Starting phenix.real_space_refine on Sun Dec 29 02:26:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkv_14054/12_2024/7qkv_14054.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkv_14054/12_2024/7qkv_14054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qkv_14054/12_2024/7qkv_14054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkv_14054/12_2024/7qkv_14054.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkv_14054/12_2024/7qkv_14054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkv_14054/12_2024/7qkv_14054.cif" } resolution = 3.23 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: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 2934 2.51 5 N 864 2.21 5 O 891 1.98 5 H 4887 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9585 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "A" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "C" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "D" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "E" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "F" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "G" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "H" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "I" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Time building chain proxies: 6.93, per 1000 atoms: 0.72 Number of scatterers: 9585 At special positions: 0 Unit cell: (128.544, 131.84, 33.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 891 8.00 N 864 7.00 C 2934 6.00 H 4887 1.00 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: 2.77 Conformation dependent library (CDL) restraints added in 790.8 milliseconds 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.960A pdb=" N VAL B 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 317 through 318 removed outlier: 6.348A pdb=" N LYS B 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 324 through 330 removed outlier: 9.642A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N ASN D 327 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 325 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY G 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN B 327 " --> pdb=" O GLY G 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.553A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLU D 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER B 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.391A pdb=" N ASP B 345 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.468A pdb=" N GLN B 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE G 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS B 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N SER G 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY B 355 " --> pdb=" O SER G 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.381A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 369 through 374 removed outlier: 6.448A pdb=" N LYS B 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLU G 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N HIS G 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR B 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.914A pdb=" N VAL A 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 317 through 318 removed outlier: 6.355A pdb=" N LYS A 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 324 through 330 removed outlier: 9.663A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N ASN E 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLY A 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS E 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 325 " --> pdb=" O SER H 324 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY H 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN A 327 " --> pdb=" O GLY H 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 337 through 342 removed outlier: 6.532A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.493A pdb=" N ASP A 345 " --> pdb=" O PHE H 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 350 through 357 removed outlier: 6.277A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLY E 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU E 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER A 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 360 through 362 removed outlier: 6.353A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 369 through 374 removed outlier: 6.321A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS A 369 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLU H 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 371 