Starting phenix.real_space_refine on Fri Feb 14 01:26:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkv_14054/02_2025/7qkv_14054.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkv_14054/02_2025/7qkv_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_14054/02_2025/7qkv_14054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkv_14054/02_2025/7qkv_14054.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkv_14054/02_2025/7qkv_14054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkv_14054/02_2025/7qkv_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.13, per 1000 atoms: 0.64 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: 2.25 Conformation dependent library (CDL) restraints added in 874.1 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: 1.16 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: 3.29 Time building geometry restraints manager: 2.70 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: 0.01 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 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: 0.160 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.190 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:3.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.580 ------------------------------------------------------------------------------- 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 : 0.706 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: 0.4441 time to fit residues: 96.6760 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 : 0.762 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.197722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.176683 restraints weight = 17428.567| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 2.49 r_work: 0.4489 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4416 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 ASN cc_start: 0.7168 (m-40) cc_final: 0.6931 (t0) REVERT: B 345 ASP cc_start: 0.6902 (m-30) cc_final: 0.6694 (m-30) REVERT: B 346 PHE cc_start: 0.8055 (m-80) cc_final: 0.7738 (m-80) REVERT: B 347 LYS cc_start: 0.8063 (mttt) cc_final: 0.7389 (tmtt) REVERT: B 376 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8476 (mt) REVERT: A 347 LYS cc_start: 0.8045 (mttt) cc_final: 0.7222 (tmtt) REVERT: A 358 ASP cc_start: 0.8055 (m-30) cc_final: 0.7808 (t0) REVERT: C 347 LYS cc_start: 0.8171 (mttt) cc_final: 0.7346 (tmtt) REVERT: C 358 ASP cc_start: 0.7861 (m-30) cc_final: 0.7622 (t0) REVERT: C 376 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8310 (mt) REVERT: D 311 LYS cc_start: 0.8370 (mtmt) cc_final: 0.8067 (mmtm) REVERT: D 343 LYS cc_start: 0.8358 (mttt) cc_final: 0.7300 (mmpt) REVERT: D 347 LYS cc_start: 0.7973 (mttt) cc_final: 0.7668 (tmtt) REVERT: E 311 LYS cc_start: 0.8440 (mtmt) cc_final: 0.7832 (mmtm) REVERT: E 343 LYS cc_start: 0.8517 (mttt) cc_final: 0.7518 (mmpt) REVERT: E 347 LYS cc_start: 0.7962 (mttt) cc_final: 0.7609 (tmtt) REVERT: F 311 LYS cc_start: 0.8670 (ttmt) cc_final: 0.7963 (mmtm) REVERT: F 347 LYS cc_start: 0.8088 (mttt) cc_final: 0.7559 (tmtt) REVERT: F 351 GLN cc_start: 0.8106 (mp10) cc_final: 0.7488 (tt0) REVERT: G 347 LYS cc_start: 0.8282 (mttt) cc_final: 0.7576 (pttp) REVERT: G 358 ASP cc_start: 0.7843 (m-30) cc_final: 0.7607 (t0) REVERT: H 345 ASP cc_start: 0.6417 (m-30) cc_final: 0.6207 (m-30) REVERT: H 347 LYS cc_start: 0.8160 (mttt) cc_final: 0.7499 (pttp) REVERT: H 358 ASP cc_start: 0.8116 (m-30) cc_final: 0.7742 (t0) REVERT: I 347 LYS cc_start: 0.8069 (mttt) cc_final: 0.7405 (pttp) REVERT: I 358 ASP cc_start: 0.7825 (m-30) cc_final: 0.7461 (t0) outliers start: 9 outliers final: 7 residues processed: 115 average time/residue: 0.4370 time to fit residues: 61.2059 Evaluate side-chains 103 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 33 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 22 optimal weight: 0.1980 chunk 25 