Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:11:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p66_13219/11_2022/7p66_13219.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p66_13219/11_2022/7p66_13219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p66_13219/11_2022/7p66_13219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p66_13219/11_2022/7p66_13219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p66_13219/11_2022/7p66_13219.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p66_13219/11_2022/7p66_13219.pdb" } resolution = 3.0 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: 4060 Number of models: 1 Model: "" Number of chains: 5 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} Time building chain proxies: 2.80, per 1000 atoms: 0.69 Number of scatterers: 4060 At special positions: 0 Unit cell: (109.25, 92, 46, 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 760 8.00 N 760 7.00 C 2530 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: 1.48 Conformation dependent library (CDL) restraints added in 776.4 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 930 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 284 removed outlier: 6.877A pdb=" N GLN C 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 277 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE C 278 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN B 279 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS C 280 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS B 281 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 276 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASN B 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE A 278 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LYS B 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LYS A 280 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASP B 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N LEU A 282 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLN A 276 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ASN D 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N ILE A 278 " --> pdb=" O ASN D 279 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N LYS D 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS A 280 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ASP D 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 282 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N GLN D 276 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N ASN E 279 " --> pdb=" O GLN D 276 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N ILE D 278 " --> pdb=" O ASN E 279 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N LYS E 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS D 280 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ASP E 283 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU D 282 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 287 through 290 removed outlier: 6.333A pdb=" N VAL A 287 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N LYS D 290 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER A 289 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL D 287 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LYS E 290 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER D 289 " --> pdb=" O LYS E 290 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 297 through 298 removed outlier: 6.690A pdb=" N ILE A 297 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 297 " --> pdb=" O LYS E 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.531A pdb=" N GLN A 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR D 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN D 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR E 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.804A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.334A pdb=" N VAL A 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS D 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER A 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL D 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LYS E 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER D 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.420A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 337 through 345 removed outlier: 6.542A pdb=" N GLU B 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N SER C 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS B 340 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LYS C 343 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU B 342 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ASP C 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 344 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 348 through 350 removed outlier: 6.995A pdb=" N ASP B 348 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASP A 348 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 355 through 362 removed outlier: 6.929A pdb=" N SER B 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU C 357 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP B 358 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN C 359 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER A 356 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 357 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP A 358 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASN B 359 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY A 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ASP D 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N LEU A 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N ILE D 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N HIS D 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR A 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N GLY D 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N ASP E 358 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N LEU D 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N ILE E 360 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N HIS E 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR D 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.932A pdb=" N LYS B 370 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS A 370 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS D 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU E 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE D 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 377 removed outlier: 6.958A pdb=" N THR A 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 80 hydrogen bonds defined for protein. 