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N HIS H 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR A 373 " --> pdb=" O HIS H 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 313 through 314 removed outlier: 6.953A pdb=" N VAL C 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 317 through 318 removed outlier: 6.425A pdb=" N LYS C 317 " --> pdb=" O VAL I 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 324 through 330 removed outlier: 9.636A pdb=" N SER C 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N ASN F 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY C 326 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N HIS F 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C 325 " --> pdb=" O SER I 324 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY I 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 327 " --> pdb=" O GLY I 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 337 through 342 removed outlier: 6.574A pdb=" N VAL C 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N LYS F 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLU F 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER C 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 345 through 346 removed outlier: 6.557A pdb=" N ASP C 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 350 through 357 removed outlier: 6.275A pdb=" N VAL C 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYS F 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER C 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLY F 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE C 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU F 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER C 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 360 through 362 removed outlier: 6.395A pdb=" N THR C 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 369 through 374 removed outlier: 6.483A pdb=" N LYS C 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLU I 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N HIS I 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR C 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) 70 hydrogen bonds defined for protein. 210 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: 3.87 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 4878 1.11 - 1.28: 792 1.28 - 1.45: 1147 1.45 - 1.63: 2831 1.63 - 1.80: 9 Bond restraints: 9657 Sorted by residual: bond pdb=" N GLN A 336 " pdb=" H GLN A 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ASN D 359 " pdb=" H ASN D 359 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY H 367 " pdb=" H GLY H 367 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 GLN B 336 " pdb="HE21 GLN B 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS D 331 " pdb=" H LYS D 331 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 9652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 14545 2.47 - 4.94: 2366 4.94 - 7.40: 657 7.40 - 9.87: 54 9.87 - 12.34: 9 Bond angle restraints: 17631 Sorted by residual: angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.42 118.54 -8.12 1.49e+00 4.50e-01 2.97e+01 angle pdb=" C LYS A 375 " pdb=" N LEU A 376 " pdb=" CA LEU A 376 " ideal model delta sigma weight residual 122.36 130.55 -8.19 1.60e+00 3.91e-01 2.62e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 121.31 128.60 -7.29 1.49e+00 4.50e-01 2.39e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.55 118.57 -8.02 1.64e+00 3.72e-01 2.39e+01 angle pdb=" C ASP F 348 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " ideal model delta sigma weight residual 121.31 128.52 -7.21 1.49e+00 4.50e-01 2.34e+01 ... (remaining 17626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.16: 3682 13.16 - 26.31: 423 26.31 - 39.47: 145 39.47 - 52.62: 62 52.62 - 65.78: 134 Dihedral angle restraints: 4446 sinusoidal: 2556 harmonic: 1890 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 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA LYS H 375 " pdb=" C LYS H 375 " pdb=" N LEU H 376 " pdb=" CA LEU H 376 " ideal model delta harmonic sigma weight residual 180.00 152.92 27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA VAL G 350 " pdb=" C VAL G 350 " pdb=" N GLN G 351 " pdb=" CA GLN G 351 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 4443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 364 0.065 - 0.130: 244 0.130 - 0.194: 90 0.194 - 0.259: 16 0.259 - 0.323: 6 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA LYS F 311 " pdb=" N LYS F 311 " pdb=" C LYS F 311 " pdb=" CB LYS F 311 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA LYS E 311 " pdb=" N LYS E 311 " pdb=" C LYS E 311 " pdb=" CB LYS E 311 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA ASN F 327 " pdb=" N ASN F 327 " pdb=" C ASN F 327 " pdb=" CB ASN F 327 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 717 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.336 2.00e-02 2.50e+03 1.44e-01 6.26e+02 pdb=" CG TYR E 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.103 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.101 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.091 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.063 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.289 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " 0.058 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " 0.113 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " 0.056 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 310 " -0.224 2.00e-02 2.50e+03 1.01e-01 3.05e+02 pdb=" CG TYR H 310 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR H 310 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR H 310 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 TYR H 310 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 TYR H 310 " 0.053 2.00e-02 2.50e+03 pdb=" CZ TYR H 310 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR H 310 " -0.215 2.00e-02 2.50e+03 pdb=" HD1 TYR H 310 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR H 310 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 TYR H 310 " 0.045 2.00e-02 2.50e+03 pdb=" HE2 TYR H 310 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.226 2.00e-02 2.50e+03 9.95e-02 2.97e+02 pdb=" CG TYR F 310 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.073 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.055 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.204 2.00e-02 2.50e+03 pdb=" HD1 TYR F 310 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR F 310 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR F 310 " -0.027 2.00e-02 2.50e+03 pdb=" HE2 TYR F 310 " -0.007 2.00e-02 2.50e+03 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 702 2.17 - 2.77: 16377 2.77 - 3.38: 25469 3.38 - 3.99: 33649 3.99 - 4.60: 47837 Nonbonded interactions: 124034 Sorted by model distance: nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.556 2.450 nonbonded pdb=" OD1 ASP H 314 " pdb=" HG SER H 316 " model vdw 1.559 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.563 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.610 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.618 2.450 ... (remaining 124029 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 11.610 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 1.260 Process input model: 26.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 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 : 0.011 0.033 4770 Z= 0.745 Angle : 1.916 8.186 6381 Z= 1.248 Chirality : 0.094 0.323 720 Planarity : 0.015 0.166 810 Dihedral : 12.281 56.991 1836 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % 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: -2.11 (0.28), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.22), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.006 HIS G 330 PHE 0.032 0.013 PHE I 346 TYR 0.290 0.091 TYR E 310 ARG 0.004 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8125 (m-80) cc_final: 0.7866 (m-80) REVERT: B 347 LYS cc_start: 0.7885 (mttt) cc_final: 0.7276 (tmtt) REVERT: B 358 ASP cc_start: 0.8448 (m-30) cc_final: 0.8055 (t0) REVERT: A 327 ASN cc_start: 0.7512 (m-40) cc_final: 0.7309 (m-40) REVERT: A 343 LYS cc_start: 0.8500 (mttt) cc_final: 0.7686 (mttm) REVERT: A 347 LYS cc_start: 0.7999 (mttt) cc_final: 0.7434 (tptp) REVERT: A 358 ASP cc_start: 0.8546 (m-30) cc_final: 0.8066 (t0) REVERT: C 346 PHE cc_start: 0.8364 (m-80) cc_final: 0.8059 (m-80) REVERT: C 358 ASP cc_start: 0.8441 (m-30) cc_final: 0.8057 (t0) REVERT: D 311 LYS cc_start: 0.7191 (mtmt) cc_final: 0.6616 (mmtm) REVERT: D 347 LYS cc_start: 0.7807 (mttt) cc_final: 0.7558 (tmtt) REVERT: E 311 LYS cc_start: 0.7213 (mtmt) cc_final: 0.6420 (mmtm) REVERT: E 347 LYS cc_start: 0.7878 (mttt) cc_final: 0.7520 (tmtt) REVERT: F 343 LYS cc_start: 0.8191 (mttt) cc_final: 0.7456 (mmpt) REVERT: F 347 LYS cc_start: 0.7980 (mttt) cc_final: 0.7577 (tmtt) REVERT: F 351 GLN cc_start: 0.7827 (mp10) cc_final: 0.7423 (tt0) REVERT: G 345 ASP cc_start: 0.6807 (m-30) cc_final: 0.6475 (m-30) REVERT: G 347 LYS cc_start: 0.8104 (mttt) cc_final: 0.7523 (pttp) REVERT: G 358 ASP cc_start: 0.8475 (m-30) cc_final: 0.8105 (t0) REVERT: H 343 LYS