Starting phenix.real_space_refine on Thu Jun 12 08:55:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qjx_14025/06_2025/7qjx_14025.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qjx_14025/06_2025/7qjx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qjx_14025/06_2025/7qjx_14025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qjx_14025/06_2025/7qjx_14025.map" model { file = "/net/cci-nas-00/data/ceres_data/7qjx_14025/06_2025/7qjx_14025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qjx_14025/06_2025/7qjx_14025.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.62, per 1000 atoms: 0.48 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: 2.84 Conformation dependent library (CDL) restraints added in 985.2 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: 1.31 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: 4.38 Time building geometry restraints manager: 3.59 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: 0.01 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: 1.250 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: 0.230 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 29.240 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.012 0.003 HIS K 330 PHE 0.022 0.006 PHE B 378 TYR 0.077 0.016 TYR C 310 ARG 0.023 0.002 ARG L 349 Details of bonding type rmsd hydrogen bonds : bond 0.17258 ( 156) hydrogen bonds : angle 7.43704 ( 477) covalent geometry : bond 0.01406 ( 6912) covalent geometry : angle 2.55752 ( 9252) *********************** 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 : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 2.6043 time to fit residues: 301.1748 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 : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.148241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.136836 restraints weight = 43057.138| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 2.51 r_work: 0.4329 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4254 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6912 Z= 0.236 Angle : 1.248 11.678 9252 Z= 0.658 Chirality : 0.289 1.624 1044 Planarity : 0.006 0.097 1176 Dihedral : 7.115 26.998 912 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.46 % Allowed : 7.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.19), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 329 PHE 0.011 0.002 PHE H 378 TYR 0.012 0.003 TYR K 310 ARG 0.008 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 156) hydrogen bonds : angle 6.06869 ( 477) covalent geometry : bond 0.00535 ( 6912) covalent geometry : angle 1.24850 ( 9252) *********************** 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: 27 poor density : 54 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: A 372 GLU cc_start: 0.7918 (tt0) cc_final: 0.7701 (tt0) REVERT: C 349 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6956 (ttm110) REVERT: G 353 LYS cc_start: 0.5815 (mttt) cc_final: 0.4678 (mmtt) REVERT: H 347 LYS cc_start: 0.3929 (pttp) cc_final: 0.2993 (pmtt) REVERT: H 372 GLU cc_start: 0.7766 (tt0) cc_final: 0.7277 (mt-10) REVERT: I 349 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7377 (ttp-170) REVERT: K 342 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: K 358 ASP cc_start: 0.5066 (p0) cc_final: 0.3983 (p0) REVERT: L 342 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6652 (mt-10) outliers start: 27 outliers final: 10 residues processed: 77 average time/residue: 2.8144 time to fit residues: 227.3700 Evaluate side-chains 53 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 36 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 0.0170 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.144583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.133161 restraints weight = 42525.974| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.54 r_work: 0.4304 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4231 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6912 Z= 0.182 Angle : 1.181 11.116 9252 Z= 0.610 Chirality : 0.315 1.691 1044 Planarity : 0.006 0.069 1176 Dihedral : 5.976 21.120 912 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.31 % Allowed : 8.33 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 329 PHE 0.003 0.001 PHE B 346 TYR 0.012 0.003 TYR K 310 ARG 0.003 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 156) hydrogen bonds : angle 5.51834 ( 477) covalent geometry : bond 0.00460 ( 6912) covalent geometry : angle 1.18078 ( 9252) *********************** 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: 18 poor density : 52 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7012 (ttt180) cc_final: 0.6698 (pmt170) REVERT: C 338 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: C 349 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6798 (ttm110) REVERT: G 353 LYS cc_start: 0.5788 (mttt) cc_final: 0.4689 (mmtt) REVERT: H 342 GLU cc_start: 0.5255 (tp30) cc_final: 0.5003 (tp30) REVERT: H 372 GLU cc_start: 0.7705 (tt0) cc_final: 0.7453 (mt-10) REVERT: I 342 GLU cc_start: 0.4659 (tt0) cc_final: 0.4395 (tt0) REVERT: I 345 ASP cc_start: 0.7784 (m-30) cc_final: 0.7576 (m-30) REVERT: I 349 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7094 (mtm180) REVERT: K 342 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: K 358 ASP cc_start: 0.5305 (p0) cc_final: 0.4345 (p0) REVERT: K 360 ILE cc_start: 0.5613 (OUTLIER) cc_final: 0.5214 (pp) REVERT: L 342 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6550 (mt-10) outliers start: 18 outliers