Starting phenix.real_space_refine on Sun Apr 5 21:40:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qjx_14025/04_2026/7qjx_14025.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qjx_14025/04_2026/7qjx_14025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qjx_14025/04_2026/7qjx_14025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qjx_14025/04_2026/7qjx_14025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qjx_14025/04_2026/7qjx_14025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qjx_14025/04_2026/7qjx_14025.map" } resolution = 2.99 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= 0.002 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 12 5.16 5 C 4272 2.51 5 N 1236 2.21 5 O 1284 1.98 5 H 7056 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13860 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "H" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "I" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "J" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "K" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "L" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 2.69, per 1000 atoms: 0.19 Number of scatterers: 13860 At special positions: 0 Unit cell: (158.4, 161.7, 53.9, 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 12 16.00 O 1284 8.00 N 1236 7.00 C 4272 6.00 H 7056 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: 1.03 Conformation dependent library (CDL) restraints added in 447.3 milliseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 33 sheets defined 0.0% alpha, 62.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 310 removed outlier: 6.794A pdb=" N SER A 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ILE C 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 7.025A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 324 removed outlier: 6.728A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 330 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 348 removed outlier: 7.067A pdb=" N VAL C 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS A 340 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER C 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU A 342 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS C 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU A 344 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASP C 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE A 346 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS C 347 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL C 337 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU B 338 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP B 348 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.751A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 362 removed outlier: 6.514A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE C 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN B 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N HIS C 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR B 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 377 removed outlier: 6.669A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 305 through 310 removed outlier: 6.707A pdb=" N SER D 305 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE F 308 " --> pdb=" O SER D 305 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN D 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N TYR F 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL D 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.992A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 324 removed outlier: 6.588A pdb=" N VAL E 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS F 321 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER E 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N GLY F 323 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N CYS E 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 327 through 330 removed outlier: 6.809A pdb=" N ASN D 327 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N HIS F 330 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 336 through 354 removed outlier: 3.515A pdb=" N GLU D 338 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL F 339 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS D 340 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER F 341 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU D 342 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS F 343 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU D 344 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASP F 345 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE D 346 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS F 347 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D 350 " --> pdb=" O ARG F 349 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN F 351 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER D 352 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS F 353 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE D 354 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL F 337 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU E 338 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP E 348 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG F 349 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 336 through 354 removed outlier: 3.515A pdb=" N GLU D 338 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL F 339 