REVERT: n 321 LYS cc_start: 0.8363 (mtpp) cc_final: 0.7723 (mttp) REVERT: n 340 LYS cc_start: 0.8978 (mtpm) cc_final: 0.8387 (ttpt) REVERT: V 338 GLU cc_start: 0.8823 (tt0) cc_final: 0.8517 (tm-30) REVERT: V 340 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8538 (tttp) REVERT: o 324 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.8279 (p) REVERT: r 342 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: r 379 ARG cc_start: 0.7885 (tpp-160) cc_final: 0.7241 (tmm160) outliers start: 13 outliers final: 7 residues processed: 176 average time/residue: 1.5923 time to fit residues: 294.2862 Evaluate side-chains 173 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 307 GLN Chi-restraints excluded: chain k residue 369 LYS Chi-restraints excluded: chain l residue 315 LEU Chi-restraints excluded: chain U residue 342 GLU Chi-restraints excluded: chain m residue 324 SER Chi-restraints excluded: chain m residue 369 LYS Chi-restraints excluded: chain V residue 307 GLN Chi-restraints excluded: chain o residue 324 SER Chi-restraints excluded: chain p residue 307 GLN Chi-restraints excluded: chain r 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: 8.9990 chunk 78 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 307 GLN m 307 GLN o 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.120203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.103332 restraints weight = 30320.926| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.58 r_work: 0.3607 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8760 Z= 0.126 Angle : 0.638 6.473 11730 Z= 0.327 Chirality : 0.052 0.136 1320 Planarity : 0.004 0.045 1500 Dihedral : 6.464 49.093 1170 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 1.01 % Allowed : 20.00 % Favored : 78.99 % 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: -2.77 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG l 379 TYR 0.007 0.001 TYR r 310 PHE 0.004 0.001 PHE S 378 HIS 0.004 0.001 HIS l 330 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8760) covalent geometry : angle 0.63765 (11730) hydrogen bonds : bond 0.03132 ( 92) hydrogen bonds : angle 6.71499 ( 276) ********************** 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 185 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 379 ARG cc_start: 0.7405 (mpt-90) cc_final: 0.7183 (mmm-85) REVERT: T 307 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: T 342 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7925 (mt-10) REVERT: k 314 ASP cc_start: 0.9007 (t0) cc_final: 0.8729 (t0) REVERT: l 340 LYS cc_start: 0.8813 (mtpm) cc_final: 0.8351 (ttpt) REVERT: U 319 THR cc_start: 0.8815 (m) cc_final: 0.8542 (p) REVERT: m 314 ASP cc_start: 0.8858 (t70) cc_final: 0.8646 (t0) REVERT: n 321 LYS cc_start: 0.8448 (mtpp) cc_final: 0.7756 (mttp) REVERT: n 340 LYS cc_start: 0.8972 (mtpm) cc_final: 0.8388 (ttpt) REVERT: V 338 GLU cc_start: 0.8841 (tt0) cc_final: 0.8510 (tm-30) REVERT: o 324 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8250 (p) REVERT: W 342 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7293 (mp0) REVERT: r 342 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: r 379 ARG cc_start: 0.7873 (tpp-160) cc_final: 0.7249 (tmm160) outliers start: 10 outliers final: 6 residues processed: 183 average time/residue: 1.6751 time to fit residues: 321.6140 Evaluate side-chains 172 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 307 GLN Chi-restraints excluded: chain k residue 369 LYS Chi-restraints excluded: chain U residue 342 GLU Chi-restraints excluded: chain m residue 324 SER Chi-restraints excluded: chain m residue 369 LYS Chi-restraints excluded: chain V residue 307 GLN Chi-restraints excluded: chain o residue 324 SER Chi-restraints excluded: chain p residue 307 GLN Chi-restraints excluded: chain r 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: 3.9990 chunk 13 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 307 GLN i 307 GLN m 307 GLN o 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.118738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.101808 restraints weight = 30411.131| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.57 r_work: 0.3585 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8760 Z= 0.171 Angle : 0.669 7.562 11730 Z= 0.347 Chirality : 0.052 0.144 1320 Planarity : 0.005 0.104 1500 Dihedral : 6.642 51.152 1170 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 1.01 % Allowed : 20.20 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.21), residues: 1095 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG l 379 TYR 0.008 0.002 TYR S 310 PHE 0.006 0.001 PHE i 346 HIS 0.003 0.001 HIS l 330 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8760) covalent geometry : angle 0.66891 (11730) hydrogen bonds : bond 0.03448 ( 92) hydrogen bonds : angle 6.76329 ( 276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7888.03 seconds wall clock time: 134 minutes 10.93 seconds (8050.93 seconds total)