240 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: 1.04 Time building geometry restraints manager: 1.62 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: 1355 1.34 - 1.46: 632 1.46 - 1.58: 2118 1.58 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 4115 Sorted by residual: bond pdb=" N SER B 352 " pdb=" CA SER B 352 " ideal model delta sigma weight residual 1.455 1.491 -0.037 1.27e-02 6.20e+03 8.31e+00 bond pdb=" N SER A 352 " pdb=" CA SER A 352 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.15e+00 bond pdb=" N SER D 352 " pdb=" CA SER D 352 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.13e+00 bond pdb=" N SER E 352 " pdb=" CA SER E 352 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.13e+00 bond pdb=" N SER C 352 " pdb=" CA SER C 352 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.07e+00 ... (remaining 4110 not shown) Histogram of bond angle deviations from ideal: 102.33 - 108.12: 229 108.12 - 113.92: 2360 113.92 - 119.71: 1015 119.71 - 125.51: 1841 125.51 - 131.30: 50 Bond angle restraints: 5495 Sorted by residual: angle pdb=" N GLN A 351 " pdb=" CA GLN A 351 " pdb=" C GLN A 351 " ideal model delta sigma weight residual 112.30 107.69 4.61 1.36e+00 5.41e-01 1.15e+01 angle pdb=" N GLN C 351 " pdb=" CA GLN C 351 " pdb=" C GLN C 351 " ideal model delta sigma weight residual 112.30 107.70 4.60 1.36e+00 5.41e-01 1.14e+01 angle pdb=" N GLN E 351 " pdb=" CA GLN E 351 " pdb=" C GLN E 351 " ideal model delta sigma weight residual 112.30 107.70 4.60 1.36e+00 5.41e-01 1.14e+01 angle pdb=" N GLN B 351 " pdb=" CA GLN B 351 " pdb=" C GLN B 351 " ideal model delta sigma weight residual 112.30 107.72 4.58 1.36e+00 5.41e-01 1.13e+01 angle pdb=" N GLN D 351 " pdb=" CA GLN D 351 " pdb=" C GLN D 351 " ideal model delta sigma weight residual 112.30 107.72 4.58 1.36e+00 5.41e-01 1.13e+01 ... (remaining 5490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.40: 2160 11.40 - 22.79: 235 22.79 - 34.18: 95 34.18 - 45.58: 20 45.58 - 56.97: 15 Dihedral angle restraints: 2525 sinusoidal: 1055 harmonic: 1470 Sorted by residual: dihedral pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " pdb=" OD1 ASP D 358 " ideal model delta sinusoidal sigma weight residual -30.00 -82.26 52.26 1 2.00e+01 2.50e-03 9.31e+00 dihedral pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " pdb=" OD1 ASP E 358 " ideal model delta sinusoidal sigma weight residual -30.00 -82.23 52.23 1 2.00e+01 2.50e-03 9.30e+00 dihedral pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " pdb=" OD1 ASP A 358 " ideal model delta sinusoidal sigma weight residual -30.00 -82.22 52.22 1 2.00e+01 2.50e-03 9.30e+00 ... (remaining 2522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 417 0.041 - 0.082: 83 0.082 - 0.122: 91 0.122 - 0.163: 9 0.163 - 0.204: 15 Chirality restraints: 615 Sorted by residual: chirality pdb=" CB ILE C 360 " pdb=" CA ILE C 360 " pdb=" CG1 ILE C 360 " pdb=" CG2 ILE C 360 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE E 360 " pdb=" CA ILE E 360 " pdb=" CG1 ILE E 360 " pdb=" CG2 ILE E 360 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE D 360 " pdb=" CA ILE D 360 " pdb=" CG1 ILE D 360 " pdb=" CG2 ILE D 360 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 612 not shown) Planarity restraints: 705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 349 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C ARG C 349 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG C 349 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL C 350 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 349 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C ARG A 349 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG A 349 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 350 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 349 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C ARG D 349 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG D 349 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL D 350 " 0.012 2.00e-02 2.50e+03 ... (remaining 702 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1398 2.89 - 3.39: 3508 3.39 - 3.90: 6963 3.90 - 4.40: 7450 4.40 - 4.90: 15049 Nonbonded interactions: 34368 Sorted by model distance: nonbonded pdb=" OG SER C 289 " pdb=" OG SER C 320 " model vdw 2.388 2.440 nonbonded pdb=" OG SER A 289 " pdb=" OG SER A 320 " model vdw 2.389 2.440 nonbonded pdb=" OG SER D 289 " pdb=" OG SER D 320 " model vdw 2.389 2.440 nonbonded pdb=" OG SER B 289 " pdb=" OG SER B 320 " model vdw 2.389 2.440 nonbonded pdb=" OG SER E 289 " pdb=" OG SER E 320 " model vdw 2.389 2.440 ... (remaining 34363 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' } 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 2530 2.51 5 N 760 2.21 5 O 760 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: 1.400 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: 7.850 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 16.180 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 0.037 4115 Z= 0.238 Angle : 0.661 4.610 5495 Z= 0.423 Chirality : 0.059 0.204 615 Planarity : 0.004 0.020 705 Dihedral : 12.126 56.974 1595 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.21 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: -2.50 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.22), residues: 530 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.451 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.7208 time to fit residues: 82.7667 Evaluate side-chains 84 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7093 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 45 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 296 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN B 296 ASN B 351 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS C 296 ASN C 351 GLN C 374 HIS D 296 ASN D 351 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN E 296 ASN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN E 368 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.060 4115 Z= 0.635 Angle : 0.743 7.584 5495 Z= 0.385 Chirality : 0.055 0.152 615 Planarity : 0.005 0.039 705 Dihedral : 5.572 18.933 550 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 5.16 % 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 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.22), residues: 530 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.511 Fit side-chains outliers start: 24 outliers final: 9 residues processed: 98 average time/residue: 0.8530 time to fit residues: 87.4504 Evaluate side-chains 88 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.0682 time to fit residues: 1.2933 ------------------------------------------------------------------------------- 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: 1.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN A 296 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN B 288 GLN B 296 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN C 296 ASN D 296 ASN D 374 HIS E 288 GLN E 296 ASN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4115 Z= 0.211 Angle : 0.560 6.819 5495 Z= 0.282 Chirality : 0.050 0.144 615 Planarity : 0.004 0.031 705 Dihedral : 4.892 16.073 550 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 2.80 % 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 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.21), residues: 530 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.537 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 0.7968 time to fit residues: 68.0973 Evaluate side-chains 83 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.0812 time to fit residues: 1.4072 ------------------------------------------------------------------------------- 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: 3.