Starting phenix.real_space_refine (version: dev) on Thu May 12 20:48:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6c_13225/05_2022/7p6c_13225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6c_13225/05_2022/7p6c_13225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6c_13225/05_2022/7p6c_13225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6c_13225/05_2022/7p6c_13225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6c_13225/05_2022/7p6c_13225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6c_13225/05_2022/7p6c_13225.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 283": "OD1" <-> "OD2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 283": "OD1" <-> "OD2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 283": "OD1" <-> "OD2" Residue "D ASP 348": "OD1" <-> "OD2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 283": "OD1" <-> "OD2" Residue "E ASP 348": "OD1" <-> "OD2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 283": "OD1" <-> "OD2" Residue "F ASP 348": "OD1" <-> "OD2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 283": "OD1" <-> "OD2" Residue "G ASP 348": "OD1" <-> "OD2" Residue "G PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 283": "OD1" <-> "OD2" Residue "H ASP 348": "OD1" <-> "OD2" Residue "H PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 283": "OD1" <-> "OD2" Residue "I ASP 348": "OD1" <-> "OD2" Residue "I PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 283": "OD1" <-> "OD2" Residue "J ASP 348": "OD1" <-> "OD2" Residue "J PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 8120 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "B" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "D" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "F" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "G" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "H" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "I" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "J" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 5.00, per 1000 atoms: 0.62 Number of scatterers: 8120 At special positions: 0 Unit cell: (106.142, 114.139, 49.436, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1520 8.00 N 1520 7.00 C 5060 6.00 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 - 3.50 Amino acid : False - 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: 3.32 Conformation dependent library (CDL) restraints added in 1.3 seconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 274 through 280 removed outlier: 6.825A pdb=" N LYS B 274 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE C 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN B 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN C 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS A 274 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE B 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLN A 276 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASN B 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 278 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 283 through 284 removed outlier: 6.209A pdb=" N ASP B 283 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP A 283 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 287 through 292 removed outlier: 6.444A pdb=" N VAL A 287 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LYS D 290 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N SER A 289 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N GLY D 292 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N CYS A 291 " --> pdb=" O GLY D 292 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 287 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LYS E 290 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER D 289 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLY E 292 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS D 291 " --> pdb=" O GLY E 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 297 through 298 removed outlier: 6.277A pdb=" N ILE A 297 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE D 297 " --> pdb=" O LYS E 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 305 through 310 removed outlier: 6.625A pdb=" N SER B 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE C 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N TYR C 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 305 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE B 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.817A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.274A pdb=" N VAL A 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LYS D 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N SER A 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL D 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LYS E 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER D 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.698A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE D 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.317A pdb=" N VAL A 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LYS D 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL A 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU D 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER A 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU D 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS A 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE D 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL D 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LYS E 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL D 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLU E 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER D 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LEU E 344 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS D 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE E 346 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP D 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 349 through 354 removed outlier: 6.573A pdb=" N VAL B 