Starting phenix.real_space_refine on Thu Sep 26 18:08:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjx_14025/09_2024/7qjx_14025.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjx_14025/09_2024/7qjx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjx_14025/09_2024/7qjx_14025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjx_14025/09_2024/7qjx_14025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjx_14025/09_2024/7qjx_14025.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjx_14025/09_2024/7qjx_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-5461/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: 7.41, per 1000 atoms: 0.53 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: 3.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.45 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: 4.10 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.38 - 0.67: 3 0.67 - 0.96: 47 0.96 - 1.24: 7971 1.24 - 1.53: 4279 1.53 - 1.82: 1668 Warning: very small bond lengths. Bond restraints: 13968 Sorted by residual: bond pdb=" CG2 VAL H 313 " pdb="HG22 VAL H 313 " ideal model delta sigma weight residual 0.970 0.382 0.588 2.00e-02 2.50e+03 8.65e+02 bond pdb=" CG2 VAL H 313 " pdb="HG21 VAL H 313 " ideal model delta sigma weight residual 0.970 0.391 0.579 2.00e-02 2.50e+03 8.39e+02 bond pdb=" CG2 VAL H 313 " pdb="HG23 VAL H 313 " ideal model delta sigma weight residual 0.970 0.461 0.509 2.00e-02 2.50e+03 6.48e+02 bond pdb=" CG1 VAL H 313 " pdb="HG11 VAL H 313 " ideal model delta sigma weight residual 0.970 0.715 0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" CG1 VAL H 313 " pdb="HG12 VAL H 313 " ideal model delta sigma weight residual 0.970 0.715 0.255 2.00e-02 2.50e+03 1.62e+02 ... (remaining 13963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.55: 25290 19.55 - 39.11: 161 39.11 - 58.66: 6 58.66 - 78.22: 4 78.22 - 97.77: 3 Bond angle restraints: 25464 Sorted by residual: angle pdb="HG21 VAL H 313 " pdb=" CG2 VAL H 313 " pdb="HG23 VAL H 313 " ideal model delta sigma weight residual 110.00 12.23 97.77 3.00e+00 1.11e-01 1.06e+03 angle pdb="HG21 VAL H 313 " pdb=" CG2 VAL H 313 " pdb="HG22 VAL H 313 " ideal model delta sigma weight residual 110.00 18.59 91.41 3.00e+00 1.11e-01 9.28e+02 angle pdb="HG22 VAL H 313 " pdb=" CG2 VAL H 313 " pdb="HG23 VAL H 313 " ideal model delta sigma weight residual 110.00 20.05 89.95 3.00e+00 1.11e-01 8.99e+02 angle pdb="HG21 VAL B 318 " pdb=" CG2 VAL B 318 " pdb="HG22 VAL B 318 " ideal model delta sigma weight residual 110.00 41.95 68.05 3.00e+00 1.11e-01 5.15e+02 angle pdb="HG21 VAL B 318 " pdb=" CG2 VAL B 318 " pdb="HG23 VAL B 318 " ideal model delta sigma weight residual 110.00 42.37 67.63 3.00e+00 1.11e-01 5.08e+02 ... (remaining 25459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5640 17.66 - 35.32: 417 35.32 - 52.97: 213 52.97 - 70.63: 145 70.63 - 88.29: 29 Dihedral angle restraints: 6444 sinusoidal: 3672 harmonic: 2772 Sorted by residual: dihedral pdb=" CA GLY A 365 " pdb=" C GLY A 365 " pdb=" N GLY A 366 " pdb=" CA GLY A 366 " ideal model delta harmonic sigma weight residual 180.00 149.56 30.44 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CD ARG K 349 " pdb=" NE ARG K 349 " pdb=" CZ ARG K 349 " pdb=" NH1 ARG K 349 " ideal model delta sinusoidal sigma weight residual 0.00 -48.88 48.88 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CA SER K 316 " pdb=" C SER K 316 " pdb=" N LYS K 317 " pdb=" CA LYS K 317 " ideal model delta harmonic sigma weight residual 180.00 151.41 28.59 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 6441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 963 0.286 - 0.571: 35 0.571 - 0.857: 12 0.857 - 1.142: 30 1.142 - 1.427: 4 Chirality restraints: 1044 Sorted by residual: chirality pdb=" CB VAL B 318 " pdb=" CA VAL B 318 " pdb=" CG1 VAL B 318 " pdb=" CG2 VAL B 318 " both_signs ideal model delta sigma weight residual False -2.63 -1.20 -1.43 2.00e-01 2.50e+01 5.09e+01 chirality pdb=" CB VAL I 309 " pdb=" CA VAL I 309 " pdb=" CG1 VAL I 309 " pdb=" CG2 VAL I 309 " both_signs ideal model delta sigma weight residual False -2.63 -1.44 -1.19 2.00e-01 2.50e+01 3.56e+01 chirality pdb=" CB VAL B 306 " pdb=" CA VAL B 306 " pdb=" CG1 VAL B 306 " pdb=" CG2 VAL B 306 " both_signs ideal model delta sigma weight residual False -2.63 -1.47 -1.15 2.00e-01 2.50e+01 3.33e+01 ... (remaining 1041 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 365 " -0.075 2.00e-02 2.50e+03 1.46e-01 2.13e+02 pdb=" C GLY A 365 " 0.252 2.00e-02 2.50e+03 pdb=" O GLY A 365 " -0.101 2.00e-02 2.50e+03 pdb=" N GLY A 366 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 349 " -0.893 9.50e-02 1.11e+02 3.00e-01 1.19e+02 pdb=" NE ARG K 349 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG K 349 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG K 349 " -0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG K 349 " 0.067 2.00e-02 2.50e+03 pdb="HH11 ARG K 349 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG K 349 " 0.008 2.00e-02 2.50e+03 pdb="HH21 ARG K 349 " -0.053 2.00e-02 