Starting phenix.real_space_refine on Wed Oct 9 16:43:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/10_2024/9eog_19854.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/10_2024/9eog_19854.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/9eog_19854/10_2024/9eog_19854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/10_2024/9eog_19854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/10_2024/9eog_19854.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/10_2024/9eog_19854.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2202 2.51 5 N 648 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 3522 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.54, per 1000 atoms: 0.72 Number of scatterers: 3522 At special positions: 0 Unit cell: (74.984, 153.264, 37.904, 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 6 16.00 O 666 8.00 N 648 7.00 C 2202 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 466.1 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 59.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.494A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.775A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 319 removed outlier: 6.347A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 322 through 330 removed outlier: 8.880A pdb=" N CYS A 322 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU B 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N SER A 324 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N ASN B 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLY A 326 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N HIS B 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER E 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER F 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU E 325 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY F 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN E 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 346 removed outlier: 6.859A pdb=" N VAL B 337 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU A 338 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS A 340 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER B 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU A 342 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU E 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N VAL E 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N LYS F 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N VAL E 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLU F 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER E 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU F 344 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS E 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE F 346 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP E 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 362 removed outlier: 8.868A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N SER B 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 355 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP B 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ILE B 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER A 352 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS E 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 354 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY E 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER E 352 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS F 353 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E 354 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY F 355 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 379 removed outlier: 6.603A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE E 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS E 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU F 372 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE E 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS F 374 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR E 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU F 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS E 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE F 378 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR E 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.493A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR D 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.775A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 317 through 319 Processing sheet with id=AB2, first strand: chain 'C' and resid 322 through 330 removed outlier: 6.808A pdb=" N SER D 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 325 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY D 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN C 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 346 removed outlier: 9.035A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU D 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS C 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N PHE D 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 351 through 362 removed outlier: 6.867A pdb=" N SER C 352 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS D 353 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY D 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 369 through 379 removed outlier: 6.603A pdb=" N LYS C 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLU D 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU D 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS C 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE D 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR C 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 58 hydrogen bonds defined for protein. 174 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: 0.81 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 843 1.33 - 1.45: 816 1.45 - 1.57: 1911 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3576 Sorted by residual: bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.307 0.047 1.10e-02 8.26e+03 1.80e+01 bond pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.78e+01 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.77e+01 bond pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.77e+01 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.76e+01 ... (remaining 3571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 3834 1.74 - 3.48: 678 3.48 - 5.21: 228 5.21 - 6.95: 36 6.95 - 8.69: 6 Bond angle restraints: 4782 Sorted by residual: angle pdb=" C ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta sigma weight residual 111.63 120.32 -8.69 1.36e+00 5.41e-01 4.08e+01 angle pdb=" C ARG C 349 " pdb=" CA ARG C 349 " pdb=" CB ARG C 349 " ideal model delta sigma weight residual 111.63 120.31 -8.68 1.36e+00 5.41e-01 4.07e+01 angle pdb=" C ARG A 349 " pdb=" CA ARG A 349 " pdb=" CB ARG A 349 " ideal model delta sigma weight residual 111.63 120.30 -8.67 1.36e+00 5.41e-01 4.07e+01 angle pdb=" C ARG E 349 " pdb=" CA ARG E 349 " pdb=" CB ARG E 349 " ideal model delta sigma weight residual 111.63 120.29 -8.66 1.36e+00 5.41e-01 4.05e+01 angle pdb=" C ARG F 349 " pdb=" CA ARG F 349 " pdb=" CB ARG F 349 " ideal model delta sigma weight residual 111.63 120.28 -8.65 1.36e+00 5.41e-01 4.05e+01 ... (remaining 4777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.95: 1664 9.95 - 19.91: 358 19.91 - 29.86: 102 29.86 - 39.81: 30 39.81 - 49.76: 24 Dihedral angle restraints: 2178 sinusoidal: 912 harmonic: 1266 Sorted by residual: dihedral pdb=" CA VAL C 318 " pdb=" C VAL C 318 " pdb=" N THR C 319 " pdb=" CA THR C 319 " ideal model delta harmonic sigma weight residual -180.00 -149.79 -30.21 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA VAL E 318 " pdb=" C VAL E 318 " pdb=" N THR E 319 " pdb=" CA THR E 319 " ideal model delta harmonic sigma weight residual 180.00 -149.80 -30.20 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA VAL D 318 " pdb=" C VAL D 318 " pdb=" N THR D 319 " pdb=" CA THR D 319 " ideal model delta harmonic sigma weight residual 180.00 -149.81 -30.19 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 2175 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.080: 251 0.080 - 0.158: 241 0.158 - 0.236: 36 0.236 - 0.314: 0 0.314 - 0.391: 6 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ARG E 349 " pdb=" N ARG E 349 " pdb=" C ARG E 349 " pdb=" CB ARG E 349 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA ARG A 349 " pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CB ARG A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 531 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 366 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLY B 366 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY B 366 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY B 367 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 366 " -0.017 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLY E 366 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY E 366 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY E 367 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 366 " 0.017 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLY C 366 " -0.063 2.00e-02 2.50e+03 pdb=" O GLY C 366 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY C 367 " 0.021 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.94: 1428 2.94 - 3.43: 3246 3.43 - 3.92: 5599 3.92 - 4.41: 5642 4.41 - 4.90: 11553 Nonbonded interactions: 27468 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.445 3.040 ... (remaining 27463 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.810 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 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 : 0.009 0.047 3576 Z= 0.594 Angle : 1.628 8.689 4782 Z= 1.047 Chirality : 0.104 0.391 534 Planarity : 0.011 0.039 612 Dihedral : 12.855 49.764 1374 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.48 % Allowed : 4.48 % Favored : 91.04 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.37 % 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: -4.10 (0.27), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS E 330 PHE 0.049 0.009 PHE C 346 TYR 0.049 0.017 TYR C 310 ARG 0.004 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 0.452 Fit side-chains REVERT: A 311 LYS cc_start: 0.8486 (tmtt) cc_final: 0.8059 (ttpt) REVERT: A 317 LYS cc_start: 0.8468 (ptpp) cc_final: 0.8197 (pttt) REVERT: A 321 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8522 (tppp) REVERT: A 331 LYS cc_start: 0.8749 (mttp) cc_final: 0.8450 (mtpm) REVERT: A 342 GLU cc_start: 0.8452 (tt0) cc_final: 0.8212 (mm-30) REVERT: A 375 LYS cc_start: 0.8509 (tttt) cc_final: 0.7763 (mptm) REVERT: B 311 LYS cc_start: 0.8545 (tmtt) cc_final: 0.7985 (mmtt) REVERT: B 316 SER cc_start: 0.9441 (p) cc_final: 0.9163 (p) REVERT: B 317 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8218 (ptpt) REVERT: B 331 LYS cc_start: 0.8732 (mttp) cc_final: 0.7249 (tmtt) REVERT: B 349 ARG cc_start: 0.7988 (ptp-170) cc_final: 0.7733 (ptm160) REVERT: B 375 LYS cc_start: 0.8417 (tttt) cc_final: 0.7672 (mptm) REVERT: C 311 LYS cc_start: 0.8620 (tmtt) cc_final: 0.8030 (mmtt) REVERT: C 317 LYS cc_start: 0.8541 (ptpp) cc_final: 0.8203 (ptmt) REVERT: C 331 LYS cc_start: 0.8796 (mttp) cc_final: 0.8470 (mtpm) REVERT: C 375 LYS cc_start: 0.8454 (tttt) cc_final: 0.7748 (mptm) REVERT: D 311 LYS cc_start: 0.8741 (tmtt) cc_final: 0.7754 (pptt) REVERT: D 317 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8384 (ptmt) REVERT: D 331 LYS cc_start: 0.8844 (mttp) cc_final: 0.8523 (mtpt) REVERT: D 375 LYS cc_start: 0.8954 (tttt) cc_final: 0.8356 (mttm) REVERT: E 311 LYS cc_start: 0.8526 (tmtt) cc_final: 0.8144 (ttmt) REVERT: E 317 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8149 (ptmt) REVERT: E 321 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8341 (mtpt) REVERT: E 331 LYS cc_start: 0.8964 (mttp) cc_final: 0.8575 (mtpt) REVERT: E 342 GLU cc_start: 0.8582 (tt0) cc_final: 0.8130 (mm-30) REVERT: E 375 LYS cc_start: 0.8655 (tttt) cc_final: 0.7951 (mttm) REVERT: F 311 LYS cc_start: 0.8705 (tmtt) cc_final: 0.7759 (pptt) REVERT: F 331 LYS cc_start: 0.8888 (mttp) cc_final: 0.8627 (mtpt) REVERT: F 375 LYS cc_start: 0.8865 (tttt) cc_final: 0.8486 (mtpm) outliers start: 18 outliers final: 1 residues processed: 140 average time/residue: 1.7841 time to fit residues: 254.6581 Evaluate side-chains 131 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 351 GLN A 374 HIS B 307 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN B 374 HIS C 307 GLN C 330 HIS C 351 GLN C 374 HIS D 307 GLN D 336 GLN D 351 GLN D 368 ASN D 374 HIS E 307 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS F 307 GLN F 368 ASN F 374 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3576 Z= 0.284 Angle : 0.664 5.523 4782 Z= 0.339 Chirality : 0.054 0.160 534 Planarity : 0.004 0.027 612 Dihedral : 6.216 30.899 484 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.74 % Allowed : 16.92 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 374 PHE 0.021 0.003 PHE A 346 TYR 0.012 0.003 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.478 Fit side-chains REVERT: A 348 ASP cc_start: 0.7835 (t0) cc_final: 0.7393 (m-30) REVERT: B 311 LYS cc_start: 0.8540 (tmtt) cc_final: 0.7995 (mmtt) REVERT: B 317 LYS cc_start: 0.8653 (ptpp) cc_final: 0.8333 (ptmt) REVERT: B 331 LYS cc_start: 0.8761 (mttp) cc_final: 0.8489 (mtpt) REVERT: B 348 ASP cc_start: 0.8329 (t0) cc_final: 0.8042 (m-30) REVERT: B 358 ASP cc_start: 0.8916 (p0) cc_final: 0.8453 (p0) REVERT: C 317 LYS cc_start: 0.8499 (ptpp) cc_final: 0.8196 (ptmt) REVERT: C 331 LYS cc_start: 0.8831 (mttp) cc_final: 0.8561 (mtpm) REVERT: C 348 ASP cc_start: 0.8153 (t0) cc_final: 0.7746 (m-30) REVERT: C 358 ASP cc_start: 0.8598 (p0) cc_final: 0.8214 (p0) REVERT: D 311 LYS cc_start: 0.8704 (tmtt) cc_final: 0.7776 (pptt) REVERT: D 317 LYS cc_start: 0.8775 (ptpp) cc_final: 0.8382 (ptmt) REVERT: D 331 LYS cc_start: 0.8785 (mttp) cc_final: 0.8297 (mtpt) REVERT: D 340 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8520 (mttm) REVERT: D 347 LYS cc_start: 0.8291 (ptmt) cc_final: 0.7882 (ptmt) REVERT: D 348 ASP cc_start: 0.8364 (t0) cc_final: 0.8035 (m-30) REVERT: D 358 ASP cc_start: 0.8833 (p0) cc_final: 0.8559 (p0) REVERT: D 375 LYS cc_start: 0.8681 (tttt) cc_final: 0.8048 (mttm) REVERT: E 311 LYS cc_start: 0.8437 (tmtt) cc_final: 0.8162 (ttmt) REVERT: E 317 LYS cc_start: 0.8428 (ptpp) cc_final: 0.8047 (ptmt) REVERT: E 331 LYS cc_start: 0.8837 (mttp) cc_final: 0.8458 (mtpt) REVERT: E 340 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8382 (mttm) REVERT: E 348 ASP cc_start: 0.7949 (t0) cc_final: 0.7596 (m-30) REVERT: E 358 ASP cc_start: 0.8446 (p0) cc_final: 0.8104 (p0) REVERT: E 375 LYS cc_start: 0.8537 (tttt) cc_final: 0.7782 (mttp) REVERT: F 311 LYS cc_start: 0.8618 (tmtt) cc_final: 0.7799 (pptt) REVERT: F 317 LYS cc_start: 0.8698 (ptpt) cc_final: 0.8470 (ptmt) REVERT: F 331 LYS cc_start: 0.8791 (mttp) cc_final: 0.8514 (mtpt) REVERT: F 348 ASP cc_start: 0.8373 (t0) cc_final: 0.8058 (m-30) outliers start: 11 outliers final: 1 residues processed: 120 average time/residue: 1.4031 time to fit residues: 173.0354 Evaluate side-chains 107 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 41 optimal weight: 0.0010 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 9.9990 overall best weight: 0.6766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3576 Z= 0.146 Angle : 0.560 6.004 4782 Z= 0.275 Chirality : 0.051 0.126 534 Planarity : 0.003 0.024 612 Dihedral : 4.896 36.026 476 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.00 % Allowed : 21.39 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 329 PHE 0.013 0.001 PHE A 346 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.496 Fit side-chains REVERT: A 348 ASP cc_start: 0.7788 (t0) cc_final: 0.7496 (m-30) REVERT: B 317 