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LYS C 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER B 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LYS B 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER A 352 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.871A pdb=" N ASP B 358 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASN C 359 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP A 358 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN B 359 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N LEU A 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N ILE D 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN A 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N HIS D 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N LEU D 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ILE E 360 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN D 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N HIS E 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR D 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.815A pdb=" N LYS B 370 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS A 370 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU D 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE D 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS D 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N GLU E 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE D 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N HIS E 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR D 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU E 376 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS D 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE E 378 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR D 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 274 through 280 removed outlier: 6.823A pdb=" N LYS G 274 " --> pdb=" O VAL H 275 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE H 277 " --> pdb=" O LYS G 274 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLN G 276 " --> pdb=" O ILE H 277 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASN H 279 " --> pdb=" O GLN G 276 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE G 278 " --> pdb=" O ASN H 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS F 274 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE G 277 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLN F 276 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASN G 279 " --> pdb=" O GLN F 276 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE F 278 " --> pdb=" O ASN G 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 283 through 284 removed outlier: 6.206A pdb=" N ASP G 283 " --> pdb=" O LEU H 284 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP F 283 " --> pdb=" O LEU G 284 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 287 through 292 removed outlier: 6.440A pdb=" N VAL F 287 " --> pdb=" O GLN I 288 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS I 290 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N SER F 289 " --> pdb=" O LYS I 290 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLY I 292 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS F 291 " --> pdb=" O GLY I 292 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL I 287 " --> pdb=" O GLN J 288 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LYS J 290 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N SER I 289 " --> pdb=" O LYS J 290 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N GLY J 292 " --> pdb=" O SER I 289 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS I 291 " --> pdb=" O GLY J 292 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 297 through 298 removed outlier: 6.270A pdb=" N ILE F 297 " --> pdb=" O LYS I 298 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE I 297 " --> pdb=" O LYS J 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 305 through 310 removed outlier: 6.627A pdb=" N SER G 305 " --> pdb=" O VAL H 306 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE H 308 " --> pdb=" O SER G 305 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN G 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N TYR H 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL G 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER F 305 " --> pdb=" O VAL G 306 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE G 308 " --> pdb=" O SER F 305 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN F 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N TYR G 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL F 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 313 through 314 removed outlier: 6.819A pdb=" N VAL G 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL F 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 317 through 322 removed outlier: 6.278A pdb=" N VAL F 318 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LYS I 321 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER F 320 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL I 318 " --> pdb=" O THR J 319 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LYS J 321 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER I 320 " --> pdb=" O LYS J 321 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 328 through 330 removed outlier: 6.696A pdb=" N ILE F 328 " --> pdb=" O HIS I 329 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE I 328 " --> pdb=" O HIS J 329 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 337 through 346 removed outlier: 6.311A pdb=" N VAL F 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LYS I 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL F 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLU I 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER F 341 " --> pdb=" O GLU I 342 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LEU I 344 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS F 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE I 346 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP F 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL I 337 " --> pdb=" O GLU J 338 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LYS J 340 " --> pdb=" O VAL I 337 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL I 339 " --> pdb=" O LYS J 340 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLU J 342 " --> pdb=" O VAL I 339 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER I 341 " --> pdb=" O GLU J 342 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU J 344 " --> pdb=" O SER I 341 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS I 343 " --> pdb=" O LEU J 344 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE J 346 " --> pdb=" O LYS I 343 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASP I 345 " --> pdb=" O PHE J 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 349 through 354 removed outlier: 6.563A pdb=" N VAL G 350 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LYS H 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER G 352 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL F 350 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LYS G 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER F 352 " --> pdb=" O LYS G 353 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 357 through 362 removed outlier: 6.862A pdb=" N ASP G 358 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN H 359 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP F 358 " --> pdb=" O LEU G 357 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN G 359 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N LEU F 357 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N ILE I 360 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN F 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N HIS I 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR F 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N LEU I 357 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N ILE J 360 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN I 359 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N HIS J 362 " --> pdb=" O ASN I 359 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR I 361 " --> pdb=" O HIS J 362 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 369 through 378 removed outlier: 6.808A pdb=" N LYS G 370 " --> pdb=" O LYS H 369 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS F 370 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS F 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLU I 372 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE F 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N HIS I 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR F 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU I 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS F 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE I 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR F 377 " --> pdb=" O PHE I 378 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS I 369 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N GLU J 372 " --> pdb=" O LYS I 369 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE I 371 " --> pdb=" O GLU J 372 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N HIS J 374 " --> pdb=" O ILE I 371 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR I 373 " --> pdb=" O HIS J 374 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU J 376 " --> pdb=" O THR I 373 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS I 375 " --> pdb=" O LEU J 376 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE J 378 " --> pdb=" O LYS I 375 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR I 377 " --> pdb=" O PHE J 378 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2710 1.34 - 1.46: 1245 1.46 - 1.58: 4255 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 8230 Sorted by residual: bond pdb=" N ILE F 371 " pdb=" CA ILE F 371 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.24e-02 6.50e+03 7.73e+00 bond pdb=" N ILE D 371 " pdb=" CA ILE D 371 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.56e+00 bond pdb=" N ILE E 371 " pdb=" CA ILE E 371 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.42e+00 bond pdb=" N ILE B 371 " pdb=" CA ILE B 371 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.37e+00 bond pdb=" N ILE C 371 " pdb=" CA ILE C 371 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.34e+00 ... (remaining 8225 not shown) Histogram of bond angle deviations from ideal: 102.41 - 108.23: 487 108.23 - 114.04: 4717 114.04 - 119.86: 2020 119.86 - 125.68: 3676 125.68 - 131.50: 90 Bond angle restraints: 10990 Sorted by residual: angle pdb=" CA ILE I 371 " pdb=" C ILE I 371 " pdb=" O ILE I 371 " ideal model delta sigma weight residual 120.53 117.72 2.81 1.07e+00 8.73e-01 6.90e+00 angle pdb=" CA ILE G 371 " pdb=" C ILE G 371 " pdb=" O ILE G 371 " ideal model delta sigma weight residual 120.53 117.74 2.79 1.07e+00 8.73e-01 6.81e+00 angle pdb=" CA ILE A 371 " pdb=" C ILE A 371 " pdb=" O ILE A 371 " ideal model delta sigma weight residual 120.53 117.74 2.79 1.07e+00 8.73e-01 6.81e+00 angle pdb=" CA ILE B 371 " pdb=" C ILE B 371 " pdb=" O ILE B 371 " ideal model delta sigma weight residual 120.53 117.74 2.79 1.07e+00 8.73e-01 6.80e+00 angle pdb=" CA ILE C 371 " pdb=" C ILE C 371 " pdb=" O ILE C 371 " ideal model delta sigma weight residual 120.53 117.74 2.79 1.07e+00 8.73e-01 6.80e+00 ... (remaining 10985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.13: 4200 13.13 - 26.25: 479 26.25 - 39.38: 281 39.38 - 52.51: 80 52.51 - 65.63: 10 Dihedral angle restraints: 5050 sinusoidal: 2110 harmonic: 2940 Sorted by residual: dihedral pdb=" CG LYS B 340 " pdb=" CD LYS B 340 " pdb=" CE LYS B 340 " pdb=" NZ LYS B 340 " ideal model delta sinusoidal sigma weight residual 180.00 132.86 47.14 3 1.50e+01 4.44e-03 8.45e+00 dihedral pdb=" CG LYS D 340 " pdb=" CD LYS D 340 " pdb=" CE LYS D 340 " pdb=" NZ LYS D 340 " ideal model delta sinusoidal sigma weight residual 180.00 132.89 47.11 3 1.50e+01 4.44e-03 8.44e+00 dihedral pdb=" CG LYS F 340 " pdb=" CD LYS F 340 " pdb=" CE