Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:20:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6a_13223/11_2022/7p6a_13223.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6a_13223/11_2022/7p6a_13223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6a_13223/11_2022/7p6a_13223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6a_13223/11_2022/7p6a_13223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6a_13223/11_2022/7p6a_13223.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6a_13223/11_2022/7p6a_13223.pdb" } resolution = 1.9 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 TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4166 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Conformer: "B" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} bond proxies already assigned to first conformer: 816 Chain: "B" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Conformer: "B" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} bond proxies already assigned to first conformer: 816 Chain: "C" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Conformer: "B" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} bond proxies already assigned to first conformer: 816 Chain: "D" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Conformer: "B" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} bond proxies already assigned to first conformer: 816 Chain: "E" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Conformer: "B" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} bond proxies already assigned to first conformer: 816 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 4.50, per 1000 atoms: 1.08 Number of scatterers: 4166 At special positions: 0 Unit cell: (105.415, 82.878, 39.985, 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 10 16.00 O 836 8.00 N 765 7.00 C 2555 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: 1.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 51.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 292 removed outlier: 6.322A pdb=" N VAL B 275 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE C 278 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 277 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LYS C 280 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN B 279 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU C 282 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LYS B 281 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N LEU C 284 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP B 283 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N ASN C 286 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER B 285 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLN C 288 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 287 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LYS C 290 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER B 289 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLY C 292 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N CYS B 291 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 275 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE B 278 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 277 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LYS B 280 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN A 279 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 282 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LYS A 281 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LEU B 284 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ASP A 283 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 10.009A pdb=" N ASN B 286 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N SER A 285 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N GLN B 288 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 287 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LYS B 290 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N SER A 289 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLY B 292 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS A 291 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 282 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP D 283 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 284 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER D 285 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASN A 286 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU D 282 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP E 283 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU D 284 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER E 285 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN D 286 " --> pdb=" O SER E 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 297 through 298 removed outlier: 6.329A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 297 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 305 through 310 removed outlier: 6.623A pdb=" N SER A 305 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE D 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN A 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR D 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER D 305 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ILE E 308 " --> pdb=" O SER D 305 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN D 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR E 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.758A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.263A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LYS B 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER A 320 " --> pdb=" O LYS B 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.414A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 337 through 340 removed outlier: 6.339A pdb=" N VAL B 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LYS C 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.441A pdb=" N LEU A 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU D 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 349 through 354 removed outlier: 6.525A pdb=" N VAL A 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LYS D 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER A 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LYS E 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER D 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 362 removed outlier: 8.704A pdb=" N LEU B 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 9.580A pdb=" N ILE C 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN B 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N HIS C 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR B 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N LEU A 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ILE B 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP A 358 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN D 359 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP D 358 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN E 359 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.288A pdb=" N LYS B 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N GLU C 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE B 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N HIS C 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR B 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU C 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS B 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE C 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LYS A 370 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS D 370 " --> pdb=" O LYS E 369 " (cutoff:3.500A) 96 hydrogen bonds defined for protein. 