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS D 340 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER F 341 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU D 342 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS F 343 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU D 344 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASP F 345 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE D 346 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS F 347 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D 350 " --> pdb=" O ARG F 349 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN F 351 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER D 352 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS F 353 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE D 354 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 357 through 362 removed outlier: 5.920A pdb=" N ASP D 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR F 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU E 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N ILE F 360 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASN E 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N HIS F 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.643A pdb=" N LYS D 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLU F 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE D 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N HIS F 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR D 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N LEU F 376 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS D 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 305 through 310 removed outlier: 6.866A pdb=" N SER G 305 " --> pdb=" O VAL I 306 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ILE I 308 " --> pdb=" O SER G 305 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN G 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N TYR I 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL G 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 313 through 314 removed outlier: 7.108A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 317 through 323 removed outlier: 6.689A pdb=" N VAL H 318 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N LYS I 321 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER H 320 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N GLY I 323 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS H 322 " --> pdb=" O GLY I 323 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 328 through 330 removed outlier: 6.326A pdb=" N ILE H 328 " --> pdb=" O HIS I 329 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 336 through 340 removed outlier: 7.045A pdb=" N VAL G 337 " --> pdb=" O GLN I 336 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU I 338 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N GLN H 336 " --> pdb=" O VAL I 337 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N VAL I 339 " --> pdb=" O GLN H 336 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU H 338 " --> pdb=" O VAL I 339 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 343 through 348 removed outlier: 7.000A pdb=" N LYS G 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N PHE I 346 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP G 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASP I 348 " --> pdb=" O ASP G 345 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N LYS G 347 " --> pdb=" O ASP I 348 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP H 348 " --> pdb=" O LYS I 347 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 351 through 354 removed outlier: 6.703A pdb=" N GLN G 351 " --> pdb=" O SER I 352 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ILE I 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS G 353 " --> pdb=" O ILE I 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 357 through 362 removed outlier: 6.575A pdb=" N ASP G 358 " --> pdb=" O ASN I 359 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR I 361 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE G 360 " --> pdb=" O THR I 361 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 368 through 377 removed outlier: 6.561A pdb=" N LYS G 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLU I 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE G 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N HIS I 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR G 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU I 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS G 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 305 through 310 removed outlier: 6.707A pdb=" N SER J 305 " --> pdb=" O VAL L 306 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE L 308 " --> pdb=" O SER J 305 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN J 307 " --> pdb=" O ILE L 308 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR L 310 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL J 309 " --> pdb=" O TYR L 310 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 313 through 314 removed outlier: 6.994A pdb=" N VAL J 313 " --> pdb=" O ASP L 314 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 317 through 324 removed outlier: 6.588A pdb=" N VAL K 318 " --> pdb=" O THR L 319 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS L 321 " --> pdb=" O VAL K 318 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER K 320 " --> pdb=" O LYS L 321 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLY L 323 " --> pdb=" O SER K 320 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N CYS K 322 " --> pdb=" O GLY L 323 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 327 through 330 removed outlier: 6.808A pdb=" N ASN J 327 " --> pdb=" O ILE L 328 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N HIS L 330 " --> pdb=" O ASN J 327 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N HIS J 329 " --> pdb=" O HIS L 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 336 through 348 removed outlier: 6.473A pdb=" N VAL J 337 " --> pdb=" O GLU L 338 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LYS L 340 " --> pdb=" O VAL J 337 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL J 339 " --> pdb=" O LYS L 340 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLU L 342 " --> pdb=" O VAL J 339 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER J 341 " --> pdb=" O GLU L 342 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU L 344 " --> pdb=" O SER J 341 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS J 343 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N PHE L 346 " --> pdb=" O LYS J 343 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP J 345 " --> pdb=" O PHE L 346 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASP L 348 " --> pdb=" O ASP J 345 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N LYS J 347 " --> pdb=" O ASP L 348 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL L 337 " --> pdb=" O GLN K 336 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU K 338 " --> pdb=" O VAL L 337 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASP K 348 " --> pdb=" O LYS L 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 351 through 354 removed outlier: 6.883A pdb=" N GLN J 351 " --> pdb=" O SER L 352 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ILE L 354 " --> pdb=" O GLN J 351 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS J 353 " --> pdb=" O ILE L 354 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 357 through 362 removed outlier: 5.915A pdb=" N ASP J 358 " --> pdb=" O ASN L 359 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR L 361 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE J 360 " --> pdb=" O THR L 361 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU K 357 " --> pdb=" O ASP L 358 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N ILE L 360 " --> pdb=" O LEU K 357 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASN K 359 " --> pdb=" O ILE L 360 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N HIS L 362 " --> pdb=" O ASN K 359 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR K 361 " --> pdb=" O HIS L 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 368 through 377 removed outlier: 6.644A pdb=" N LYS J 369 " --> pdb=" O LYS L 370 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLU L 372 " --> pdb=" O LYS J 369 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE J 371 " --> pdb=" O GLU L 372 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N HIS L 374 " --> pdb=" O ILE J 371 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR J 373 " --> pdb=" O HIS L 374 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N LEU L 376 " --> pdb=" O THR J 373 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS J 375 " --> pdb=" O LEU L 376 " (cutoff:3.500A) 159 hydrogen bonds defined for protein. 477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.38 - 0.67: 3 0.67 - 0.96: 47 0.96 - 1.24: 7971 1.24 - 1.53: 4279 1.53 - 1.82: 1668 Warning: very small bond lengths. Bond restraints: 13968 Sorted by residual: bond pdb=" CG2 VAL H 313 " pdb="HG22 VAL H 313 " ideal model delta sigma weight residual 0.970 0.382 0.588 2.00e-02 2.50e+03 8.65e+02 bond pdb=" CG2 VAL H 313 " pdb="HG21 VAL H 313 " ideal model delta sigma weight residual 0.970 0.391 0.579 2.00e-02 2.50e+03 8.39e+02 bond pdb=" CG2 VAL H 313 " pdb="HG23 VAL H 313 " ideal model delta sigma weight residual 0.970 0.461 0.509 2.00e-02 2.50e+03 6.48e+02 bond pdb=" CG1 VAL H 313 " pdb="HG11 VAL H 313 " ideal model delta sigma weight residual 0.970 0.715 0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" CG1 VAL H 313 " pdb="HG12 VAL H 313 " ideal model delta sigma weight residual 0.970 0.715 0.255 2.00e-02 2.50e+03 1.62e+02 ... (remaining 13963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.55: 25290 19.55 - 39.11: 161 39.11 - 58.66: 6 58.66 - 78.22: 4 78.22 - 97.77: 3 Bond angle restraints: 25464 Sorted by residual: angle pdb="HG21 VAL H 313 " pdb=" CG2 VAL H 313 " pdb="HG23 VAL H 313 " ideal model delta sigma weight residual 110.00 12.23 97.77 3.00e+00 1.11e-01 1.06e+03 angle pdb="HG21 VAL H 313 " pdb=" CG2 VAL H 313 " pdb="HG22 VAL H 313 " ideal model delta sigma weight residual 110.00 18.59 91.41 3.00e+00 1.11e-01 9.28e+02 angle pdb="HG22 VAL H 313 " pdb=" CG2 VAL H 313 " pdb="HG23 VAL H 313 " ideal model delta sigma weight residual 110.00 20.05 89.95 3.00e+00 1.11e-01 8.99e+02 angle pdb="HG21 VAL B 318 " pdb=" CG2 VAL B 318 " pdb="HG22 VAL B 318 " ideal model delta sigma weight residual 110.00 41.95 68.05 3.00e+00 1.11e-01 5.15e+02 angle pdb="HG21 VAL B 318 " pdb=" CG2 VAL B 318 " pdb="HG23 VAL B 318 " ideal model delta sigma weight residual 110.00 42.37 67.63 3.00e+00 1.11e-01 5.08e+02 ... (remaining 25459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5640 17.66 - 35.32: 417 35.32 - 52.97: 