final: 5 residues processed: 68 average time/residue: 3.0336 time to fit residues: 215.8282 Evaluate side-chains 55 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 C residue 349 ARG Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain F 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 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.139376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.128083 restraints weight = 41606.640| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.37 r_work: 0.4262 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: 0.7697 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6912 Z= 0.185 Angle : 1.180 11.185 9252 Z= 0.608 Chirality : 0.311 1.706 1044 Planarity : 0.006 0.061 1176 Dihedral : 5.820 20.014 912 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.82 % Allowed : 9.62 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 362 PHE 0.005 0.001 PHE E 378 TYR 0.010 0.002 TYR K 310 ARG 0.005 0.001 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 156) hydrogen bonds : angle 5.33324 ( 477) covalent geometry : bond 0.00441 ( 6912) covalent geometry : angle 1.18047 ( 9252) *********************** 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 68 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 353 LYS cc_start: 0.5920 (mttt) cc_final: 0.4837 (mmtt) REVERT: H 372 GLU cc_start: 0.7818 (tt0) cc_final: 0.7585 (mt-10) REVERT: I 342 GLU cc_start: 0.4895 (tt0) cc_final: 0.4630 (tt0) REVERT: I 349 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7124 (ttm170) REVERT: K 342 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: K 358 ASP cc_start: 0.5500 (p0) cc_final: 0.4692 (p0) REVERT: K 360 ILE cc_start: 0.6208 (OUTLIER) cc_final: 0.5847 (pp) outliers start: 22 outliers final: 9 residues processed: 65 average time/residue: 3.0241 time to fit residues: 205.7248 Evaluate side-chains 52 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 E residue 307 GLN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain G residue 338 GLU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 overall best weight: 7.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS D 359 ASN E 359 ASN F 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.135395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.124186 restraints weight = 42868.039| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.36 r_work: 0.4224 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4154 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6912 Z= 0.208 Angle : 1.222 11.462 9252 Z= 0.636 Chirality : 0.316 1.727 1044 Planarity : 0.006 0.065 1176 Dihedral : 6.087 21.386 912 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.85 % Allowed : 10.64 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS I 362 PHE 0.009 0.001 PHE J 346 TYR 0.011 0.003 TYR E 310 ARG 0.006 0.001 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 156) hydrogen bonds : angle 5.51700 ( 477) covalent geometry : bond 0.00487 ( 6912) covalent geometry : angle 1.22237 ( 9252) *********************** 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 77 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 47 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7055 (ttt180) cc_final: 0.6759 (ppt-90) REVERT: C 338 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: C 372 GLU cc_start: 0.8204 (tt0) cc_final: 0.7880 (tm-30) REVERT: G 353 LYS cc_start: 0.5630 (mttt) cc_final: 0.4532 (mmtt) REVERT: H 338 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: H 347 LYS cc_start: 0.4631 (pmtt) cc_final: 0.4356 (pmtt) REVERT: H 372 GLU cc_start: 0.7868 (tt0) cc_final: 0.7567 (mt-10) REVERT: I 349 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7079 (ttm170) REVERT: I 373 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8232 (t) REVERT: J 342 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: J 349 ARG cc_start: 0.5461 (OUTLIER) cc_final: 0.5204 (mtt90) REVERT: K 342 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: K 358 ASP cc_start: 0.5424 (p0) cc_final: 0.4515 (p0) REVERT: K 360 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.6059 (pp) REVERT: L 342 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6506 (mt-10) outliers start: 30 outliers final: 14 residues processed: 73 average time/residue: 2.8043 time to fit residues: 214.9935 Evaluate side-chains 65 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 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 338 GLU Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain J residue 349 ARG 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 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 72 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.136674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.125507 restraints weight = 42910.387| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.33 r_work: 0.4251 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4181 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5510 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= 0.166 Angle : 1.170 11.154 9252 Z= 0.600 Chirality : 0.313 1.709 1044 Planarity : 0.006 0.071 1176 Dihedral : 5.646 19.789 912 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.69 % Allowed : 12.18 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 362 PHE 0.004 0.001 PHE G 346 TYR 0.008 0.002 TYR A 310 ARG 0.006 0.001 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 156) hydrogen bonds : angle 5.21666 ( 477) covalent geometry : bond 0.00423 ( 6912) covalent