Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:18:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p65_13218/11_2022/7p65_13218.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p65_13218/11_2022/7p65_13218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p65_13218/11_2022/7p65_13218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p65_13218/11_2022/7p65_13218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p65_13218/11_2022/7p65_13218.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p65_13218/11_2022/7p65_13218.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 348": "OD1" <-> "OD2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "D ASP 348": "OD1" <-> "OD2" Residue "E ASP 348": "OD1" <-> "OD2" 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: 4145 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "B" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "D" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Time building chain proxies: 2.76, per 1000 atoms: 0.67 Number of scatterers: 4145 At special positions: 0 Unit cell: (67.85, 111.55, 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 785 8.00 N 775 7.00 C 2575 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: 1.52 Conformation dependent library (CDL) restraints added in 995.8 milliseconds 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 950 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 42.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 280 removed outlier: 6.541A pdb=" N GLN B 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASN C 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN A 276 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ASN B 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE A 278 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 275 " --> pdb=" O GLN D 276 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE D 278 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 277 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N LYS D 280 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASN A 279 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 284 through 289 removed outlier: 6.543A pdb=" N SER B 285 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLN C 288 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 287 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER A 285 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN B 288 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 287 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 294 through 299 removed outlier: 8.975A pdb=" N LYS B 294 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N ILE C 297 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN B 296 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HIS C 299 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS B 298 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N LYS A 294 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ILE B 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN A 296 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N HIS B 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS A 298 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP A 295 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN D 296 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP D 295 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN E 296 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.562A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR C 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL B 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.842A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.847A 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 320 removed outlier: 6.557A pdb=" N LYS B 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N SER C 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR B 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 336 through 337 removed outlier: 6.208A pdb=" N GLN A 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLN D 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 340 through 345 removed outlier: 6.419A pdb=" N LYS B 340 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LYS C 343 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU B 342 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASP C 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 344 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS A 340 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LYS B 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLU A 342 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ASP B 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 344 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 348 through 354 removed outlier: 6.345A pdb=" N ARG A 349 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N SER D 352 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN A 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ILE D 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS A 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG D 349 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N SER E 352 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN D 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE E 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LYS D 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.572A pdb=" N ASP A 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N THR D 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE A 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP D 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N THR E 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE D 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 368 through 373 removed outlier: 6.220A pdb=" N ASN A 368 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE D 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS A 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N THR D 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU A 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASN D 368 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE E 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS D 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR E 373 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU D 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.642A pdb=" N LEU B 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARG C 379 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE B 378 " --> pdb=" O ARG C 379 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 376 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARG B 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE A 378 " --> pdb=" O ARG B 379 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 255 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: 1.11 Time building geometry restraints manager: 1.68 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: 