213 52.97 - 70.63: 145 70.63 - 88.29: 29 Dihedral angle restraints: 6444 sinusoidal: 3672 harmonic: 2772 Sorted by residual: dihedral pdb=" CA GLY A 365 " pdb=" C GLY A 365 " pdb=" N GLY A 366 " pdb=" CA GLY A 366 " ideal model delta harmonic sigma weight residual 180.00 149.56 30.44 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CD ARG K 349 " pdb=" NE ARG K 349 " pdb=" CZ ARG K 349 " pdb=" NH1 ARG K 349 " ideal model delta sinusoidal sigma weight residual 0.00 -48.88 48.88 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CA SER K 316 " pdb=" C SER K 316 " pdb=" N LYS K 317 " pdb=" CA LYS K 317 " ideal model delta harmonic sigma weight residual 180.00 151.41 28.59 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 6441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 963 0.286 - 0.571: 35 0.571 - 0.857: 12 0.857 - 1.142: 30 1.142 - 1.427: 4 Chirality restraints: 1044 Sorted by residual: chirality pdb=" CB VAL B 318 " pdb=" CA VAL B 318 " pdb=" CG1 VAL B 318 " pdb=" CG2 VAL B 318 " both_signs ideal model delta sigma weight residual False -2.63 -1.20 -1.43 2.00e-01 2.50e+01 5.09e+01 chirality pdb=" CB VAL I 309 " pdb=" CA VAL I 309 " pdb=" CG1 VAL I 309 " pdb=" CG2 VAL I 309 " both_signs ideal model delta sigma weight residual False -2.63 -1.44 -1.19 2.00e-01 2.50e+01 3.56e+01 chirality pdb=" CB VAL B 306 " pdb=" CA VAL B 306 " pdb=" CG1 VAL B 306 " pdb=" CG2 VAL B 306 " both_signs ideal model delta sigma weight residual False -2.63 -1.47 -1.15 2.00e-01 2.50e+01 3.33e+01 ... (remaining 1041 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 365 " -0.075 2.00e-02 2.50e+03 1.46e-01 2.13e+02 pdb=" C GLY A 365 " 0.252 2.00e-02 2.50e+03 pdb=" O GLY A 365 " -0.101 2.00e-02 2.50e+03 pdb=" N GLY A 366 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 349 " -0.893 9.50e-02 1.11e+02 3.00e-01 1.19e+02 pdb=" NE ARG K 349 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG K 349 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG K 349 " -0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG K 349 " 0.067 2.00e-02 2.50e+03 pdb="HH11 ARG K 349 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG K 349 " 0.008 2.00e-02 2.50e+03 pdb="HH21 ARG K 349 " -0.053 2.00e-02 2.50e+03 pdb="HH22 ARG K 349 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 349 " -0.535 9.50e-02 1.11e+02 1.85e-01 8.49e+01 pdb=" NE ARG L 349 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG L 349 " 0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG L 349 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG L 349 " 0.096 2.00e-02 2.50e+03 pdb="HH11 ARG L 349 " -0.026 2.00e-02 2.50e+03 pdb="HH12 ARG L 349 " -0.010 2.00e-02 2.50e+03 pdb="HH21 ARG L 349 " -0.061 2.00e-02 2.50e+03 pdb="HH22 ARG L 349 " -0.055 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1019 2.18 - 2.78: 22399 2.78 - 3.39: 34259 3.39 - 3.99: 44103 3.99 - 4.60: 63093 Nonbonded interactions: 164873 Sorted by model distance: nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.572 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.580 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.585 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.597 2.450 nonbonded pdb=" OD1 ASP L 314 " pdb=" HG SER L 316 " model vdw 1.605 2.450 ... (remaining 164868 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.050 Set scattering table: 0.040 Process input model: 13.550 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 : 0.014 0.372 6912 Z= 0.870 Angle : 2.558 21.806 9252 Z= 1.636 Chirality : 0.238 1.427 1044 Planarity : 0.016 0.375 1176 Dihedral : 13.832 86.955 2628 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.71 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.64 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.52 (0.21), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG L 349 TYR 0.077 0.016 TYR C 310 PHE 0.022 0.006 PHE B 378 HIS 0.012 0.003 HIS K 330 Details of bonding type rmsd covalent geometry : bond 0.01406 ( 6912) covalent geometry : angle 2.55752 ( 9252) hydrogen bonds : bond 0.17258 ( 156) hydrogen bonds : angle 7.43704 ( 477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7897 (ttt180) cc_final: 0.7508 (tmm160) REVERT: G 353 LYS cc_start: 0.5919 (mttt) cc_final: 0.4999 (mmtt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 1.3592 time to fit residues: 156.1061 Evaluate side-chains 43 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 330 HIS K 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.147295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.135819 restraints weight = 43380.966| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 2.51 r_work: 0.4321 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4247 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6912 Z= 0.234 Angle : 1.242 12.018 9252 Z= 0.649 Chirality : 0.288 1.626 1044 Planarity : 0.006 0.088 1176 Dihedral : 7.147 27.444 912 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.59 % Allowed : 6.92 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.19), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 349 TYR 0.015 0.003 TYR K 310 PHE 0.010 0.002 PHE H 378 HIS 0.007 0.002 HIS J 329 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 6912) covalent geometry : angle 1.24153 ( 9252) hydrogen bonds : bond 0.03899 ( 156) hydrogen bonds : angle 6.06600 ( 477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: A 372 GLU cc_start: 0.7910 (tt0) cc_final: 0.7683 (tt0) REVERT: B 349 ARG