geometry : angle 1.16975 ( 9252) *********************** 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 66 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7078 (ttt180) cc_final: 0.6530 (ppt-90) REVERT: C 338 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7972 (tm-30) REVERT: D 342 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7022 (mt-10) REVERT: G 353 LYS cc_start: 0.5605 (mttt) cc_final: 0.4520 (mmtt) REVERT: I 349 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7068 (ttm170) REVERT: J 349 ARG cc_start: 0.5824 (OUTLIER) cc_final: 0.5528 (mtt90) REVERT: K 307 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7010 (pm20) REVERT: K 342 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: K 358 ASP cc_start: 0.5498 (p0) cc_final: 0.4603 (p0) REVERT: K 360 ILE cc_start: 0.6479 (OUTLIER) cc_final: 0.6027 (pp) outliers start: 21 outliers final: 8 residues processed: 63 average time/residue: 3.1299 time to fit residues: 206.2668 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 : 1.108 ------------------------------------------------------------------------------- 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 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 J 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 35 optimal weight: 0.4980 chunk 24 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 67 optimal weight: 0.0070 chunk 19 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 overall best weight: 3.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 359 ASN K 359 ASN L 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.137282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.126123 restraints weight = 42530.218| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 2.33 r_work: 0.4263 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.4195 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6912 Z= 0.155 Angle : 1.152 11.098 9252 Z= 0.589 Chirality : 0.314 1.707 1044 Planarity : 0.005 0.068 1176 Dihedral : 5.364 18.462 912 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.31 % Allowed : 13.46 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.002 0.000 PHE K 346 TYR 0.008 0.002 TYR B 310 ARG 0.003 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02872 ( 156) hydrogen bonds : angle 5.02700 ( 477) covalent geometry : bond 0.00413 ( 6912) covalent geometry : angle 1.15181 ( 9252) *********************** 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 60 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7097 (ttt180) cc_final: 0.6571 (ppt-90) REVERT: C 338 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: C 372 GLU cc_start: 0.8167 (tt0) cc_final: 0.7818 (tm-30) REVERT: E 307 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: G 353 LYS cc_start: 0.5649 (mttt) cc_final: 0.4534 (mmtt) REVERT: I 349 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7033 (ttm170) REVERT: J 349 ARG cc_start: 0.5628 (OUTLIER) cc_final: 0.5390 (mtt90) REVERT: K 307 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.6928 (pm20) REVERT: K 342 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: K 358 ASP cc_start: 0.5485 (p0) cc_final: 0.4610 (p0) REVERT: K 360 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.5912 (pp) outliers start: 18 outliers final: 7 residues processed: 58 average time/residue: 3.0718 time to fit residues: 186.6609 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 : 1.162 ------------------------------------------------------------------------------- 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 J 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 Chi-restraints excluded: chain L residue 307 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.134905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.123610 restraints weight = 42624.144| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.32 r_work: 0.4223 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4152 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6912 Z= 0.195 Angle : 1.199 11.503 9252 Z= 0.619 Chirality : 0.314 1.703 1044 Planarity : 0.006 0.077 1176 Dihedral : 5.761 20.191 912 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.69 % Allowed : 13.46 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 362 PHE 0.007 0.001 PHE D 346 TYR 0.011 0.003 TYR J 310 ARG 0.002 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 156) hydrogen bonds : angle 5.32287 ( 477) covalent geometry : bond 0.00470 ( 6912) covalent geometry : angle 1.19876 ( 9252) *********************** 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 61 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7262 (ttt180) cc_final: 0.6701 (ppt-90) REVERT: C 338 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: E 307 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: G 353 LYS cc_start: 0.5771 (mttt) cc_final: 0.4626 (mmtt) REVERT: I 349 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7071 (ttm170) REVERT: J 349 ARG cc_start: 0.5450 (OUTLIER) cc_final: 0.5217 (mtt90) REVERT: K 307 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7192 (pt0) REVERT: K 342 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: K 358 ASP cc_start: 0.5736 (p0) cc_final: 0.4757 (p0) REVERT: K 360 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6078 (pp) outliers start: 21 outliers final: 9 residues processed: 59 average time/residue: 3.0452 time to fit residues: 188.3408 Evaluate side-chains 54 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 I residue 372 