288 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: 1.13 Time building geometry restraints manager: 1.66 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: 1354 1.34 - 1.46: 678 1.46 - 1.58: 2108 1.58 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 4150 Sorted by residual: bond pdb=" N SER A 285 " pdb=" CA SER A 285 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.23e-02 6.61e+03 6.64e+00 bond pdb=" N LEU D 284 " pdb=" CA LEU D 284 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.40e+00 bond pdb=" N LEU E 284 " pdb=" CA LEU E 284 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.39e+00 bond pdb=" N LEU C 284 " pdb=" CA LEU C 284 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.21e-02 6.83e+03 6.25e+00 bond pdb=" N LEU B 284 " pdb=" CA LEU B 284 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.21e-02 6.83e+03 6.18e+00 ... (remaining 4145 not shown) Histogram of bond angle deviations from ideal: 102.52 - 108.27: 259 108.27 - 114.03: 2389 114.03 - 119.78: 960 119.78 - 125.53: 1882 125.53 - 131.29: 55 Bond angle restraints: 5545 Sorted by residual: angle pdb=" N SER B 285 " pdb=" CA SER B 285 " pdb=" C SER B 285 " ideal model delta sigma weight residual 108.79 113.80 -5.01 1.53e+00 4.27e-01 1.07e+01 angle pdb=" N SER D 285 " pdb=" CA SER D 285 " pdb=" C SER D 285 " ideal model delta sigma weight residual 108.79 113.79 -5.00 1.53e+00 4.27e-01 1.07e+01 angle pdb=" N SER E 285 " pdb=" CA SER E 285 " pdb=" C SER E 285 " ideal model delta sigma weight residual 108.79 113.78 -4.99 1.53e+00 4.27e-01 1.06e+01 angle pdb=" N SER C 285 " pdb=" CA SER C 285 " pdb=" C SER C 285 " ideal model delta sigma weight residual 108.79 113.75 -4.96 1.53e+00 4.27e-01 1.05e+01 angle pdb=" N SER A 285 " pdb=" CA SER A 285 " pdb=" C SER A 285 " ideal model delta sigma weight residual 108.79 113.74 -4.95 1.53e+00 4.27e-01 1.05e+01 ... (remaining 5540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 2360 15.94 - 31.88: 155 31.88 - 47.82: 40 47.82 - 63.76: 5 63.76 - 79.70: 5 Dihedral angle restraints: 2565 sinusoidal: 1075 harmonic: 1490 Sorted by residual: dihedral pdb=" CB GLU D 372 " pdb=" CG GLU D 372 " pdb=" CD GLU D 372 " pdb=" OE1 GLU D 372 " ideal model delta sinusoidal sigma weight residual 0.00 -79.70 79.70 1 3.00e+01 1.11e-03 8.76e+00 dihedral pdb=" CB GLU B 372 " pdb=" CG GLU B 372 " pdb=" CD GLU B 372 " pdb=" OE1 GLU B 372 " ideal model delta sinusoidal sigma weight residual 0.00 -79.68 79.68 1 3.00e+01 1.11e-03 8.76e+00 dihedral pdb=" CB GLU A 372 " pdb=" CG GLU A 372 " pdb=" CD GLU A 372 " pdb=" OE1 GLU A 372 " ideal model delta sinusoidal sigma weight residual 0.00 -79.67 79.67 1 3.00e+01 1.11e-03 8.75e+00 ... (remaining 2562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 409 0.047 - 0.095: 108 0.095 - 0.142: 91 0.142 - 0.190: 7 0.190 - 0.237: 5 Chirality restraints: 620 Sorted by residual: chirality pdb=" CG LEU D 282 " pdb=" CB LEU D 282 " pdb=" CD1 LEU D 282 " pdb=" CD2 LEU D 282 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CG LEU B 282 " pdb=" CB LEU B 282 " pdb=" CD1 LEU B 282 " pdb=" CD2 LEU B 282 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU C 282 " pdb=" CB LEU C 282 " pdb=" CD1 LEU C 282 " pdb=" CD2 LEU C 282 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 617 not shown) Planarity restraints: 710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 349 " 0.121 9.50e-02 1.11e+02 5.44e-02 2.27e+00 pdb=" NE ARG C 349 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 349 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 349 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 349 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 349 " 0.122 9.50e-02 1.11e+02 5.48e-02 2.25e+00 pdb=" NE ARG B 349 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 349 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 349 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 349 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 349 " 0.121 9.50e-02 1.11e+02 5.44e-02 2.25e+00 pdb=" NE ARG E 349 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG E 349 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG E 349 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG E 349 " 0.001 2.00e-02 2.50e+03 ... (remaining 707 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 463 2.78 - 3.31: 3710 3.31 - 3.84: 7626 3.84 - 4.37: 8842 4.37 - 4.90: 16483 Nonbonded interactions: 37124 Sorted by model distance: nonbonded pdb=" O LEU B 357 " pdb=" O HOH B 501 " model vdw 2.247 2.440 nonbonded pdb=" OD1 ASP D 358 " pdb=" O HOH D 501 " model vdw 2.306 2.440 nonbonded pdb=" OD1 ASP B 358 " pdb=" O HOH B 502 " model vdw 2.358 2.440 nonbonded pdb=" O LEU C 357 " pdb=" O HOH B 502 " model vdw 2.360 2.440 nonbonded pdb=" O ASP D 295 " pdb=" OH TYR D 310 " model vdw 2.372 2.440 ... (remaining 37119 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' and (resid 272 through 342 or resid 344 through 379)) selection = (chain 'B' and (resid 272 through 342 or resid 344 through 379)) selection = (chain 'C' and (resid 272 through 342 or resid 344 through 379)) selection = (chain 'D' and (resid 272 through 342 or resid 344 through 379)) selection = (chain 'E' and (resid 272 through 342 or resid 344 through 379)) } 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 10 5.16 5 C 2555 2.51 5 N 765 2.21 5 O 836 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.010 Extract box with map and model: 8.010 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.040 Process input model: 18.580 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.004 0.032 4150 Z= 0.245 Angle : 0.718 6.294 5545 Z= 0.415 Chirality : 0.059 0.237 620 Planarity : 0.006 0.055 710 Dihedral : 12.298 79.700 1625 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 0.00 % 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: -3.07 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.19), residues: 535 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.505 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.8083 time to fit residues: 96.6950 Evaluate side-chains 94 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 0.0770 chunk 45 optimal weight: 9.9990 overall best weight: 2.