2.50e+03 pdb="HH22 ARG K 349 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 349 " -0.535 9.50e-02 1.11e+02 1.85e-01 8.49e+01 pdb=" NE ARG L 349 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG L 349 " 0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG L 349 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG L 349 " 0.096 2.00e-02 2.50e+03 pdb="HH11 ARG L 349 " -0.026 2.00e-02 2.50e+03 pdb="HH12 ARG L 349 " -0.010 2.00e-02 2.50e+03 pdb="HH21 ARG L 349 " -0.061 2.00e-02 2.50e+03 pdb="HH22 ARG L 349 " -0.055 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1019 2.18 - 2.78: 22399 2.78 - 3.39: 34259 3.39 - 3.99: 44103 3.99 - 4.60: 63093 Nonbonded interactions: 164873 Sorted by model distance: nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.572 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.580 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.585 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.597 2.450 nonbonded pdb=" OD1 ASP L 314 " pdb=" HG SER L 316 " model vdw 1.605 2.450 ... (remaining 164868 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.230 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 31.410 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.910 ------------------------------------------------------------------------------- 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= 0.964 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.086 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: 2.5912 time to fit residues: 299.2343 Evaluate side-chains 43 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3298 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= 0.357 Angle : 1.249 11.697 9252 Z= 0.659 Chirality : 0.289 1.625 1044 Planarity : 0.007 0.097 1176 Dihedral : 7.120 26.985 912 Min Nonbonded Distance : 2.261 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 : -2.68 (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 *********************** 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 fitting. rotamer outliers: 27 poor density : 54 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: C 349 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7373 (ttm110) REVERT: G 353 LYS cc_start: 0.5811 (mttt) cc_final: 0.4874 (mmtt) REVERT: H 347 LYS cc_start: 0.4025 (pttp) cc_final: 0.3383 (pmtt) REVERT: I 349 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7634 (ttp-170) REVERT: K 342 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: L 342 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6306 (mt-10) outliers start: 27 outliers final: 10 residues processed: 77 average time/residue: 2.8179 time to fit residues: 227.8007 Evaluate side-chains 53 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 42 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6912 Z= 0.302 Angle : 1.188 11.284 9252 Z= 0.617 Chirality : 0.313 1.687 1044 Planarity : 0.006 0.065 1176 Dihedral : 6.013 21.403 912 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.44 % Allowed : 8.08 % 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: -3.63 (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 0.005 0.001 HIS J 329 PHE 0.004 0.001 PHE E 378 TYR 0.012 0.003 TYR K 310 ARG 0.004 0.001 ARG A 349 *********************** 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 68 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 49 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7291 (ttm110) REVERT: G 353 LYS cc_start: 0.5831 (mttt) cc_final: 0.4922 (mmtt) REVERT: I 349 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7403 (ttm170) REVERT: K 342 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: K 360 ILE cc_start: 0.6052 (OUTLIER) cc_final: 0.5511 (pp) REVERT: L 342 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6298 (mt-10) outliers start: 19 outliers final: 5 residues processed: 67 average time/residue: 3.0852 time to fit residues: 216.9642 Evaluate side-chains 51 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 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 75 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6912 Z= 0.321 Angle : 1.217 11.459 9252 Z= 0.631 Chirality : 0.311 1.725 1044 Planarity : 0.006 0.064 1176 Dihedral : 6.099 20.291 912 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.69 % Allowed : 10.00 % Favored : 87.31 % 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: -3.82 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (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 E 378 TYR 0.011 0.003 TYR K 310 ARG 0.006 0.001 ARG H 349 *********************** 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 66 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 45 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 338 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: C 349 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7350 (ttm110) REVERT: G 353 LYS cc_start: 0.5587 (mttt) cc_final: 0.4716 (mmtt) REVERT: I 349 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7382 (ttm170) REVERT: K 342 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: K 360 ILE cc_start: 0.6500 (OUTLIER) cc_final: 0.5956 (pp) REVERT: L 342 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6271 (mt-10) outliers start: 21 outliers final: 9 residues processed: 62 average time/residue: 3.0369 time to fit residues: 197.1431 Evaluate side-chains 53 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 349 ARG Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain K residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 359 ASN F 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6912 Z= 0.291 Angle : 1.188 11.277 9252 Z= 0.613 Chirality : 0.315 1.716 1044 Planarity : 0.006 0.066 1176 Dihedral : 5.800 19.509 912 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.59 % Allowed : 10.77 % Favored : 85.64 % 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 0.006 0.001 HIS I 362 PHE 0.004 0.001 PHE F 378 TYR 0.009 0.002 TYR B 310 ARG 0.004 0.001 ARG B 349 *********************** 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 72 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 44 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: G 353 LYS cc_start: 0.5600 (mttt) cc_final: 0.4711 (mmtt) REVERT: I 349 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7369 (ttm170) REVERT: K 342 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: K 360 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6111 (pp) outliers start: 28 outliers final: 11 residues processed: 69 average time/residue: 2.8354 time to fit residues: 205.4192 Evaluate side-chains 54 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 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 373 THR Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 307 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 368 ASN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6912 Z= 0.284 Angle : 1.175 11.309 9252 Z= 0.603 Chirality : 0.313 1.711 1044 Planarity : 0.006 0.069 1176 Dihedral : 5.619 19.672 912 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.69 % Allowed : 12.31 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.81 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 374 PHE 0.004 0.001 PHE G 346 TYR 0.008 0.002 TYR E 310 ARG 0.003 0.001 ARG G 349 *********************** 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 64 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: D 345 ASP cc_start: 0.8386 (t0) cc_final: 0.8169 (m-30) REVERT: G 353 LYS cc_start: 0.5666 (mttt) cc_final: 0.4745 (mmtt) REVERT: I 349 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7343 (ttm170) REVERT: K 307 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6705 (pm20) REVERT: K 342 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: K 360 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.6022 (pp) REVERT: L 342 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6004 (mt-10) outliers start: 21 outliers final: 11 residues processed: 62 average time/residue: 2.8207 time to fit residues: 183.9072 Evaluate side-chains 56 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 373 THR Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 321 LYS Chi-restraints excluded: chain L residue 342 GLU Chi-restraints excluded: chain L residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 chunk 46 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 overall best weight: 3.7986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5701 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= 0.271 Angle : 1.160 11.099 9252 Z= 0.593 Chirality : 0.314 1.704 1044 Planarity : 0.005 0.069 1176 Dihedral : 5.409 20.464 912 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.31 % Allowed : 13.33 % Favored : 84.36 % 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: -3.77 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.15), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.003 0.001 PHE C 346 TYR 0.008 0.002 TYR A 310 ARG 0.002 0.000 ARG J 349 *********************** 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 63 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: E 307 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7336 (mt0) REVERT: G 353 LYS cc_start: 0.5647 (mttt) cc_final: 0.4741 (mmtt) REVERT: I 349 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7325 (ttm170) REVERT: K 307 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6611 (pm20) REVERT: K 342 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: K 360 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.5990 (pp) outliers start: 18 outliers final: 11 residues processed: 61 average time/residue: 2.7278 time to fit residues: 175.3850 Evaluate side-chains 55 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 39 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 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 373 THR Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 307 GLN Chi-restraints excluded: chain L residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6912 Z= 0.267 Angle : 1.149 11.082 9252 Z= 0.586 Chirality : 0.314 