1395 1.34 - 1.46: 624 1.46 - 1.57: 2171 1.57 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 4200 Sorted by residual: bond pdb=" N LYS A 317 " pdb=" CA LYS A 317 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.19e+00 bond pdb=" N ARG E 349 " pdb=" CA ARG E 349 " ideal model delta sigma weight residual 1.462 1.492 -0.029 1.20e-02 6.94e+03 6.04e+00 bond pdb=" N LYS B 317 " pdb=" CA LYS B 317 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.22e-02 6.72e+03 5.93e+00 bond pdb=" N LYS C 317 " pdb=" CA LYS C 317 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.22e-02 6.72e+03 5.91e+00 bond pdb=" N LYS E 317 " pdb=" CA LYS E 317 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.22e-02 6.72e+03 5.81e+00 ... (remaining 4195 not shown) Histogram of bond angle deviations from ideal: 101.90 - 107.76: 185 107.76 - 113.63: 2382 113.63 - 119.50: 1039 119.50 - 125.37: 1959 125.37 - 131.24: 45 Bond angle restraints: 5610 Sorted by residual: angle pdb=" CA LEU B 315 " pdb=" CB LEU B 315 " pdb=" CG LEU B 315 " ideal model delta sigma weight residual 116.30 124.97 -8.67 3.50e+00 8.16e-02 6.13e+00 angle pdb=" CA LEU A 315 " pdb=" CB LEU A 315 " pdb=" CG LEU A 315 " ideal model delta sigma weight residual 116.30 124.96 -8.66 3.50e+00 8.16e-02 6.12e+00 angle pdb=" CA LEU E 315 " pdb=" CB LEU E 315 " pdb=" CG LEU E 315 " ideal model delta sigma weight residual 116.30 124.95 -8.65 3.50e+00 8.16e-02 6.11e+00 angle pdb=" CA LEU C 315 " pdb=" CB LEU C 315 " pdb=" CG LEU C 315 " ideal model delta sigma weight residual 116.30 124.95 -8.65 3.50e+00 8.16e-02 6.11e+00 angle pdb=" CA LEU D 315 " pdb=" CB LEU D 315 " pdb=" CG LEU D 315 " ideal model delta sigma weight residual 116.30 124.95 -8.65 3.50e+00 8.16e-02 6.11e+00 ... (remaining 5605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.96: 2229 11.96 - 23.92: 216 23.92 - 35.88: 100 35.88 - 47.84: 21 47.84 - 59.80: 14 Dihedral angle restraints: 2580 sinusoidal: 1080 harmonic: 1500 Sorted by residual: dihedral pdb=" CG LYS D 331 " pdb=" CD LYS D 331 " pdb=" CE LYS D 331 " pdb=" NZ LYS D 331 " ideal model delta sinusoidal sigma weight residual 60.00 119.80 -59.80 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS A 331 " pdb=" CD LYS A 331 " pdb=" CE LYS A 331 " pdb=" NZ LYS A 331 " ideal model delta sinusoidal sigma weight residual 60.00 119.77 -59.77 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS C 331 " pdb=" CD LYS C 331 " pdb=" CE LYS C 331 " pdb=" NZ LYS C 331 " ideal model delta sinusoidal sigma weight residual 60.00 119.76 -59.76 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 310 0.025 - 0.050: 167 0.050 - 0.075: 38 0.075 - 0.101: 64 0.101 - 0.126: 46 Chirality restraints: 625 Sorted by residual: chirality pdb=" CA LYS C 340 " pdb=" N LYS C 340 " pdb=" C LYS C 340 " pdb=" CB LYS C 340 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA LYS D 340 " pdb=" N LYS D 340 " pdb=" C LYS D 340 " pdb=" CB LYS D 340 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE E 277 " pdb=" N ILE E 277 " pdb=" C ILE E 277 " pdb=" CB ILE E 277 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 622 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 300 " 0.016 5.00e-02 4.00e+02 2.46e-02 9.69e-01 pdb=" N PRO C 301 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 301 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 301 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 300 " 0.016 5.00e-02 4.00e+02 2.45e-02 9.61e-01 pdb=" N PRO E 301 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO E 301 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 301 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 300 " 0.016 5.00e-02 4.00e+02 2.43e-02 9.48e-01 pdb=" N PRO A 301 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " 0.013 5.00e-02 4.00e+02 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1459 2.88 - 3.39: 3289 3.39 - 3.89: 7295 3.89 - 4.40: 7622 4.40 - 4.90: 15606 Nonbonded interactions: 35271 Sorted by model distance: nonbonded pdb=" O PHE A 346 " pdb=" NZ LYS B 311 " model vdw 2.381 2.520 nonbonded pdb=" O PHE B 346 " pdb=" NZ LYS C 311 " model vdw 2.398 2.520 nonbonded pdb=" NZ LYS A 311 " pdb=" O PHE D 346 " model vdw 2.398 2.520 nonbonded pdb=" NZ LYS D 311 " pdb=" O PHE E 346 " model vdw 2.404 2.520 nonbonded pdb=" ND1 HIS E 299 " pdb=" OH TYR E 310 " model vdw 2.475 2.520 ... (remaining 35266 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 2575 2.51 5 N 775 2.21 5 O 785 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: 0.000 Extract box with map and model: 7.950 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 16.310 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 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 0.055 4200 Z= 0.263 Angle : 0.627 8.666 5610 Z= 0.319 Chirality : 0.050 0.126 625 Planarity : 0.003 0.025 725 Dihedral : 12.602 59.802 1630 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: -2.90 (0.29), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.22), residues: 540 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.548 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.9336 time to fit residues: 124.3527 Evaluate side-chains 99 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 381 ASN B 276 GLN B 296 ASN B 359 ASN B 381 ASN C 276 GLN C 296 ASN C 359 ASN C 381 ASN D 296 ASN D 307 GLN D 359 ASN D 368 ASN D 381 ASN E 359 ASN E 381 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 4200 Z= 0.294 Angle : 0.588 9.123 5610 Z= 0.274 Chirality : 0.049 0.153 625 Planarity : 0.002 0.016 725 Dihedral : 4.148 11.765 560 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.30), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.23), residues: 540 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.553 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 106 average time/residue: 0.8092 time to fit residues: 90.0584 Evaluate side-chains 101 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5120 time to fit residues: 2.3646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 381 ASN B 296 ASN B 381 ASN C 359 ASN C 381 ASN D 381 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 4200 Z= 0.438 Angle : 0.639 9.199 5610 Z= 0.300 Chirality : 0.049 0.122 625 Planarity : 0.002 0.013 725 Dihedral : 4.324 12.959 560 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.05 % 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: -2.80 (0.29), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.22), residues: 540 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.569 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 104 average time/residue: 0.8294 time to fit residues: 90.4434 Evaluate side-chains 102 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.611 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0653 time to fit residues: 0.9617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 50 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 381 ASN B 276 GLN B 296 ASN B 359 ASN B 381 ASN C 296 ASN C 381 