LYS F 340 " pdb=" NZ LYS F 340 " ideal model delta sinusoidal sigma weight residual 180.00 132.89 47.11 3 1.50e+01 4.44e-03 8.44e+00 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 752 0.043 - 0.086: 184 0.086 - 0.129: 284 0.129 - 0.172: 0 0.172 - 0.214: 10 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CA ILE H 371 " pdb=" N ILE H 371 " pdb=" C ILE H 371 " pdb=" CB ILE H 371 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE E 371 " pdb=" N ILE E 371 " pdb=" C ILE E 371 " pdb=" CB ILE E 371 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE I 371 " pdb=" N ILE I 371 " pdb=" C ILE I 371 " pdb=" CB ILE I 371 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1227 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 300 " -0.014 5.00e-02 4.00e+02 2.09e-02 7.00e-01 pdb=" N PRO D 301 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO D 301 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO D 301 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 300 " -0.014 5.00e-02 4.00e+02 2.09e-02 6.99e-01 pdb=" N PRO J 301 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO J 301 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO J 301 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 300 " -0.014 5.00e-02 4.00e+02 2.08e-02 6.93e-01 pdb=" N PRO A 301 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " -0.012 5.00e-02 4.00e+02 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1669 2.81 - 3.33: 6711 3.33 - 3.85: 14379 3.85 - 4.38: 16376 4.38 - 4.90: 31438 Nonbonded interactions: 70573 Sorted by model distance: nonbonded pdb=" OG1 THR A 373 " pdb=" OG1 THR B 361 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR I 361 " pdb=" OG1 THR J 373 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR F 373 " pdb=" OG1 THR G 361 " model vdw 2.285 2.440 nonbonded pdb=" OG1 THR A 361 " pdb=" OG1 THR D 373 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR G 373 " pdb=" OG1 THR H 361 " model vdw 2.286 2.440 ... (remaining 70568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 5060 2.51 5 N 1520 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.250 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: 0.000 Extract box with map and model: 13.390 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 26.640 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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 : 0.005 0.040 8230 Z= 0.344 Angle : 0.803 4.959 10990 Z= 0.486 Chirality : 0.061 0.214 1230 Planarity : 0.003 0.021 1410 Dihedral : 15.343 65.635 3190 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.43 % 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: -3.05 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.13), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 260 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 260 average time/residue: 1.0631 time to fit residues: 293.6885 Evaluate side-chains 209 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.6658 time to fit residues: 6.6262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 0.1980 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 0.4980 chunk 58 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN D 288 GLN E 296 ASN F 296 ASN G 296 ASN H 288 GLN I 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 8230 Z= 0.311 Angle : 0.633 5.718 10990 Z= 0.333 Chirality : 0.051 0.134 1230 Planarity : 0.003 0.022 1410 Dihedral : 5.943 14.296 1100 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 1.61 % 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: -2.91 (0.17), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.13), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 1.014 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 210 average time/residue: 1.1900 time to fit residues: 264.4781 Evaluate side-chains 199 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 189 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 1.6005 time to fit residues: 18.0636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.1980 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN E 296 ASN F 296 ASN I 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 8230 Z= 0.321 Angle : 0.635 5.992 10990 Z= 0.331 Chirality : 0.050 0.132 1230 Planarity : 0.003 0.023 1410 Dihedral : 6.013 14.233 1100 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 2.15 % 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: -2.84 (0.17), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.13), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 1.090 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 210 average time/residue: 1.1670 time to fit residues: 261.5774 Evaluate side-chains 200 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 192 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 1.8225 time to fit residues: 16.6917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN C 288 GLN E 296 ASN F 296 ASN G 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.044 8230 Z= 0.452 Angle : 0.701 6.046 10990 Z= 0.365 Chirality : 0.052 0.131 1230 Planarity : 0.003 0.025 1410 Dihedral : 6.225 15.131 1100 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 3.33 % 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: -2.74 (0.17), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.13), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 1.188 Fit side-chains outliers start: 31 outliers final: 14 residues processed: 215 average time/residue: 1.1472 time to fit residues: 261.8724 Evaluate side-chains 210 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 5 residues processed: 9 average time/residue: 1.4846 time to fit residues: 15.4006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN B 351 GLN E 296 ASN F 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 8230 Z= 0.352 Angle : 0.643 6.825 10990 Z= 0.334 Chirality : 0.050 0.129 1230 Planarity : 0.003 0.024 1410 Dihedral : 6.107 15.893 1100 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.71 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.13), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 1.054 