cc_start: 0.8536 (mttt) cc_final: 0.8127 (mttm) REVERT: H 347 LYS cc_start: 0.7854 (mttt) cc_final: 0.7345 (pttp) REVERT: H 358 ASP cc_start: 0.8445 (m-30) cc_final: 0.8003 (t0) REVERT: I 343 LYS cc_start: 0.8423 (mttt) cc_final: 0.7840 (mttm) REVERT: I 347 LYS cc_start: 0.7730 (mttt) cc_final: 0.7290 (pttp) REVERT: I 358 ASP cc_start: 0.8454 (m-30) cc_final: 0.8043 (t0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.4313 time to fit residues: 93.3202 Evaluate side-chains 109 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS A 362 HIS C 362 HIS D 362 HIS E 362 HIS F 362 HIS G 362 HIS H 362 HIS I 362 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4770 Z= 0.398 Angle : 0.730 6.607 6381 Z= 0.388 Chirality : 0.051 0.143 720 Planarity : 0.003 0.024 810 Dihedral : 7.879 28.829 630 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.67 % Allowed : 17.04 % Favored : 81.30 % 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: -2.49 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 330 PHE 0.007 0.001 PHE E 346 TYR 0.033 0.007 TYR D 310 ARG 0.001 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8036 (m-80) cc_final: 0.7807 (m-80) REVERT: B 347 LYS cc_start: 0.8062 (mttt) cc_final: 0.7560 (tmtt) REVERT: B 358 ASP cc_start: 0.8454 (m-30) cc_final: 0.8161 (t0) REVERT: B 376 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6952 (mt) REVERT: A 347 LYS cc_start: 0.8071 (mttt) cc_final: 0.7463 (tmtt) REVERT: A 358 ASP cc_start: 0.8467 (m-30) cc_final: 0.8146 (t0) REVERT: A 376 LEU cc_start: 0.7646 (mt) cc_final: 0.7420 (mp) REVERT: C 347 LYS cc_start: 0.8158 (mttt) cc_final: 0.7538 (tmtt) REVERT: C 358 ASP cc_start: 0.8290 (m-30) cc_final: 0.7974 (t0) REVERT: C 376 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6764 (mt) REVERT: D 311 LYS cc_start: 0.7157 (mtmt) cc_final: 0.6711 (mmtm) REVERT: D 343 LYS cc_start: 0.8262 (mttt) cc_final: 0.7453 (mmpt) REVERT: E 311 LYS cc_start: 0.7280 (mtmt) cc_final: 0.6676 (mmtm) REVERT: E 343 LYS cc_start: 0.8390 (mttt) cc_final: 0.7652 (mmpt) REVERT: E 347 LYS cc_start: 0.7951 (mttt) cc_final: 0.7723 (tmtt) REVERT: F 311 LYS cc_start: 0.7115 (ttmt) cc_final: 0.6684 (mmtm) REVERT: F 347 LYS cc_start: 0.8062 (mttt) cc_final: 0.7675 (tmtt) REVERT: F 351 GLN cc_start: 0.8245 (mp10) cc_final: 0.7607 (tt0) REVERT: G 347 LYS cc_start: 0.8250 (mttt) cc_final: 0.7688 (pttp) REVERT: G 358 ASP cc_start: 0.8383 (m-30) cc_final: 0.7942 (t0) REVERT: G 376 LEU cc_start: 0.7248 (mt) cc_final: 0.6597 (mp) REVERT: H 347 LYS cc_start: 0.8107 (mttt) cc_final: 0.7586 (pttp) REVERT: H 358 ASP cc_start: 0.8486 (m-30) cc_final: 0.8016 (t0) REVERT: I 347 LYS cc_start: 0.7981 (mttt) cc_final: 0.7475 (pttp) REVERT: I 358 ASP cc_start: 0.8309 (m-30) cc_final: 0.7831 (t0) outliers start: 9 outliers final: 7 residues processed: 115 average time/residue: 0.4369 time to fit residues: 61.1790 Evaluate side-chains 104 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain I residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 368 ASN H 368 ASN I 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4770 Z= 0.202 Angle : 0.575 4.222 6381 Z= 0.304 Chirality : 0.050 0.140 720 Planarity : 0.003 0.025 810 Dihedral : 6.379 21.649 630 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.04 % Allowed : 17.59 % Favored : 80.37 % 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: -2.73 (0.25), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.19), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.012 0.001 PHE D 346 TYR 0.013 0.003 TYR D 310 ARG 0.001 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7414 (ttmt) cc_final: 0.7117 (ttpt) REVERT: B 347 LYS cc_start: 0.7861 (mttt) cc_final: 0.7426 (tmtt) REVERT: B 358 ASP cc_start: 0.8435 (m-30) cc_final: 0.8140 (t0) REVERT: B 376 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7034 (mp) REVERT: A 347 LYS cc_start: 0.8045 (mttt) cc_final: 0.7428 (tmtt) REVERT: A 358 ASP cc_start: 0.8473 (m-30) cc_final: 0.8039 (t0) REVERT: A 376 LEU cc_start: 0.7588 (mt) cc_final: 0.7249 (mp) REVERT: C 327 ASN cc_start: 0.7222 (m-40) cc_final: 0.6887 (t0) REVERT: C 347 LYS cc_start: 0.8147 (mttt) cc_final: 0.7523 (tmtt) REVERT: C 358 ASP cc_start: 0.8432 (m-30) cc_final: 0.7992 (t0) REVERT: C 376 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6843 (mp) REVERT: D 311 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6989 (pttt) REVERT: D 343 LYS cc_start: 0.8056 (mttt) cc_final: 0.7323 (mmpt) REVERT: E 342 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: E 343 LYS cc_start: 0.8225 (mttt) cc_final: 0.7568 (mmpt) REVERT: F 311 LYS cc_start: 