cc_start: 0.7287 (ttt180) cc_final: 0.6912 (ppt-90) REVERT: C 349 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6908 (ttm110) REVERT: G 353 LYS cc_start: 0.5806 (mttt) cc_final: 0.4678 (mmtt) REVERT: H 372 GLU cc_start: 0.7792 (tt0) cc_final: 0.7313 (mt-10) REVERT: I 349 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7372 (ttp-170) REVERT: K 342 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: K 358 ASP cc_start: 0.5383 (p0) cc_final: 0.4076 (p0) REVERT: L 342 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6665 (mt-10) outliers start: 28 outliers final: 10 residues processed: 77 average time/residue: 1.3863 time to fit residues: 111.3676 Evaluate side-chains 54 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 349 ARG Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 65 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS K 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.139018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.127600 restraints weight = 42234.261| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 2.39 r_work: 0.4255 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4182 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6912 Z= 0.226 Angle : 1.241 11.813 9252 Z= 0.653 Chirality : 0.317 1.721 1044 Planarity : 0.006 0.064 1176 Dihedral : 6.304 22.092 912 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.69 % Allowed : 8.33 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 349 TYR 0.014 0.003 TYR K 310 PHE 0.006 0.001 PHE E 378 HIS 0.007 0.002 HIS J 329 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 6912) covalent geometry : angle 1.24129 ( 9252) hydrogen bonds : bond 0.04150 ( 156) hydrogen bonds : angle 5.71735 ( 477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6955 (ttm110) REVERT: G 353 LYS cc_start: 0.5879 (mttt) cc_final: 0.4747 (mmtt) REVERT: H 342 GLU cc_start: 0.5020 (tp30) cc_final: 0.4670 (tp30) REVERT: H 372 GLU cc_start: 0.7793 (tt0) cc_final: 0.7590 (mt-10) REVERT: I 342 GLU cc_start: 0.4716 (tt0) cc_final: 0.4406 (tt0) REVERT: I 349 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7167 (mtm180) REVERT: K 342 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: K 358 ASP cc_start: 0.5388 (p0) cc_final: 0.4617 (p0) REVERT: K 360 ILE cc_start: 0.6068 (OUTLIER) cc_final: 0.5609 (pp) REVERT: L 342 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6573 (mt-10) outliers start: 21 outliers final: 8 residues processed: 69 average time/residue: 1.5414 time to fit residues: 110.6002 Evaluate side-chains 51 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 349 ARG Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 0.0020 chunk 49 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 59 optimal weight: 10.0000 overall best weight: 4.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 359 ASN F 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.138762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.127470 restraints weight = 41582.252| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.36 r_work: 0.4264 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4191 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6912 Z= 0.161 Angle : 1.162 11.369 9252 Z= 0.595 Chirality : 0.311 1.708 1044 Planarity : 0.006 0.066 1176 Dihedral : 5.761 19.851 912 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.82 % Allowed : 10.13 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 349 TYR 0.009 0.002 TYR J 310 PHE 0.003 0.001 PHE C 378 HIS 0.004 0.001 HIS J 374 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6912) covalent geometry : angle 1.16232 ( 9252) hydrogen bonds : bond 0.03075 ( 156) hydrogen bonds : angle 5.33083 ( 477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7003 (ttt180) cc_final: 0.6525 (ppt-90) REVERT: C 338 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: G 353 LYS cc_start: 0.5885 (mttt) cc_final: 0.4781 (mmtt) REVERT: H 372 GLU cc_start: 0.7803 (tt0) cc_final: 0.7529 (mt-10) REVERT: I 342 GLU cc_start: 0.5036 (tt0) cc_final: 0.4798 (tt0) REVERT: I 349 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7086 (ttm170) REVERT: K 342 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: K 358 ASP cc_start: 0.5514 (p0) cc_final: 0.4729 (p0) REVERT: K 360 ILE cc_start: 0.6157 (OUTLIER) cc_final: 0.5744 (pp) outliers start: 22 outliers final: 8 residues processed: 64 average time/residue: 1.5436 time to fit residues: 102.7234 Evaluate side-chains 53 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.137695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.126629 restraints weight = 42592.331| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 2.32 r_work: 0.4256 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4186 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6912 Z= 0.171 Angle : 1.175 11.576 9252 Z= 0.605 Chirality : 0.316 1.716 1044 Planarity : 0.006 0.064 1176 Dihedral : 5.560 19.103 912 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.44 % Allowed : 11.28 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 349 TYR 0.009 0.002 TYR H 310 PHE 0.005 0.001 PHE A 346 HIS 0.005 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6912) covalent geometry : angle 1.17536 ( 9252) hydrogen bonds : bond 0.03319 ( 156) hydrogen bonds : angle 5.19157 ( 477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7007 (ttt180) cc_final: 0.6576 (ppt-90) REVERT: C 372 GLU cc_start: 0.8242 (tt0) cc_final: 0.7880 (tm-30) REVERT: D 342 