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN A 296 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN B 296 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 288 GLN C 296 ASN D 296 ASN E 276 GLN E 288 GLN E 296 ASN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4115 Z= 0.276 Angle : 0.551 7.095 5495 Z= 0.281 Chirality : 0.050 0.142 615 Planarity : 0.004 0.033 705 Dihedral : 4.875 15.859 550 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 4.09 % 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: -2.77 (0.27), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.21), residues: 530 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.528 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 85 average time/residue: 0.7968 time to fit residues: 71.2796 Evaluate side-chains 85 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.5136 time to fit residues: 3.5067 ------------------------------------------------------------------------------- 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: 10.0000 chunk 19 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 24 optimal weight: 0.0770 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 288 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4115 Z= 0.252 Angle : 0.561 7.173 5495 Z= 0.281 Chirality : 0.050 0.142 615 Planarity : 0.003 0.032 705 Dihedral : 4.815 15.506 550 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 2.80 % 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: -2.81 (0.27), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.21), residues: 530 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.537 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 0.7159 time to fit residues: 62.1329 Evaluate side-chains 85 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.0726 time to fit residues: 1.1865 ------------------------------------------------------------------------------- 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: 8.9990 chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 0.0870 chunk 35 optimal weight: 0.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN B 296 ASN C 279 ASN C 288 GLN C 296 ASN D 296 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN E 288 GLN E 296 ASN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 4115 Z= 0.148 Angle : 0.500 6.860 5495 Z= 0.251 Chirality : 0.049 0.137 615 Planarity : 0.003 0.029 705 Dihedral : 4.549 15.253 550 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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: -2.79 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 530 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.514 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 89 average time/residue: 0.7403 time to fit residues: 69.4538 Evaluate side-chains 85 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.503 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0840 time to fit residues: 0.9326 ------------------------------------------------------------------------------- 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: 7.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN A 296 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN B 296 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN C 288 GLN C 296 ASN D 296 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN E 296 ASN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 4115 Z= 0.324 Angle : 0.573 6.538 5495 Z= 0.289 Chirality : 0.050 0.169 615 Planarity : 0.003 0.033 705 Dihedral : 4.873 16.632 550 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 3.01 % 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: -2.89 (0.27), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.21), residues: 530 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.433 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 84 average time/residue: 0.7016 time to fit residues: 62.4096 Evaluate side-chains 87 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.0671 time to fit residues: 1.1981 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN C 288 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4115 Z= 0.170 Angle : 0.531 6.915 5495 Z= 0.267 Chirality : 0.049 0.137 615 Planarity : 0.003 0.031 705 Dihedral : 4.672 15.139 550 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 1.94 % 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: -2.85 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.21), residues: 530 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.490 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 84 average time/residue: 0.6592 time to fit residues: 58.8240 Evaluate side-chains 86 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.516 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0899 time to fit residues: 0.9540 ------------------------------------------------------------------------------- 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: 0.5980 chunk 42 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 4115 Z= 0.309 Angle : 0.586 6.933 5495 Z= 0.296 Chirality : 0.051 0.187 615 Planarity : 0.003 0.032 705 Dihedral : 4.883 15.735 550 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 1.94 % 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: -2.92 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.21), residues: 530 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.525 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 85 average time/residue: 0.6237 time to fit residues: 56.2501 Evaluate side-chains 85 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.497 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.0813 time to fit residues: 1.0228 ------------------------------------------------------------------------------- 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: 2.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN C 288 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 4115 Z= 0.245 Angle : 0.559 6.801 5495 Z= 0.282 Chirality : 0.050 0.176 615 Planarity : 0.003 0.033 705 Dihedral : 4.826 15.679 550 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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: -2.90 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.21), residues: 530 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.543 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 82 average time/residue: 0.6317 time to fit residues: 55.1839 Evaluate side-chains 83 residues out of total 465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.0885 time to fit residues: 1.0393 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN C 288 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.104187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.093579 restraints weight = 5981.092| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.02 r_work: 0.3488 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 1.80 restraints_weight: 0.2500 r_work: 0.3467 rms_B_bonded: 1.82 restraints_weight: 0.1250 r_work: 0.3457 rms_B_bonded: 1.88 restraints_weight: 0.0625 r_work: 0.3445 rms_B_bonded: 1.98 restraints_weight: 0.0312 r_work: 0.3433 rms_B_bonded: 2.10 restraints_weight: 0.0156 r_work: 0.3421 rms_B_bonded: 2.25 restraints_weight: 0.0078 r_work: 0.3407 rms_B_bonded: 2.42 restraints_weight: 0.0039 r_work: 0.3393 rms_B_bonded: 2.63 restraints_weight: 0.0020 r_work: 0.3377 rms_B_bonded: 2.86 restraints_weight: 0.0010 r_work: 0.3361 rms_B_bonded: 3.13 restraints_weight: 0.0005 r_work: 0.3343 rms_B_bonded: 3.43 restraints_weight: 0.0002 r_work: 0.3324 rms_B_bonded: 3.77 restraints_weight: 0.0001 r_work: 0.3303 rms_B_bonded: 4.16 restraints_weight: 0.0001 r_work: 0.3281 rms_B_bonded: 4.59 restraints_weight: 0.0000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 4115 Z= 0.305 Angle : 0.587 6.920 5495 Z= 0.296 Chirality : 0.051 0.196 615 Planarity : 0.003 0.034 705 Dihedral : 4.916 15.890 550 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 1.94 % 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: -2.92 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.21), residues: 530 =============================================================================== Job complete usr+sys time: 1804.97 seconds wall clock time: 33 minutes 33.11 seconds (2013.11 seconds total)