1.704 1044 Planarity : 0.005 0.066 1176 Dihedral : 5.171 20.170 912 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % 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: -3.70 (0.20), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.002 0.000 PHE F 346 TYR 0.007 0.002 TYR E 310 ARG 0.002 0.000 ARG J 349 *********************** 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 fitting. rotamer outliers: 21 poor density : 40 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: E 307 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7366 (mt0) REVERT: G 353 LYS cc_start: 0.5643 (mttt) cc_final: 0.4742 (mmtt) REVERT: I 349 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7263 (ttm170) REVERT: K 307 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.6537 (pm20) REVERT: K 342 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: K 360 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.6081 (pp) outliers start: 21 outliers final: 9 residues processed: 60 average time/residue: 2.7292 time to fit residues: 172.3807 Evaluate side-chains 51 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 373 THR Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain J residue 328 ILE Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 321 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 45 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5964 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= 0.266 Angle : 1.152 11.121 9252 Z= 0.588 Chirality : 0.314 1.705 1044 Planarity : 0.005 0.067 1176 Dihedral : 5.153 18.983 912 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.44 % Allowed : 13.85 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.67 (0.21), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 362 PHE 0.002 0.000 PHE B 346 TYR 0.007 0.002 TYR E 310 ARG 0.002 0.000 ARG G 349 *********************** 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 55 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 36 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: E 307 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7375 (mt0) REVERT: G 353 LYS cc_start: 0.5665 (mttt) cc_final: 0.4755 (mmtt) REVERT: I 349 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7243 (ttm170) REVERT: K 307 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6491 (pm20) REVERT: K 360 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6209 (pp) outliers start: 19 outliers final: 12 residues processed: 54 average time/residue: 2.5958 time to fit residues: 148.6151 Evaluate side-chains 53 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 373 THR Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain J residue 328 ILE Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 307 GLN Chi-restraints excluded: chain L residue 321 LYS Chi-restraints excluded: chain L residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 0.0670 chunk 40 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.6070 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= 0.272 Angle : 1.140 11.027 9252 Z= 0.579 Chirality : 0.314 1.690 1044 Planarity : 0.005 0.061 1176 Dihedral : 4.828 17.594 912 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.41 % Allowed : 14.74 % 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: -3.57 (0.21), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.004 0.000 PHE F 346 TYR 0.005 0.001 TYR H 310 ARG 0.002 0.000 ARG J 349 ********************** 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 53 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: G 353 LYS cc_start: 0.5634 (mttt) cc_final: 0.4748 (mmtt) REVERT: I 349 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7205 (ttm170) REVERT: K 307 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7150 (mt0) REVERT: K 360 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6198 (pp) outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 2.3276 time to fit residues: 129.1728 Evaluate side-chains 45 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain J residue 328 ILE Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 10.0000 chunk 9 optimal weight: 0.0010 chunk 18 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.137773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.126855 restraints weight = 42041.106| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.25 r_work: 0.4270 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.4202 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.6117 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= 0.268 Angle : 1.155 11.169 9252 Z= 0.590 Chirality : 0.314 1.714 1044 Planarity : 0.005 0.065 1176 Dihedral : 4.997 16.904 912 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.54 % Allowed : 14.62 % 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: -3.62 (0.21), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.004 0.001 PHE L 346 TYR 0.008 0.002 TYR E 310 ARG 0.002 0.000 ARG J 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4276.48 seconds wall clock time: 74 minutes 49.06 seconds (4489.06 seconds total)