GLU Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J 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 Chi-restraints excluded: chain L residue 307 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.136167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.124954 restraints weight = 42258.488| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.32 r_work: 0.4249 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4179 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5923 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= 0.163 Angle : 1.163 11.137 9252 Z= 0.596 Chirality : 0.314 1.703 1044 Planarity : 0.005 0.074 1176 Dihedral : 5.510 19.348 912 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.92 % Allowed : 14.62 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (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 HIS 0.004 0.001 HIS I 362 PHE 0.002 0.000 PHE H 378 TYR 0.007 0.002 TYR A 310 ARG 0.001 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.03174 ( 156) hydrogen bonds : angle 5.15894 ( 477) covalent geometry : bond 0.00421 ( 6912) covalent geometry : angle 1.16332 ( 9252) *********************** 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 54 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7246 (ttt180) cc_final: 0.6863 (ppt90) REVERT: C 338 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: E 307 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7989 (mt0) REVERT: G 353 LYS cc_start: 0.5725 (mttt) cc_final: 0.4597 (mmtt) REVERT: I 349 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7100 (ttm170) REVERT: J 349 ARG cc_start: 0.5709 (OUTLIER) cc_final: 0.5470 (mtt90) REVERT: K 307 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: K 342 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: K 358 ASP cc_start: 0.5657 (p0) cc_final: 0.4785 (p0) REVERT: K 360 ILE cc_start: 0.6343 (OUTLIER) cc_final: 0.5785 (pp) outliers start: 15 outliers final: 10 residues processed: 52 average time/residue: 3.0894 time to fit residues: 169.1372 Evaluate side-chains 55 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 348 ASP 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 J 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 Chi-restraints excluded: chain L residue 307 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 82 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.135969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.124783 restraints weight = 42603.779| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 2.30 r_work: 0.4247 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.4177 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6912 Z= 0.173 Angle : 1.173 11.214 9252 Z= 0.602 Chirality : 0.314 1.705 1044 Planarity : 0.006 0.075 1176 Dihedral : 5.515 19.778 912 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.92 % Allowed : 14.74 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.004 0.001 HIS L 330 PHE 0.004 0.001 PHE J 346 TYR 0.009 0.002 TYR J 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 156) hydrogen bonds : angle 5.17456 ( 477) covalent geometry : bond 0.00439 ( 6912) covalent geometry : angle 1.17285 ( 9252) ********************** 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 54 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7310 (ttt180) cc_final: 0.6735 (ppt-90) REVERT: C 338 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: E 307 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: G 353 LYS cc_start: 0.5720 (mttt) cc_final: 0.4582 (mmtt) REVERT: I 349 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7086 (ttm170) REVERT: J 349 ARG cc_start: 0.5771 (OUTLIER) cc_final: 0.5547 (mtt90) REVERT: K 307 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: K 342 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: K 358 ASP cc_start: 0.5741 (p0) cc_final: 0.4831 (p0) REVERT: K 360 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.5750 (pp) outliers start: 15 outliers final: 10 residues processed: 52 average time/residue: 3.1163 time to fit residues: 170.0179 Evaluate side-chains 55 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 348 ASP 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 J 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 Chi-restraints excluded: chain L residue 307 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 3 optimal weight: 0.0980 chunk 5 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 overall best weight: 5.8188 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.135718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.124553 restraints weight = 42508.628| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.29 r_work: 0.4239 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.4169 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.6003 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= 0.175 Angle : 1.173 11.264 9252 Z= 0.603 Chirality : 0.314 1.701 1044 Planarity : 0.006 0.072 1176 Dihedral : 5.540 19.621 912 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.31 % Allowed : 14.36 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.004 0.001 HIS I 362 PHE 0.004 0.001 PHE J 346 TYR 0.009 0.002 TYR J 310 ARG 0.001 0.000 ARG L 349 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 156) hydrogen bonds : angle 5.19018 ( 477) covalent geometry : bond 0.00440 ( 6912) covalent geometry : angle 1.17349 ( 9252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8405.50 seconds wall clock time: 143 minutes 11.76 seconds (8591.76 seconds total)