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 205 average time/residue: 1.1405 time to fit residues: 248.0151 Evaluate side-chains 210 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 5 residues processed: 9 average time/residue: 1.5245 time to fit residues: 15.6103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN D 288 GLN E 296 ASN F 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 8230 Z= 0.427 Angle : 0.684 7.238 10990 Z= 0.356 Chirality : 0.051 0.130 1230 Planarity : 0.003 0.027 1410 Dihedral : 6.253 16.086 1100 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 2.58 % 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: -2.67 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.13), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.025 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 208 average time/residue: 1.1307 time to fit residues: 249.4547 Evaluate side-chains 206 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 194 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 5 residues processed: 7 average time/residue: 1.6238 time to fit residues: 13.3001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 96 optimal weight: 0.0030 chunk 60 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 overall best weight: 5.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN D 288 GLN E 296 ASN F 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 8230 Z= 0.412 Angle : 0.682 8.071 10990 Z= 0.353 Chirality : 0.051 0.141 1230 Planarity : 0.003 0.033 1410 Dihedral : 6.244 17.539 1100 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.62 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.14), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 1.069 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 208 average time/residue: 1.1443 time to fit residues: 252.2876 Evaluate side-chains 210 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 5 residues processed: 9 average time/residue: 1.6725 time to fit residues: 17.0656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN C 288 GLN D 288 GLN E 296 ASN F 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 8230 Z= 0.401 Angle : 0.682 8.045 10990 Z= 0.354 Chirality : 0.051 0.129 1230 Planarity : 0.003 0.036 1410 Dihedral : 6.258 19.272 1100 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 1.29 % 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: -2.61 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.14), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 1.108 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 206 average time/residue: 1.1366 time to fit residues: 248.3920 Evaluate side-chains 203 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.6532 time to fit residues: 4.8949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN D 288 GLN E 296 ASN F 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8230 Z= 0.280 Angle : 0.621 6.939 10990 Z= 0.320 Chirality : 0.050 0.130 1230 Planarity : 0.003 0.034 1410 Dihedral : 6.068 19.500 1100 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 1.18 % 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: -2.61 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.14), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 201 time to evaluate : 1.095 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 207 average time/residue: 1.1691 time to fit residues: 256.6039 Evaluate side-chains 203 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 1.1894 time to fit residues: 5.2368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.0970 chunk 91 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 48 optimal weight: 0.0770 chunk 63 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 overall best weight: 4.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN E 296 ASN F 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 8230 Z= 0.319 Angle : 0.660 7.286 10990 Z= 0.340 Chirality : 0.050 0.131 1230 Planarity : 0.003 0.036 1410 Dihedral : 6.149 19.456 1100 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.86 % 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: -2.60 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.14), residues: 1060 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 1.168 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 199 average time/residue: 1.1428 time to fit residues: 241.4370 Evaluate side-chains 199 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 192 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 1.7046 time to fit residues: 6.6884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 288 GLN E 296 ASN F 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.132217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.113117 restraints weight = 8825.271| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.45 r_work: 0.3685 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 1.25 restraints_weight: 0.2500 r_work: 0.3658 rms_B_bonded: 1.32 restraints_weight: 0.1250 r_work: 0.3643 rms_B_bonded: 1.44 restraints_weight: 0.0625 r_work: 0.3626 rms_B_bonded: 1.61 restraints_weight: 0.0312 r_work: 0.3606 rms_B_bonded: 1.83 restraints_weight: 0.0156 r_work: 0.3584 rms_B_bonded: 2.11 restraints_weight: 0.0078 r_work: 0.3559 rms_B_bonded: 2.46 restraints_weight: 0.0039 r_work: 0.3529 rms_B_bonded: 2.90 restraints_weight: 0.0020 r_work: 0.3495 rms_B_bonded: 3.43 restraints_weight: 0.0010 r_work: 0.3455 rms_B_bonded: 4.08 restraints_weight: 0.0005 r_work: 0.3408 rms_B_bonded: 4.89 restraints_weight: 0.0002 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 8230 Z= 0.362 Angle : 0.680 8.270 10990 Z= 0.352 Chirality : 0.051 0.132 1230 Planarity : 0.003 0.036 1410 Dihedral : 6.207 19.165 1100 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.86 % 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: -2.59 (0.18), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.14), residues: 1060 =============================================================================== Job complete usr+sys time: 4003.02 seconds wall clock time: 71 minutes 54.45 seconds (4314.45 seconds total)