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: G 353 LYS cc_start: 0.5593 (mttt) cc_final: 0.4536 (mmtt) REVERT: H 372 GLU cc_start: 0.7789 (tt0) cc_final: 0.7553 (mt-10) REVERT: I 349 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7079 (ttm170) REVERT: K 342 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: K 358 ASP cc_start: 0.5447 (p0) cc_final: 0.4603 (p0) REVERT: K 360 ILE cc_start: 0.6385 (OUTLIER) cc_final: 0.5917 (pp) REVERT: L 342 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6397 (mt-10) outliers start: 19 outliers final: 9 residues processed: 64 average time/residue: 1.4060 time to fit residues: 94.2442 Evaluate side-chains 54 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 330 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 359 ASN K 359 ASN L 359 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.135504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.124285 restraints weight = 42260.870| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 2.31 r_work: 0.4226 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.4156 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6912 Z= 0.192 Angle : 1.192 11.356 9252 Z= 0.615 Chirality : 0.313 1.718 1044 Planarity : 0.006 0.072 1176 Dihedral : 5.769 20.470 912 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.46 % Allowed : 11.79 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 349 TYR 0.009 0.002 TYR J 310 PHE 0.006 0.001 PHE J 346 HIS 0.007 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 6912) covalent geometry : angle 1.19174 ( 9252) hydrogen bonds : bond 0.03806 ( 156) hydrogen bonds : angle 5.34749 ( 477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7050 (ttt180) cc_final: 0.6770 (ppt-90) REVERT: C 338 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: D 342 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: E 307 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: G 353 LYS cc_start: 0.5657 (mttt) cc_final: 0.4564 (mmtt) REVERT: H 372 GLU cc_start: 0.7865 (tt0) cc_final: 0.7592 (mt-10) REVERT: I 349 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7105 (ttm170) REVERT: I 373 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8199 (t) REVERT: K 307 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7697 (mp10) REVERT: K 342 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: K 358 ASP cc_start: 0.5865 (p0) cc_final: 0.5151 (p0) REVERT: K 360 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.5928 (pp) REVERT: L 321 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7105 (mttt) REVERT: L 342 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6445 (mt-10) outliers start: 27 outliers final: 12 residues processed: 70 average time/residue: 1.3923 time to fit residues: 101.7513 Evaluate side-chains 65 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain I residue 372 GLU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 307 GLN Chi-restraints excluded: chain L residue 321 LYS Chi-restraints excluded: chain L residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.137396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.126280 restraints weight = 42311.236| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.30 r_work: 0.4261 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.4191 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6912 Z= 0.155 Angle : 1.152 11.121 9252 Z= 0.589 Chirality : 0.314 1.707 1044 Planarity : 0.005 0.070 1176 Dihedral : 5.365 18.413 912 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.05 % Allowed : 13.33 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 349 TYR 0.007 0.002 TYR E 310 PHE 0.002 0.000 PHE F 346 HIS 0.003 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 6912) covalent geometry : angle 1.15167 ( 9252) hydrogen bonds : bond 0.02843 ( 156) hydrogen bonds : angle 5.07359 ( 477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7032 (ttt180) cc_final: 0.6516 (ppt90) REVERT: C 338 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: C 372 GLU cc_start: 0.8159 (tt0) cc_final: 0.7803 (tm-30) REVERT: E 307 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7900 (mt0) REVERT: G 353 LYS cc_start: 0.5656 (mttt) cc_final: 0.4533 (mmtt) REVERT: I 349 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7053 (ttm170) REVERT: K 342 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: K 358 ASP cc_start: 0.5625 (p0) cc_final: 0.4833 (p0) REVERT: K 360 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.5874 (pp) outliers start: 16 outliers final: 10 residues processed: 56 average time/residue: 1.4261 time to fit residues: 83.4229 Evaluate side-chains 54 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 307 GLN Chi-restraints excluded: chain L residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.135326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.124070 restraints weight = 42539.341| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 2.30 r_work: 0.4237 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.4167 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6912 Z= 0.184 Angle : 1.182 11.405 9252 Z= 0.609 Chirality : 0.313 1.712 1044 Planarity : 0.006 0.074 1176 Dihedral : 5.626 20.044 912 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.46 % Allowed : 12.56 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 349 TYR 0.011 0.002 TYR J 310 PHE 0.006 0.001 PHE J 346 HIS 0.006 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 6912) covalent geometry : angle 