0.7234 (ttmt) cc_final: 0.6779 (mmtm) REVERT: F 347 LYS cc_start: 0.8099 (mttt) cc_final: 0.7729 (tmtt) REVERT: F 351 GLN cc_start: 0.8180 (mp10) cc_final: 0.7610 (tt0) REVERT: G 316 SER cc_start: 0.7876 (m) cc_final: 0.7585 (p) REVERT: G 347 LYS cc_start: 0.8254 (mttt) cc_final: 0.7692 (pttp) REVERT: G 358 ASP cc_start: 0.8383 (m-30) cc_final: 0.7966 (t0) REVERT: H 311 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7250 (ttpt) REVERT: H 347 LYS cc_start: 0.8131 (mttt) cc_final: 0.7556 (pttp) REVERT: H 358 ASP cc_start: 0.8477 (m-30) cc_final: 0.7936 (t0) REVERT: H 376 LEU cc_start: 0.7365 (mt) cc_final: 0.6892 (mp) REVERT: I 347 LYS cc_start: 0.7947 (mttt) cc_final: 0.7480 (pttp) REVERT: I 358 ASP cc_start: 0.8454 (m-30) cc_final: 0.7870 (t0) REVERT: I 376 LEU cc_start: 0.7379 (mt) cc_final: 0.6992 (mp) outliers start: 11 outliers final: 6 residues processed: 110 average time/residue: 0.4543 time to fit residues: 61.4162 Evaluate side-chains 98 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4770 Z= 0.149 Angle : 0.510 3.970 6381 Z= 0.268 Chirality : 0.049 0.142 720 Planarity : 0.003 0.034 810 Dihedral : 5.598 16.769 630 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.56 % Allowed : 18.70 % Favored : 80.74 % 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: -2.65 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 329 PHE 0.008 0.001 PHE B 346 TYR 0.007 0.002 TYR D 310 ARG 0.001 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7493 (ttmt) cc_final: 0.7278 (ttpt) REVERT: B 347 LYS cc_start: 0.7809 (mttt) cc_final: 0.7400 (tptp) REVERT: B 358 ASP cc_start: 0.8411 (m-30) cc_final: 0.8078 (t0) REVERT: A 327 ASN cc_start: 0.7896 (t0) cc_final: 0.7602 (t0) REVERT: A 347 LYS cc_start: 0.7928 (mttt) cc_final: 0.7457 (tmtt) REVERT: A 358 ASP cc_start: 0.8442 (m-30) cc_final: 0.7956 (t0) REVERT: C 347 LYS cc_start: 0.8059 (mttt) cc_final: 0.7478 (tmtt) REVERT: C 358 ASP cc_start: 0.8433 (m-30) cc_final: 0.7929 (t0) REVERT: C 376 LEU cc_start: 0.7258 (mt) cc_final: 0.6780 (mp) REVERT: D 311 LYS cc_start: 0.7307 (mtmt) cc_final: 0.6981 (pttt) REVERT: D 342 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7284 (mm-30) REVERT: D 343 LYS cc_start: 0.8064 (mttt) cc_final: 0.7385 (mmmt) REVERT: E 342 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7474 (mm-30) REVERT: F 331 LYS cc_start: 0.6727 (mmtt) cc_final: 0.6423 (mmmt) REVERT: F 347 LYS cc_start: 0.8080 (mttt) cc_final: 0.7725 (tmtt) REVERT: F 351 GLN cc_start: 0.8067 (mp10) cc_final: 0.7568 (tt0) REVERT: G 316 SER cc_start: 0.8068 (m) cc_final: 0.7754 (p) REVERT: G 347 LYS cc_start: 0.8267 (mttt) cc_final: 0.7689 (pttm) REVERT: G 358 ASP cc_start: 0.8369 (m-30) cc_final: 0.7942 (t0) REVERT: G 376 LEU cc_start: 0.7451 (mt) cc_final: 0.6886 (mp) REVERT: H 311 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7269 (ttpt) REVERT: H 347 LYS cc_start: 0.8094 (mttt) cc_final: 0.7548 (pttp) REVERT: H 358 ASP cc_start: 0.8417 (m-30) cc_final: 0.7816 (t0) REVERT: I 347 LYS cc_start: 0.7931 (mttt) cc_final: 0.7492 (pttp) REVERT: I 358 ASP cc_start: 0.8464 (m-30) cc_final: 0.7844 (t0) REVERT: I 376 LEU cc_start: 0.7384 (mt) cc_final: 0.6941 (mp) outliers start: 3 outliers final: 3 residues processed: 108 average time/residue: 0.4458 time to fit residues: 58.7459 Evaluate side-chains 94 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4770 Z= 0.195 Angle : 0.528 5.459 6381 Z= 0.278 Chirality : 0.049 0.142 720 Planarity : 0.004 0.040 810 Dihedral : 5.478 17.013 630 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.67 % Allowed : 18.70 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.006 0.001 PHE B 346 TYR 0.012 0.003 TYR F 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7466 (ttmt) cc_final: 0.7184 (ttpt) REVERT: B 347 LYS cc_start: 0.7742 (mttt) cc_final: 0.7324 (tmtt) REVERT: B 358 ASP cc_start: 0.8471 (m-30) cc_final: 0.8084 (t0) REVERT: B 376 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7134 (mt) REVERT: A 347 LYS cc_start: 0.7952 (mttt) cc_final: 0.7414 (tmtt) REVERT: A 358 ASP cc_start: 0.8505 (m-30) cc_final: 0.7989 (t0) REVERT: C 347 LYS cc_start: 0.8110 (mttt) cc_final: 0.7479 (tmtt) REVERT: C 358 ASP cc_start: 0.8501 (m-30) cc_final: 0.7921 (t0) REVERT: C 376 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6596 (mt) REVERT: D 311 LYS cc_start: 0.7205 (mtmt) cc_final: 0.6901 (pttt) REVERT: D 342 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7271 (mm-30) REVERT: D 343 LYS cc_start: 0.8121 (mttt) cc_final: 0.7462 (mmmt) REVERT: E 342 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7407 (mm-30) REVERT: F 347 LYS cc_start: 0.8101 (mttt) cc_final: 0.7696 (tmtt) REVERT: F 351 GLN cc_start: 0.8114 (mp10) cc_final: 0.7610 (tt0) REVERT: G 316 SER cc_start: 0.8102 (m) cc_final: 0.7778 (p) REVERT: G 347 LYS cc_start: 0.8284 (mttt) cc_final: 0.7652 (pttm) REVERT: G 358 ASP cc_start: 0.8456 (m-30) cc_final: 0.7973 (t0) REVERT: H 311 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7271 (ttpt) REVERT: H 347 LYS cc_start: 0.8084 (mttt) cc_final: 0.7536 (pttp) REVERT: H 358 ASP cc_start: 0.8503 (m-30) cc_final: 0.7881 (t0) REVERT: I 347 LYS cc_start: 0.7933 (mttt) cc_final: 0.7467 (pttp) REVERT: I 358 ASP cc_start: 0.8511 (m-30) cc_final: 0.7890 (t0) outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 0.4566 time to fit residues: 56.1635 Evaluate side-chains 97 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4770 Z= 0.352 Angle : 0.592 4.929 6381 Z= 0.316 Chirality : 0.050 0.147 720 Planarity : 0.004 0.040 810 Dihedral : 5.940 19.189 630 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.15 % Allowed : 17.41 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.005 0.001 PHE B 346 TYR 0.020 0.005 TYR D 310 ARG 0.001 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7510 (ttmt) cc_final: 0.6716 (ttpt) REVERT: B 347 LYS cc_start: 0.7788 (mttt) cc_final: 0.7432 (tmtt) REVERT: B 358 ASP cc_start: 0.8518 (m-30) cc_final: 0.8074 (t0) REVERT: B 376 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7146 (mt) REVERT: A 347 LYS cc_start: 0.7995 (mttt) cc_final: 0.7398 (tmtt) REVERT: A 358 ASP cc_start: 0.8574 (m-30) cc_final: 0.8079 (t0) REVERT: A 376 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.6934 (mt) REVERT: C 347 LYS cc_start: 0.8022 (mttt) cc_final: 0.7378 (tmtt) REVERT: C 358 ASP cc_start: 0.8575 (m-30) cc_final: 0.8052 (t0) REVERT: C 376 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6644 (mt) REVERT: D 311 LYS cc_start: 0.7035 (mtmt) cc_final: 0.6728 (mmtm) REVERT: D 343 LYS cc_start: 0.8439 (mttt) cc_final: 0.7601 (mmpt) REVERT: E 311 LYS cc_start: 0.7240 (ttmt) cc_final: 0.6794 (mmtm) REVERT: F 311 LYS cc_start: 0.7090 (ttmt) cc_final: 0.6641 (mmtm) REVERT: F 347 LYS cc_start: 0.8093 (mttt) cc_final: 0.7665 (tmtt) REVERT: F 351 GLN cc_start: 0.8146 (mp10) cc_final: 0.7542 (tt0) REVERT: G 347 LYS cc_start: 0.8272 (mttt) cc_final: 0.7688 (pttm) REVERT: G 358 ASP cc_start: 0.8517 (m-30) cc_final: 0.7986 (t0) REVERT: G 376 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.6960 (mt) REVERT: H 311 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7211 (ttpt) REVERT: H 347 LYS cc_start: 0.8044 (mttt) cc_final: 0.7484 (pttp) REVERT: H 358 ASP cc_start: 0.8533 (m-30) cc_final: 0.7946 (t0) REVERT: H 376 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.6806 (mt) REVERT: I 347 LYS cc_start: 0.7893 (mttt) cc_final: 0.7363 (pttp) REVERT: I 358 ASP cc_start: 0.8502 (m-30) cc_final: 0.7950 (t0) outliers start: 17 outliers final: 9 residues processed: 102 average time/residue: 0.4515 time to fit residues: 56.9263 Evaluate side-chains 103 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4770 Z= 0.305 Angle : 0.574 4.861 6381 Z= 0.305 Chirality : 0.050 0.153 720 Planarity : 0.004 0.040 810 Dihedral : 5.839 19.126 630 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.70 % Allowed : 17.59 % Favored : 78.70 % 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: -2.99 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 362 PHE 0.005 0.001 PHE B 346 TYR 0.018 0.004 TYR F 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7444 (ttmt) cc_final: 0.7164 (ttpt) REVERT: B 347 LYS cc_start: 0.7806 (mttt) cc_final: 0.7303 (tmtt) REVERT: B 358 ASP cc_start: 0.8551 (m-30) cc_final: 0.8055 (t0) REVERT: B 376 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7164 (mt) REVERT: A 347 LYS cc_start: 0.8004 (mttt) cc_final: 0.7532 (tmtt) REVERT: A 358 ASP cc_start: 0.8548 (m-30) cc_final: 0.8062 (t0) REVERT: A 376 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.6925 (mt) REVERT: C 347 LYS cc_start: 0.8033 (mttt) cc_final: 0.7379 (tmtt) REVERT: C 358 ASP cc_start: 0.8571 (m-30) cc_final: 0.8051 (t0) REVERT: C 376 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6623 (mt) REVERT: D 311 LYS cc_start: 0.7083 (mtmt) cc_final: 0.6725 (pttt) REVERT: D 343 LYS cc_start: 0.8476 (mttt) cc_final: 0.7631 (mmpt) REVERT: D 349 ARG cc_start: 0.7539 (mtm180) cc_final: 0.6991 (mmp-170) REVERT: D 351 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7352 (mt0) REVERT: E 311 LYS cc_start: 0.7217 (ttmt) cc_final: 0.6777 (mmtm) REVERT: F 311 LYS cc_start: 0.7265 (ttmt) cc_final: 0.6834 (mmtm) REVERT: F 347 