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8439 (ptmt) REVERT: B 348 ASP cc_start: 0.8196 (t0) cc_final: 0.7868 (m-30) REVERT: B 358 ASP cc_start: 0.8739 (p0) cc_final: 0.8457 (p0) REVERT: C 317 LYS cc_start: 0.8478 (ptpp) cc_final: 0.8149 (ptmt) REVERT: C 331 LYS cc_start: 0.8809 (mttp) cc_final: 0.8514 (mtpt) REVERT: C 348 ASP cc_start: 0.8086 (t0) cc_final: 0.7753 (m-30) REVERT: C 375 LYS cc_start: 0.8394 (tttt) cc_final: 0.7702 (mttm) REVERT: D 311 LYS cc_start: 0.8580 (tmtt) cc_final: 0.7681 (pptt) REVERT: D 317 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8286 (ptmm) REVERT: D 331 LYS cc_start: 0.8571 (mttp) cc_final: 0.8252 (mtpt) REVERT: D 340 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8281 (mttt) REVERT: D 347 LYS cc_start: 0.8169 (ptmt) cc_final: 0.7766 (ptmt) REVERT: D 348 ASP cc_start: 0.8188 (t0) cc_final: 0.7908 (m-30) REVERT: D 358 ASP cc_start: 0.8596 (p0) cc_final: 0.8329 (m-30) REVERT: D 375 LYS cc_start: 0.8724 (tttt) cc_final: 0.8051 (mttm) REVERT: E 311 LYS cc_start: 0.8256 (tmtt) cc_final: 0.8020 (ttmt) REVERT: E 317 LYS cc_start: 0.8404 (ptpp) cc_final: 0.8032 (ptmt) REVERT: E 321 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8345 (ttmt) REVERT: E 331 LYS cc_start: 0.8716 (mttp) cc_final: 0.8450 (mtpt) REVERT: E 348 ASP cc_start: 0.7876 (t0) cc_final: 0.7663 (m-30) REVERT: E 375 LYS cc_start: 0.8471 (tttt) cc_final: 0.7709 (mttp) REVERT: F 311 LYS cc_start: 0.8464 (tmtt) cc_final: 0.7669 (pptt) outliers start: 4 outliers final: 1 residues processed: 109 average time/residue: 1.3939 time to fit residues: 156.0569 Evaluate side-chains 95 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3576 Z= 0.422 Angle : 0.688 7.075 4782 Z= 0.341 Chirality : 0.055 0.151 534 Planarity : 0.004 0.029 612 Dihedral : 5.315 28.384 476 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.24 % Allowed : 22.39 % Favored : 75.37 % 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: -2.12 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.022 0.003 PHE E 346 TYR 0.018 0.005 TYR E 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.435 Fit side-chains REVERT: A 311 LYS cc_start: 0.8461 (tttt) cc_final: 0.8126 (ttpt) REVERT: A 331 LYS cc_start: 0.8789 (mttp) cc_final: 0.8509 (mtpm) REVERT: A 348 ASP cc_start: 0.7950 (t0) cc_final: 0.7524 (m-30) REVERT: A 375 LYS cc_start: 0.8447 (tttt) cc_final: 0.7755 (mttm) REVERT: B 311 LYS cc_start: 0.8493 (tttt) cc_final: 0.7976 (mmtt) REVERT: B 317 LYS cc_start: 0.8684 (ptpp) cc_final: 0.8364 (ptmt) REVERT: B 348 ASP cc_start: 0.8327 (t0) cc_final: 0.8001 (m-30) REVERT: B 358 ASP cc_start: 0.8945 (p0) cc_final: 0.8621 (p0) REVERT: C 311 LYS cc_start: 0.8565 (tttt) cc_final: 0.8051 (mmtt) REVERT: C 317 LYS cc_start: 0.8560 (ptpp) cc_final: 0.8259 (ptmt) REVERT: C 331 LYS cc_start: 0.8860 (mttp) cc_final: 0.8553 (mtpt) REVERT: C 348 ASP cc_start: 0.8231 (t0) cc_final: 0.7916 (m-30) REVERT: C 375 LYS cc_start: 0.8314 (tttt) cc_final: 0.7570 (mttm) REVERT: D 311 LYS cc_start: 0.8705 (tttt) cc_final: 0.7802 (pptt) REVERT: D 317 LYS cc_start: 0.8722 (ptpp) cc_final: 0.8269 (ptmt) REVERT: D 331 LYS cc_start: 0.8855 (mttp) cc_final: 0.8464 (mtpt) REVERT: D 340 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8731 (mttp) REVERT: D 375 LYS cc_start: 0.8809 (tttt) cc_final: 0.8108 (mttm) REVERT: E 311 LYS cc_start: 0.8456 (tttt) cc_final: 0.8189 (ttmt) REVERT: E 331 LYS cc_start: 0.8928 (mttp) cc_final: 0.8586 (mtpt) REVERT: E 348 ASP cc_start: 0.8102 (t0) cc_final: 0.7612 (m-30) REVERT: E 356 SER cc_start: 0.8908 (t) cc_final: 0.8611 (m) REVERT: F 311 LYS cc_start: 0.8629 (tttt) cc_final: 0.7718 (pptt) outliers start: 9 outliers final: 5 residues processed: 108 average time/residue: 1.5404 time to fit residues: 170.6310 Evaluate side-chains 105 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 0.0670 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3576 Z= 0.170 Angle : 0.590 8.131 4782 Z= 0.281 Chirality : 0.050 0.133 534 Planarity : 0.003 0.029 612 Dihedral : 4.770 35.923 476 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.24 % Allowed : 24.88 % Favored : 73.88 % 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: -1.85 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 329 PHE 0.011 0.001 PHE E 346 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.426 Fit side-chains REVERT: A 331 LYS cc_start: 0.8675 (mttp) cc_final: 0.8453 (mtpm) REVERT: A 348 ASP cc_start: 0.7902 (t0) cc_final: 0.7554 (m-30) REVERT: B 317 LYS cc_start: 0.8708 (ptpp) cc_final: 0.8441 (ptmt) REVERT: B 348 ASP cc_start: 0.8223 (t0) cc_final: 0.7873 (m-30) REVERT: B 358 ASP cc_start: 0.8786 (p0) cc_final: 0.8508 (p0) REVERT: C 317 LYS cc_start: 0.8564 (ptpp) cc_final: 0.8261 (ptmt) REVERT: C 331 LYS cc_start: 0.8812 (mttp) cc_final: 0.8535 (mtpt) REVERT: C 375 LYS cc_start: 0.8429 (tttt) cc_final: 0.7720 (mttm) REVERT: D 311 LYS cc_start: 0.8581 (tttt) cc_final: 0.7705 (pptt) REVERT: D 317 LYS cc_start: 0.8632 (ptpp) cc_final: 0.8248 (ptmt) REVERT: D 331 LYS cc_start: 0.8656 (mttp) cc_final: 0.8328 (mtpt) REVERT: D 340 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8474 (mttm) REVERT: D 375 LYS cc_start: 0.8746 (tttt) cc_final: 0.8085 (mttp) REVERT: E 311 LYS cc_start: 0.8302 (tttt) cc_final: 0.8092 (ttmt) REVERT: E 331 LYS cc_start: 0.8794 (mttp) cc_final: 0.8502 (mtpt) REVERT: E 348 ASP cc_start: 0.8064 (t0) cc_final: 0.7799 (m-30) REVERT: F 311 LYS cc_start: 0.8521 (tttt) cc_final: 0.7641 (pptt) REVERT: F 358 ASP cc_start: 0.8387 (p0) cc_final: 0.8036 (m-30) outliers start: 5 outliers final: 2 residues processed: 95 average time/residue: 1.3929 time to fit residues: 135.8823 Evaluate side-chains 87 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3576 Z= 0.364 Angle : 0.673 8.516 4782 Z= 0.324 Chirality : 0.053 0.153 534 Planarity : 0.004 0.037 612 Dihedral : 5.019 31.046 476 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.49 % Allowed : 26.62 % Favored : 71.89 % 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: -1.92 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.021 0.002 PHE E 346 TYR 0.016 0.004 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.433 Fit side-chains REVERT: A 331 LYS cc_start: 0.8753 (mttp) cc_final: 0.8304 (mtpt) REVERT: A 348 ASP cc_start: 0.7915 (t0) cc_final: 0.7469 (m-30) REVERT: B 311 LYS cc_start: 0.8516 (tttt) cc_final: 0.7986 (mmtt) REVERT: B 317 LYS cc_start: 0.8702 (ptpp) cc_final: 0.8420 (ptmt) REVERT: B 348 ASP cc_start: 0.8274 (t0) cc_final: 0.7938 (m-30) REVERT: B 358 ASP cc_start: 0.8948 (p0) cc_final: 0.8634 (p0) REVERT: C 317 LYS cc_start: 0.8572 (ptpp) cc_final: 0.8268 (ptmt) REVERT: C 331 LYS cc_start: 0.8892 (mttp) cc_final: 0.8547 (mtpt) REVERT: D 311 LYS cc_start: 0.8684 (tttt) cc_final: 0.7792 (pptt) REVERT: D 317 LYS cc_start: 0.8686 (ptpp) cc_final: 0.8247 (ptmt) REVERT: D 331 LYS cc_start: 0.8809 (mttp) cc_final: 0.8449 (mtpt) REVERT: D 375 LYS cc_start: 0.8758 (tttt) cc_final: 0.8091 (mttp) REVERT: E 311 LYS cc_start: 0.8422 (tttt) cc_final: 0.8181 (ttmt) REVERT: E 331 LYS cc_start: 0.8898 (mttp) cc_final: 0.8558 (mtpt) REVERT: E 348 ASP cc_start: 0.8122 (t0) cc_final: 0.7630 (m-30) REVERT: F 311 LYS cc_start: 0.8677 (tttt) cc_final: 0.7839 (pptt) REVERT: F 358 ASP cc_start: 0.8464 (p0) cc_final: 0.8099 (m-30) outliers start: 6 outliers final: 2 residues processed: 94 average time/residue: 1.4485 time to fit residues: 139.9092 Evaluate side-chains 86 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3576 Z= 0.311 Angle : 0.665 8.928 4782 Z= 0.315 Chirality : 0.052 0.143 534 Planarity : 0.003 0.036 612 Dihedral : 4.969 31.819 476 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.49 % Allowed : 25.37 % Favored : 73.13 % 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: -1.89 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.018 0.002 PHE E 346 TYR 0.014 0.003 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.454 Fit side-chains REVERT: A 331 LYS cc_start: 0.8778 (mttp) cc_final: 0.8360 (mtpt) REVERT: A 348 ASP cc_start: 0.7936 (t0) cc_final: 0.7447 (m-30) REVERT: B 311 LYS cc_start: 0.8510 (tttt) cc_final: 0.7966 (mmtm) REVERT: B 317 LYS cc_start: 0.8680 (ptpp) cc_final: 0.8397 (ptmt) REVERT: B 348 ASP cc_start: 0.8261 (t0) cc_final: 0.7915 (m-30) REVERT: B 358 ASP cc_start: 0.8928 (p0) cc_final: 0.8596 (p0) REVERT: C 317 LYS cc_start: 0.8607 (ptpp) cc_final: 0.8297 (ptmt) REVERT: C 331 LYS cc_start: 0.8887 (mttp) cc_final: 0.8575 (mtpt) REVERT: D 311 LYS cc_start: 0.8679 (tttt) cc_final: 0.7783 (pptt) REVERT: D 317 LYS cc_start: 0.8683 (ptpp) cc_final: 0.8245 (ptmt) REVERT: D 331 LYS cc_start: 0.8783 (mttp) cc_final: 0.8415 (mtpt) REVERT: D 375 LYS cc_start: 0.8708 (tttt) cc_final: 0.8075 (mttp) REVERT: E 311 LYS cc_start: 0.8424 (tttt) cc_final: 0.8182 (ttmt) REVERT: E 317 LYS cc_start: 0.8465 (ptpp) cc_final: 0.8127 (ptmt) REVERT: E 331 LYS cc_start: 0.8885 (mttp) cc_final: 0.8529 (mtpt) REVERT: E 348 ASP cc_start: 0.8116 (t0) cc_final: 0.7641 (m-30) REVERT: F 311 LYS cc_start: 0.8647 (tttt) cc_final: 0.7796 (pptt) REVERT: F 358 ASP cc_start: 0.8463 (p0) cc_final: 0.8095 (m-30) outliers start: 6 outliers final: 4 residues processed: 93 average time/residue: 1.4212 time to fit residues: 135.6692 Evaluate side-chains 88 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.0060 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3576 Z= 0.189 Angle : 0.626 9.194 4782 Z= 0.290 Chirality : 0.050 0.133 534 Planarity : 0.003 0.038 612 Dihedral : 4.766 35.608 476 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.00 % Allowed : 25.62 % Favored : 73.38 % 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: -1.77 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 329 PHE 0.010 0.001 PHE E 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8698 (mttp) cc_final: 0.8464 (mtpm) REVERT: A 348 ASP cc_start: 0.7931 (t0) cc_final: 0.7549 (m-30) REVERT: B 317 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8426 (ptmt) REVERT: B 343 LYS cc_start: 0.8409 (ttmm) cc_final: 0.7517 (tptp) REVERT: B 348 ASP cc_start: 0.8170 (t0) cc_final: 0.7803 (m-30) REVERT: B 358 ASP cc_start: 0.8829 (p0) cc_final: 0.8521 (p0) REVERT: C 317 LYS cc_start: 0.8587 (ptpp) cc_final: 0.8278 (ptmt) REVERT: C 331 LYS cc_start: 0.8851 (mttp) cc_final: 0.8541 (mtmt) REVERT: D 311 LYS cc_start: 0.8611 (tttt) cc_final: 0.7740 (pptt) REVERT: D 317 LYS cc_start: 0.8634 (ptpp) cc_final: 0.8191 (ptmt) REVERT: D 331 LYS cc_start: 0.8688 (mttp) cc_final: 0.8340 (mtpt) REVERT: D 358 ASP cc_start: 0.8629 (p0) cc_final: 0.8175 (m-30) REVERT: D 375 LYS cc_start: 0.8688 (tttt) cc_final: 0.8083 (mttp) REVERT: E 311 LYS cc_start: 0.8334 (tttt) cc_final: 0.8113 (ttmt) REVERT: E 317 LYS cc_start: 0.8442 (ptpp) cc_final: 0.8107 (ptmt) REVERT: E 331 LYS cc_start: 0.8838 (mttp) cc_final: 0.8508 (mtpt) REVERT: E 348 ASP cc_start: 0.8100 (t0) cc_final: 0.7795 (m-30) REVERT: F 311 LYS cc_start: 0.8596 (tttt) cc_final: 0.7766 (pptt) REVERT: F 358 ASP cc_start: 0.8371 (p0) cc_final: 0.8129 (m-30) outliers start: 4 outliers final: 3 residues processed: 90 average time/residue: 1.3673 time to fit residues: 126.2967 Evaluate side-chains 89 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.0470 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.0970 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 0.3980 overall best weight: 1.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3576 Z= 0.227 Angle : 0.652 9.668 4782 Z= 0.301 Chirality : 0.051 0.144 534 Planarity : 0.003 0.042 612 Dihedral : 4.765 34.484 476 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.00 % Allowed : 25.87 % Favored : 73.13 % 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: -1.73 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.014 0.002 PHE E 346 TYR 0.011 0.002 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.472 Fit side-chains REVERT: A 331 LYS cc_start: 0.8715 (mttp) cc_final: 0.8494 (mtpm) REVERT: A 348 ASP cc_start: 0.7942 (t0) cc_final: 0.7573 (m-30) REVERT: B 311 LYS cc_start: 0.8532 (tttt) cc_final: 0.8005 (mmtt) REVERT: B 317 LYS cc_start: 0.8673 (ptpp) cc_final: 0.8408 (ptmt) REVERT: B 343 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7526 (tptp) REVERT: B 348 ASP cc_start: 0.8187 (t0) cc_final: 0.7836 (m-30) REVERT: B 358 ASP cc_start: 0.8878 (p0) cc_final: 0.8575 (p0) REVERT: C 317 LYS cc_start: 0.8597 (ptpp) cc_final: 0.8290 (ptmt) REVERT: C 331 LYS cc_start: 0.8854 (mttp) cc_final: 0.8551 (mtpt) REVERT: D 311 LYS cc_start: 0.8618 (tttt) cc_final: 0.7753 (pptt) REVERT: D 317 LYS cc_start: 0.8652 (ptpp) cc_final: 0.8219 (ptmt) REVERT: D 331 LYS cc_start: 0.8740 (mttp) cc_final: 0.8387 (mtpt) REVERT: D 358 ASP cc_start: 0.8642 (p0) cc_final: 0.8277 (m-30) REVERT: D 375 LYS cc_start: 0.8670 (tttt) cc_final: 0.8069 (mttp) REVERT: E 311 LYS cc_start: 0.8355 (tttt) cc_final: 0.8138 (ttmt) REVERT: E 317 LYS cc_start: 0.8455 (ptpp) cc_final: 0.8126 (ptmt) REVERT: E 331 LYS cc_start: 0.8893 (mttp) cc_final: 0.8560 (mtpt) REVERT: E 348 ASP cc_start: 0.8110 (t0) cc_final: 0.7819 (m-30) REVERT: F 311 LYS cc_start: 0.8621 (tttt) cc_final: 0.7797 (pptt) outliers start: 4 outliers final: 3 residues processed: 91 average time/residue: 1.4129 time to fit residues: 131.8150 Evaluate side-chains 89 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3576 Z= 0.309 Angle : 0.683 10.126 4782 Z= 0.319 Chirality : 0.052 0.155 534 Planarity : 0.004 0.042 612 Dihedral : 4.918 32.250 476 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.00 % Allowed : 26.87 % Favored : 72.14 % 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: -1.81 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.018 0.002 PHE E 346 TYR 0.014 0.004 TYR A 310 ARG 0.001 0.000 ARG D 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.408 Fit side-chains REVERT: A 331 LYS cc_start: 0.8767 (mttp) cc_final: 0.8355 (mtpt) REVERT: A 348 ASP cc_start: 0.7964 (t0) cc_final: 0.7432 (m-30) REVERT: B 311 LYS cc_start: 0.8516 (tttt) cc_final: 0.7983 (mmtt) REVERT: B 317 LYS cc_start: 0.8672 (ptpp) cc_final: 0.8392 (ptmt) REVERT: B 348 ASP cc_start: 0.8240 (t0) cc_final: 0.7893 (m-30) REVERT: B 358 ASP cc_start: 0.8931 (p0) cc_final: 0.8636 (p0) REVERT: C 317 LYS cc_start: 0.8594 (ptpp) cc_final: 0.8278 (ptmt) REVERT: C 331 LYS cc_start: 0.8876 (mttp) cc_final: 0.8557 (mtmt) REVERT: D 311 LYS cc_start: 0.8646 (tttt) cc_final: 0.7778 (pptt) REVERT: D 317 LYS cc_start: 0.8680 (ptpp) cc_final: 0.8303 (ptmt) REVERT: D 331 LYS cc_start: 0.8806 (mttp) cc_final: 0.8443 (mtpt) REVERT: D 358 ASP cc_start: 0.8602 (p0) cc_final: 0.8303 (m-30) REVERT: D 375 LYS cc_start: 0.8686 (tttt) cc_final: 0.8060 (mttp) REVERT: D 379 ARG cc_start: 0.8785 (mpt-90) cc_final: 0.6598 (pmt170) REVERT: E 311 LYS cc_start: 0.8421 (tttt) cc_final: 0.8187 (ttmt) REVERT: E 317 LYS cc_start: 0.8441 (ptpp) cc_final: 0.8120 (ptmt) REVERT: E 331 LYS cc_start: 0.8912 (mttp) cc_final: 0.8561 (mtpt) REVERT: E 348 ASP cc_start: 0.8135 (t0) cc_final: 0.7661 (m-30) REVERT: F 311 LYS cc_start: 0.8643 (tttt) cc_final: 0.7759 (pptt) outliers start: 4 outliers final: 3 residues processed: 90 average time/residue: 1.5991 time to fit residues: 147.2359 Evaluate side-chains 89 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 41 optimal weight: 0.0980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.140963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.121462 restraints weight = 4169.888| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.43 r_work: 0.3813 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3576 Z= 0.402 Angle : 0.733 10.319 4782 Z= 0.346 Chirality : 0.054 0.161 534 Planarity : 0.004 0.041 612 Dihedral : 5.152 30.873 476 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.24 % Allowed : 27.11 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.023 0.003 PHE E 346 TYR 0.018 0.005 TYR A 310 ARG 0.001 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2651.82 seconds wall clock time: 51 minutes 5.24 seconds (3065.24 seconds total)