1.18163 ( 9252) hydrogen bonds : bond 0.03731 ( 156) hydrogen bonds : angle 5.25267 ( 477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 39 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7220 (ttt180) cc_final: 0.6684 (ppt-90) REVERT: C 338 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: D 342 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7021 (mt-10) REVERT: E 307 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8058 (mt0) REVERT: G 353 LYS cc_start: 0.5743 (mttt) cc_final: 0.4609 (mmtt) REVERT: I 349 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7093 (ttm170) REVERT: K 307 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7759 (mp10) REVERT: K 342 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: K 358 ASP cc_start: 0.5612 (p0) cc_final: 0.4858 (p0) REVERT: K 360 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.5990 (pp) outliers start: 27 outliers final: 15 residues processed: 64 average time/residue: 1.3316 time to fit residues: 89.3462 Evaluate side-chains 61 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain I residue 372 GLU Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 307 GLN Chi-restraints excluded: chain L residue 321 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 0.0980 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.139327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.128239 restraints weight = 42286.264| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.32 r_work: 0.4294 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4225 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6912 Z= 0.154 Angle : 1.138 11.083 9252 Z= 0.578 Chirality : 0.314 1.693 1044 Planarity : 0.005 0.062 1176 Dihedral : 5.002 17.654 912 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.54 % Allowed : 14.74 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.21), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.005 0.001 TYR C 310 PHE 0.006 0.001 PHE F 346 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 6912) covalent geometry : angle 1.13812 ( 9252) hydrogen bonds : bond 0.02258 ( 156) hydrogen bonds : angle 4.86235 ( 477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7110 (ttt180) cc_final: 0.6591 (ppt90) REVERT: C 338 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: C 372 GLU cc_start: 0.8088 (tt0) cc_final: 0.7728 (tm-30) REVERT: G 353 LYS cc_start: 0.5629 (mttt) cc_final: 0.4511 (mmtt) REVERT: I 349 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7045 (ttm170) REVERT: K 358 ASP cc_start: 0.5313 (p0) cc_final: 0.4510 (p0) REVERT: K 360 ILE cc_start: 0.6466 (OUTLIER) cc_final: 0.5851 (pp) outliers start: 12 outliers final: 6 residues processed: 57 average time/residue: 1.3662 time to fit residues: 81.7001 Evaluate side-chains 47 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain I residue 372 GLU Chi-restraints excluded: chain J residue 328 ILE Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 67 optimal weight: 0.0870 chunk 75 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.137215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.125997 restraints weight = 42203.505| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.32 r_work: 0.4261 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4190 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6912 Z= 0.156 Angle : 1.148 11.286 9252 Z= 0.587 Chirality : 0.314 1.718 1044 Planarity : 0.005 0.067 1176 Dihedral : 5.125 18.702 912 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.15 % Allowed : 15.26 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.21), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 349 TYR 0.008 0.002 TYR E 310 PHE 0.004 0.001 PHE J 346 HIS 0.004 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 6912) covalent geometry : angle 1.14828 ( 9252) hydrogen bonds : bond 0.02962 ( 156) hydrogen bonds : angle 4.90756 ( 477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7234 (ttt180) cc_final: 0.6689 (ppt-90) REVERT: G 353 LYS cc_start: 0.5778 (mttt) cc_final: 0.4642 (mmtt) REVERT: I 349 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7028 (ttm170) REVERT: K 358 ASP cc_start: 0.5538 (p0) cc_final: 0.4709 (p0) REVERT: K 360 ILE cc_start: 0.6305 (OUTLIER) cc_final: 0.5677 (pp) outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 1.4605 time to fit residues: 70.3155 Evaluate side-chains 46 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain J residue 328 ILE Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.138464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.127395 restraints weight = 42194.237| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.25 r_work: 0.4284 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.4220 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6912 Z= 0.148 Angle : 1.136 11.088 9252 Z= 0.578 Chirality : 0.313 1.693 1044 Planarity : 0.005 0.065 1176 Dihedral : 4.941 17.622 912 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.28 % Allowed : 15.00 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.21), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 349 TYR 0.006 0.002 TYR A 310 PHE 0.002 0.000 PHE F 346 HIS 0.003 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6912) covalent geometry : angle 1.13584 ( 9252) hydrogen bonds : bond 0.02495 ( 156) hydrogen bonds : angle 4.76713 ( 477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4104.24 seconds wall clock time: 70 minutes 0.81 seconds (4200.81 seconds total)