LYS cc_start: 0.8090 (mttt) cc_final: 0.7640 (tmtt) REVERT: F 351 GLN cc_start: 0.8133 (mp10) cc_final: 0.7511 (tt0) REVERT: G 316 SER cc_start: 0.8034 (m) cc_final: 0.7777 (p) REVERT: G 347 LYS cc_start: 0.8275 (mttt) cc_final: 0.7657 (pttm) REVERT: G 358 ASP cc_start: 0.8519 (m-30) cc_final: 0.7987 (t0) REVERT: G 376 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.6917 (mt) REVERT: H 311 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7254 (ttpt) REVERT: H 347 LYS cc_start: 0.8020 (mttt) cc_final: 0.7510 (pttp) REVERT: H 358 ASP cc_start: 0.8536 (m-30) cc_final: 0.7940 (t0) REVERT: H 376 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.6834 (mt) REVERT: I 347 LYS cc_start: 0.7884 (mttt) cc_final: 0.7373 (pttp) REVERT: I 358 ASP cc_start: 0.8494 (m-30) cc_final: 0.7930 (t0) REVERT: I 376 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.6911 (mt) outliers start: 20 outliers final: 11 residues processed: 99 average time/residue: 0.4949 time to fit residues: 59.3465 Evaluate side-chains 103 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN D 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4770 Z= 0.195 Angle : 0.524 4.350 6381 Z= 0.276 Chirality : 0.049 0.151 720 Planarity : 0.004 0.047 810 Dihedral : 5.426 17.467 630 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.33 % Allowed : 18.52 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.005 0.001 PHE B 346 TYR 0.011 0.002 TYR D 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7434 (ttmt) cc_final: 0.7120 (ttpt) REVERT: B 347 LYS cc_start: 0.7837 (mttt) cc_final: 0.7327 (tmtt) REVERT: B 358 ASP cc_start: 0.8546 (m-30) cc_final: 0.8095 (t0) REVERT: B 376 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7161 (mt) REVERT: A 347 LYS cc_start: 0.7980 (mttt) cc_final: 0.7528 (tmtt) REVERT: A 358 ASP cc_start: 0.8533 (m-30) cc_final: 0.8039 (t0) REVERT: A 376 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.6905 (mt) REVERT: C 347 LYS cc_start: 0.7977 (mttt) cc_final: 0.7387 (tmtt) REVERT: C 358 ASP cc_start: 0.8521 (m-30) cc_final: 0.7997 (t0) REVERT: C 376 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6592 (mt) REVERT: D 311 LYS cc_start: 0.7204 (mtmt) cc_final: 0.6858 (pttt) REVERT: D 343 LYS cc_start: 0.8352 (mttt) cc_final: 0.7575 (mmpt) REVERT: D 351 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7380 (mt0) REVERT: E 311 LYS cc_start: 0.7302 (ttmt) cc_final: 0.6857 (mmtm) REVERT: F 311 LYS cc_start: 0.7241 (ttmt) cc_final: 0.6796 (mmtm) REVERT: F 347 LYS cc_start: 0.8050 (mttt) cc_final: 0.7614 (tmtt) REVERT: F 351 GLN cc_start: 0.8096 (mp10) cc_final: 0.7562 (tt0) REVERT: G 316 SER cc_start: 0.8047 (m) cc_final: 0.7776 (p) REVERT: G 347 LYS cc_start: 0.8201 (mttt) cc_final: 0.7628 (pttm) REVERT: G 358 ASP cc_start: 0.8470 (m-30) cc_final: 0.8001 (t0) REVERT: H 311 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7204 (ttpt) REVERT: H 347 LYS cc_start: 0.8066 (mttt) cc_final: 0.7560 (pttp) REVERT: H 358 ASP cc_start: 0.8499 (m-30) cc_final: 0.7871 (t0) REVERT: H 376 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.6874 (mt) REVERT: I 347 LYS cc_start: 0.7861 (mttt) cc_final: 0.7342 (pttp) REVERT: I 358 ASP cc_start: 0.8479 (m-30) cc_final: 0.7864 (t0) REVERT: I 376 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.6915 (mt) outliers start: 18 outliers final: 10 residues processed: 99 average time/residue: 0.4600 time to fit residues: 55.4618 Evaluate side-chains 104 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 0.0070 chunk 35 optimal weight: 0.0270 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4770 Z= 0.139 Angle : 0.494 4.319 6381 Z= 0.260 Chirality : 0.049 0.147 720 Planarity : 0.004 0.056 810 Dihedral : 4.757 14.757 630 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.41 % Allowed : 19.26 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.005 0.001 PHE B 346 TYR 0.006 0.001 TYR G 310 ARG 0.002 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7525 (ttmt) cc_final: 0.7310 (ttpt) REVERT: B 347 LYS cc_start: 0.7824 (mttt) cc_final: 0.7302 (tmtt) REVERT: B 358 ASP cc_start: 0.8459 (m-30) cc_final: 0.8001 (t0) REVERT: B 376 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7217 (mt) REVERT: A 347 LYS cc_start: 0.7935 (mttt) cc_final: 0.7530 (tmtt) REVERT: A 358 ASP cc_start: 0.8621 (m-30) cc_final: 0.8107 (t0) REVERT: A 375 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.5938 (mtpt) REVERT: A 376 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6827 (mt) REVERT: C 347 LYS cc_start: 0.8027 (mttt) cc_final: 0.7427 (tmtt) REVERT: C 358 ASP cc_start: 0.8375 (m-30) cc_final: 0.7984 (t0) REVERT: C 376 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6456 (mt) REVERT: D 311 LYS cc_start: 0.7360 (mtmt) cc_final: 0.7003 (pttt) REVERT: D 343 LYS cc_start: 0.8168 (mttt) cc_final: 0.7442 (mmpt) REVERT: E 311 LYS cc_start: 0.7359 (ttmt) cc_final: 0.6871 (mmtm) REVERT: F 342 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7330 (mt-10) REVERT: F 347 LYS cc_start: 0.8014 (mttt) cc_final: 0.7605 (tmtt) REVERT: G 316 SER cc_start: 0.8121 (m) cc_final: 0.7864 (p) REVERT: G 347 LYS cc_start: 0.8222 (mttt) cc_final: 0.7647 (pttm) REVERT: G 358 ASP cc_start: 0.8420 (m-30) cc_final: 0.7896 (t0) REVERT: G 376 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.6897 (mt) REVERT: H 311 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7235 (ttpt) REVERT: H 347 LYS cc_start: 0.8071 (mttt) cc_final: 0.7565 (pttp) REVERT: H 358 ASP cc_start: 0.8466 (m-30) cc_final: 0.7880 (t0) REVERT: I 347 LYS cc_start: 0.7932 (mttt) cc_final: 0.7396 (pttp) REVERT: I 358 ASP cc_start: 0.8433 (m-30) cc_final: 0.7849 (t0) REVERT: I 376 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.6768 (mt) outliers start: 13 outliers final: 7 residues processed: 113 average time/residue: 0.4867 time to fit residues: 66.9270 Evaluate side-chains 109 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 17 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4770 Z= 0.230 Angle : 0.535 4.216 6381 Z= 0.284 Chirality : 0.049 0.139 720 Planarity : 0.004 0.054 810 Dihedral : 5.153 16.353 630 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.04 % Allowed : 20.00 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.004 0.001 PHE D 346 TYR 0.014 0.003 TYR F 310 ARG 0.002 0.000 ARG H 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7429 (ttmt) cc_final: 0.7128 (ttpt) REVERT: B 347 LYS cc_start: 0.7822 (mttt) cc_final: 0.7390 (tmtt) REVERT: B 358 ASP cc_start: 0.8548 (m-30) cc_final: 0.8000 (t0) REVERT: B 376 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7246 (mt) REVERT: A 347 LYS cc_start: 0.7963 (mttt) cc_final: 0.7503 (tmtt) REVERT: A 358 ASP cc_start: 0.8656 (m-30) cc_final: 0.8105 (t0) REVERT: A 375 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.5853 (mtpt) REVERT: A 376 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6827 (mt) REVERT: C 347 LYS cc_start: 0.7988 (mttt) cc_final: 0.7402 (tmtt) REVERT: C 358 ASP cc_start: 0.8542 (m-30) cc_final: 0.8001 (t0) REVERT: C 376 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6535 (mt) REVERT: D 311 LYS cc_start: 0.7219 (mtmt) cc_final: 0.6868 (pttt) REVERT: D 343 LYS cc_start: 0.8197 (mttt) cc_final: 0.7492 (mmpt) REVERT: E 311 LYS cc_start: 0.7305 (ttmt) cc_final: 0.6847 (mmtm) REVERT: F 342 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7393 (mt-10) REVERT: F 347 LYS cc_start: 0.8045 (mttt) cc_final: 0.7617 (tmtt) REVERT: G 316 SER cc_start: 0.7965 (m) cc_final: 0.7702 (p) REVERT: G 347 LYS cc_start: 0.8199 (mttt) cc_final: 0.7655 (pttm) REVERT: G 358 ASP cc_start: 0.8496 (m-30) cc_final: 0.7913 (t0) REVERT: G 376 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.6924 (mt) REVERT: H 311 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7214 (ttpt) REVERT: H 347 LYS cc_start: 0.8035 (mttt) cc_final: 0.7506 (pttp) REVERT: H 358 ASP cc_start: 0.8489 (m-30) cc_final: 0.7864 (t0) REVERT: I 347 LYS cc_start: 0.7858 (mttt) cc_final: 0.7340 (pttp) REVERT: I 358 ASP cc_start: 0.8499 (m-30) cc_final: 0.7896 (t0) REVERT: I 376 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7034 (mt) outliers start: 11 outliers final: 5 residues processed: 94 average time/residue: 0.5174 time to fit residues: 58.4423 Evaluate side-chains 100 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.239700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.199708 restraints weight = 18426.187| |-----------------------------------------------------------------------------| r_work (start): 0.4659 rms_B_bonded: 2.98 r_work: 0.4650 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4578 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4770 Z= 0.170 Angle : 0.513 3.975 6381 Z= 0.271 Chirality : 0.049 0.138 720 Planarity : 0.004 0.055 810 Dihedral : 4.987 15.998 630 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.59 % Allowed : 19.63 % Favored : 77.78 % 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 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.004 0.001 PHE B 346 TYR 0.009 0.002 TYR F 310 ARG 0.000 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3166.27 seconds wall clock time: 57 minutes 54.37 seconds (3474.37 seconds total)