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS B 330 HIS ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 4150 Z= 0.282 Angle : 0.613 7.185 5545 Z= 0.314 Chirality : 0.053 0.179 620 Planarity : 0.003 0.035 710 Dihedral : 5.779 14.530 560 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.85 % 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: -2.76 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.20), residues: 535 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.530 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 101 average time/residue: 0.8159 time to fit residues: 86.4846 Evaluate side-chains 97 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 1.8429 time to fit residues: 4.4105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 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 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 4150 Z= 0.386 Angle : 0.660 7.372 5545 Z= 0.343 Chirality : 0.054 0.173 620 Planarity : 0.004 0.028 710 Dihedral : 6.101 15.685 560 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.64 % 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: -2.60 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.20), residues: 535 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.401 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 99 average time/residue: 0.8056 time to fit residues: 83.6798 Evaluate side-chains 97 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4150 Z= 0.272 Angle : 0.600 7.093 5545 Z= 0.308 Chirality : 0.052 0.131 620 Planarity : 0.003 0.021 710 Dihedral : 5.945 15.561 560 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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: -2.63 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.20), residues: 535 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.551 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.7573 time to fit residues: 75.7669 Evaluate side-chains 94 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 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 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 4150 Z= 0.434 Angle : 0.689 7.466 5545 Z= 0.359 Chirality : 0.055 0.160 620 Planarity : 0.004 0.030 710 Dihedral : 6.265 16.319 560 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.64 % 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: -2.54 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.20), residues: 535 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.520 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 98 average time/residue: 0.7617 time to fit residues: 78.6124 Evaluate side-chains 97 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 276 GLN B 279 ASN D 276 GLN D 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 4150 Z= 0.319 Angle : 0.636 7.253 5545 Z= 0.327 Chirality : 0.054 0.183 620 Planarity : 0.003 0.023 710 Dihedral : 6.122 15.945 560 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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: -2.58 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.20), residues: 535 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.580 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.7949 time to fit residues: 79.7024 Evaluate side-chains 93 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.500 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 279 ASN B 276 GLN D 276 GLN E 276 GLN E 279 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4150 Z= 0.219 Angle : 0.592 7.238 5545 Z= 0.301 Chirality : 0.052 0.147 620 Planarity : 0.003 0.020 710 Dihedral : 5.898 15.511 560 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.64 % 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: -2.60 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.20), residues: 535 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.532 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.7724 time to fit residues: 78.1141 Evaluate side-chains 93 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 276 GLN B 279 ASN D 276 GLN D 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4150 Z= 0.216 Angle : 0.587 6.898 5545 Z= 0.299 Chirality : 0.052 0.163 620 Planarity : 0.003 0.023 710 Dihedral : 5.824 15.162 560 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.00 % 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: -2.62 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.20), residues: 535 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.542 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.8241 time to fit residues: 82.2259 Evaluate side-chains 90 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 276 GLN D 276 GLN D 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4150 Z= 0.282 Angle : 0.623 7.032 5545 Z= 0.320 Chirality : 0.054 0.224 620 Planarity : 0.003 0.022 710 Dihedral : 5.990 15.338 560 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.00 % 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: -2.59 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.20), residues: 535 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.561 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.7880 time to fit residues: 76.3588 Evaluate side-chains 92 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.510 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 276 GLN B 279 ASN D 276 GLN E 276 GLN E 279 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 4150 Z= 0.446 Angle : 0.703 7.571 5545 Z= 0.366 Chirality : 0.058 0.313 620 Planarity : 0.004 0.025 710 Dihedral : 6.311 16.423 560 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.00 % 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: -2.50 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.20), residues: 535 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.541 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.8121 time to fit residues: 81.9393 Evaluate side-chains 96 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 28 optimal weight: 0.0070 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.0070 chunk 1 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 276 GLN D 276 GLN D 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.129540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.111901 restraints weight = 16476.694| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.28 r_work: 0.3738 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.3680 rms_B_bonded: 2.21 restraints_weight: 0.1250 r_work: 0.3644 rms_B_bonded: 2.65 restraints_weight: 0.0625 r_work: 0.3603 rms_B_bonded: 3.31 restraints_weight: 0.0312 r_work: 0.3555 rms_B_bonded: 4.27 restraints_weight: 0.0156 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4150 Z= 0.220 Angle : 0.599 7.310 5545 Z= 0.304 Chirality : 0.053 0.200 620 Planarity : 0.003 0.022 710 Dihedral : 5.919 15.488 560 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.00 % 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: -2.61 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.20), residues: 535 =============================================================================== Job complete usr+sys time: 1939.87 seconds wall clock time: 35 minutes 43.49 seconds (2143.49 seconds total)