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 4200 Z= 0.263 Angle : 0.579 8.441 5610 Z= 0.270 Chirality : 0.049 0.165 625 Planarity : 0.002 0.009 725 Dihedral : 4.194 12.236 560 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.68 % 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: -2.78 (0.29), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.22), residues: 540 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.549 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 104 average time/residue: 0.8130 time to fit residues: 88.6913 Evaluate side-chains 104 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 5 average time/residue: 1.0548 time to fit residues: 6.1746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 381 ASN B 296 ASN B 359 ASN B 381 ASN C 381 ASN D 381 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.037 4200 Z= 0.444 Angle : 0.615 8.945 5610 Z= 0.295 Chirality : 0.049 0.121 625 Planarity : 0.002 0.013 725 Dihedral : 4.364 13.026 560 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.89 % 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: -2.82 (0.29), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.22), residues: 540 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.557 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 99 average time/residue: 0.8307 time to fit residues: 86.3726 Evaluate side-chains 100 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.0463 time to fit residues: 0.7771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN B 276 GLN B 296 ASN B 381 ASN C 381 ASN D 381 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4200 Z= 0.191 Angle : 0.553 8.147 5610 Z= 0.260 Chirality : 0.049 0.156 625 Planarity : 0.002 0.010 725 Dihedral : 4.120 11.973 560 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.47 % 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: -2.75 (0.29), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.22), residues: 540 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.483 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 0.7714 time to fit residues: 83.3518 Evaluate side-chains 98 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.6884 time to fit residues: 2.1569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 7.9990 chunk 30 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN B 296 ASN B 359 ASN B 381 ASN C 296 ASN C 381 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 4200 Z= 0.151 Angle : 0.568 11.455 5610 Z= 0.259 Chirality : 0.049 0.118 625 Planarity : 0.002 0.011 725 Dihedral : 3.922 11.042 560 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.26 % 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: -2.68 (0.30), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.23), residues: 540 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.567 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 99 average time/residue: 0.8057 time to fit residues: 83.8552 Evaluate side-chains 96 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.485 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 381 ASN B 276 GLN B 296 ASN B 359 ASN B 381 ASN C 359 ASN C 381 ASN D 381 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 4200 Z= 0.348 Angle : 0.623 9.102 5610 Z= 0.290 Chirality : 0.049 0.117 625 Planarity : 0.002 0.012 725 Dihedral : 4.132 12.847 560 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 2.11 % 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: -2.78 (0.29), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.22), residues: 540 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.563 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 102 average time/residue: 0.7802 time to fit residues: 83.7700 Evaluate side-chains 100 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.6378 time to fit residues: 4.0865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN B 296 ASN B 359 ASN B 381 ASN C 359 ASN C 381 ASN D 381 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4200 Z= 0.220 Angle : 0.595 8.823 5610 Z= 0.275 Chirality : 0.049 0.118 625 Planarity : 0.002 0.011 725 Dihedral : 4.043 12.345 560 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.30), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.23), residues: 540 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.581 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 0.8076 time to fit residues: 83.9981 Evaluate side-chains 95 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN B 276 GLN B 296 ASN B 359 ASN B 381 ASN C 359 ASN C 381 ASN D 381 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 4200 Z= 0.272 Angle : 0.615 8.511 5610 Z= 0.285 Chirality : 0.049 0.117 625 Planarity : 0.002 0.012 725 Dihedral : 4.084 12.679 560 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.84 % 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 (0.29), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.22), residues: 540 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.585 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 98 average time/residue: 0.7730 time to fit residues: 79.6913 Evaluate side-chains 96 residues out of total 475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.3784 time to fit residues: 2.1842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 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 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN B 296 ASN B 359 ASN B 381 ASN C 359 ASN C 381 ASN D 381 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.091225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.077929 restraints weight = 5533.298| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.11 r_work: 0.3236 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.3213 rms_B_bonded: 1.87 restraints_weight: 0.1250 r_work: 0.3201 rms_B_bonded: 1.93 restraints_weight: 0.0625 r_work: 0.3188 rms_B_bonded: 2.02 restraints_weight: 0.0312 r_work: 0.3175 rms_B_bonded: 2.14 restraints_weight: 0.0156 r_work: 0.3161 rms_B_bonded: 2.28 restraints_weight: 0.0078 r_work: 0.3146 rms_B_bonded: 2.45 restraints_weight: 0.0039 r_work: 0.3130 rms_B_bonded: 2.66 restraints_weight: 0.0020 r_work: 0.3113 rms_B_bonded: 2.89 restraints_weight: 0.0010 r_work: 0.3095 rms_B_bonded: 3.16 restraints_weight: 0.0005 r_work: 0.3075 rms_B_bonded: 3.46 restraints_weight: 0.0002 r_work: 0.3054 rms_B_bonded: 3.81 restraints_weight: 0.0001 r_work: 0.3032 rms_B_bonded: 4.20 restraints_weight: 0.0001 r_work: 0.3007 rms_B_bonded: 4.64 restraints_weight: 0.0000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.036 4200 Z= 0.453 Angle : 0.666 9.221 5610 Z= 0.316 Chirality : 0.049 0.119 625 Planarity : 0.002 0.016 725 Dihedral : 4.310 14.440 560 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.29), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.22), residues: 540 =============================================================================== Job complete usr+sys time: 1953.56 seconds wall clock time: 36 minutes 15.92 seconds (2175.92 seconds total)