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.207164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.185415 restraints weight = 17079.708| |-----------------------------------------------------------------------------| r_work (start): 0.4648 rms_B_bonded: 2.56 r_work: 0.4585 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4509 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4770 Z= 0.152 Angle : 0.556 4.230 6381 Z= 0.293 Chirality : 0.050 0.133 720 Planarity : 0.003 0.025 810 Dihedral : 6.275 21.281 630 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.48 % Allowed : 17.59 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.25), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.19), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.007 0.001 PHE D 346 TYR 0.008 0.002 TYR D 310 ARG 0.001 0.000 ARG B 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 124 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 ASP cc_start: 0.6611 (m-30) cc_final: 0.6125 (m-30) REVERT: B 346 PHE cc_start: 0.8077 (m-80) cc_final: 0.7837 (m-80) REVERT: B 347 LYS cc_start: 0.7971 (mttt) cc_final: 0.7272 (tmtt) REVERT: A 347 LYS cc_start: 0.8007 (mttt) cc_final: 0.7199 (tmtt) REVERT: A 358 ASP cc_start: 0.8043 (m-30) cc_final: 0.7628 (t0) REVERT: C 327 ASN cc_start: 0.7298 (m-40) cc_final: 0.6705 (t0) REVERT: C 347 LYS cc_start: 0.8140 (mttt) cc_final: 0.7284 (tmtt) REVERT: C 358 ASP cc_start: 0.7899 (m-30) cc_final: 0.7529 (t0) REVERT: D 343 LYS cc_start: 0.8123 (mttt) cc_final: 0.7112 (mmpt) REVERT: D 347 LYS cc_start: 0.7899 (mttt) cc_final: 0.7617 (tmtt) REVERT: E 327 ASN cc_start: 0.7264 (m-40) cc_final: 0.6994 (t0) REVERT: E 342 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: E 343 LYS cc_start: 0.8207 (mttt) cc_final: 0.7317 (mmpt) REVERT: E 347 LYS cc_start: 0.7974 (mttt) cc_final: 0.7633 (tmtt) REVERT: F 311 LYS cc_start: 0.8550 (ttmt) cc_final: 0.7835 (mmtm) REVERT: F 347 LYS cc_start: 0.8164 (mttt) cc_final: 0.7618 (tmtt) REVERT: F 351 GLN cc_start: 0.8025 (mp10) cc_final: 0.7492 (tt0) REVERT: F 363 VAL cc_start: 0.8954 (t) cc_final: 0.8728 (m) REVERT: G 347 LYS cc_start: 0.8311 (mttt) cc_final: 0.7609 (pttp) REVERT: H 347 LYS cc_start: 0.8220 (mttt) cc_final: 0.7462 (pttp) REVERT: H 358 ASP cc_start: 0.8007 (m-30) cc_final: 0.7562 (t0) REVERT: I 347 LYS cc_start: 0.8021 (mttt) cc_final: 0.7387 (pttp) REVERT: I 358 ASP cc_start: 0.7949 (m-30) cc_final: 0.7494 (t0) outliers start: 8 outliers final: 4 residues processed: 118 average time/residue: 0.4246 time to fit residues: 61.5392 Evaluate side-chains 101 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 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 376 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.203066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.181570 restraints weight = 17067.437| |-----------------------------------------------------------------------------| r_work (start): 0.4597 rms_B_bonded: 2.56 r_work: 0.4537 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4463 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4770 Z= 0.249 Angle : 0.570 4.864 6381 Z= 0.299 Chirality : 0.049 0.142 720 Planarity : 0.003 0.032 810 Dihedral : 6.081 18.518 630 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.48 % Allowed : 18.52 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.19), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 362 PHE 0.005 0.001 PHE C 346 TYR 0.016 0.004 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 104 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 ASP cc_start: 0.6598 (m-30) cc_final: 0.6085 (m-30) REVERT: B 346 PHE cc_start: 0.8090 (m-80) cc_final: 0.7807 (m-80) REVERT: B 347 LYS cc_start: 0.8006 (mttt) cc_final: 0.7216 (tmtt) REVERT: A 327 ASN cc_start: 0.7851 (t0) cc_final: 0.7527 (t0) REVERT: A 347 LYS cc_start: 0.7972 (mttt) cc_final: 0.7226 (tmtt) REVERT: A 358 ASP cc_start: 0.8081 (m-30) cc_final: 0.7692 (t0) REVERT: C 347 LYS cc_start: 0.8141 (mttt) cc_final: 0.7260 (tmtt) REVERT: C 358 ASP cc_start: 0.8036 (m-30) cc_final: 0.7607 (t0) REVERT: C 376 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8231 (mt) REVERT: D 311 LYS cc_start: 0.8559 (pttt) cc_final: 0.8038 (mmtm) REVERT: D 342 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7043 (mm-30) REVERT: D 343 LYS cc_start: 0.8210 (mttt) cc_final: 0.7177 (mmpt) REVERT: D 347 LYS cc_start: 0.7829 (mttt) cc_final: 0.7591 (tmtt) REVERT: E 311 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8033 (mmtm) REVERT: E 327 ASN cc_start: 0.7450 (m-40) cc_final: 0.7058 (t0) REVERT: E 342 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7269 (mm-30) REVERT: E 343 LYS cc_start: 0.8438 (mttt) cc_final: 0.7431 (mmpt) REVERT: E 347 LYS cc_start: 0.7983 (mttt) cc_final: 0.7593 (tmtt) REVERT: F 311 LYS cc_start: 0.8582 (ttmt) cc_final: 0.7884 (mmtm) REVERT: F 327 ASN cc_start: 0.7518 (m-40) cc_final: 0.7312 (t0) REVERT: F 347 LYS cc_start: 0.8182 (mttt) cc_final: 0.7632 (tmtt) REVERT: F 351 GLN cc_start: 0.8039 (mp10) cc_final: 0.7466 (tt0) REVERT: G 347 LYS cc_start: 0.8292 (mttt) cc_final: 0.7509 (pttp) REVERT: H 347 LYS cc_start: 0.8180 (mttt) cc_final: 0.7461 (pttp) REVERT: H 358 ASP cc_start: 0.8104 (m-30) cc_final: 0.7617 (t0) REVERT: I 347 LYS cc_start: 0.7986 (mttt) cc_final: 0.7380 (pttp) REVERT: I 358 ASP cc_start: 0.8011 (m-30) cc_final: 0.7583 (t0) outliers start: 8 outliers final: 7 residues processed: 101 average time/residue: 0.4662 time to fit residues: 57.8671 Evaluate side-chains 99 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.206000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.184261 restraints weight = 16994.548| |-----------------------------------------------------------------------------| r_work (start): 0.4624 rms_B_bonded: 2.63 r_work: 0.4563 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4488 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4770 Z= 0.175 Angle : 0.523 4.519 6381 Z= 0.275 Chirality : 0.049 0.143 720 Planarity : 0.003 0.038 810 Dihedral : 5.569 17.314 630 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.67 % Allowed : 17.96 % 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: -2.70 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.003 0.001 PHE D 346 TYR 0.008 0.002 TYR F 310 ARG 0.001 0.000 ARG B 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 107 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8164 (m-80) cc_final: 0.7907 (m-80) REVERT: B 347 LYS cc_start: 0.7911 (mttt) cc_final: 0.7291 (tmtt) REVERT: A 347 LYS cc_start: 0.7935 (mttt) cc_final: 0.7192 (tmtt) REVERT: A 358 ASP cc_start: 0.8110 (m-30) cc_final: 0.7654 (t0) REVERT: C 347 LYS cc_start: 0.8144 (mttt) cc_final: 0.7301 (tmtt) REVERT: C 358 ASP cc_start: 0.8054 (m-30) cc_final: 0.7593 (t0) REVERT: C 376 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8193 (mt) REVERT: D 311 LYS cc_start: 0.8543 (pttt) cc_final: 0.7999 (mmtm) REVERT: D 343 LYS cc_start: 0.8176 (mttt) cc_final: 0.7270 (mmmt) REVERT: D 347 LYS cc_start: 0.7829 (mttt) cc_final: 0.7528 (tmtt) REVERT: E 311 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8086 (mmtm) REVERT: E 327 ASN cc_start: 0.7369 (m-40) cc_final: 0.7060 (t0) REVERT: E 342 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7043 (mm-30) REVERT: E 343 LYS cc_start: 0.8443 (mttt) cc_final: 0.7369 (mmpt) REVERT: E 347 LYS cc_start: 0.7983 (mttt) cc_final: 0.7606 (tmtt) REVERT: F 311 LYS cc_start: 0.8570 (ttmt) cc_final: 0.7931 (mmtm) REVERT: F 347 LYS cc_start: 0.8100 (mttt) cc_final: 0.7604 (tmtt) REVERT: F 351 GLN cc_start: 0.8030 (mp10) cc_final: 0.7479 (tt0) REVERT: G 347 LYS cc_start: 0.8276 (mttt) cc_final: 0.7538 (pttm) REVERT: H 311 LYS cc_start: 0.8687 (ttmt) cc_final: 0.7973 (ttpt) REVERT: H 347 LYS cc_start: 0.8147 (mttt) cc_final: 0.7417 (pttp) REVERT: H 358 ASP cc_start: 0.8091 (m-30) cc_final: 0.7605 (t0) REVERT: I 347 LYS cc_start: 0.8030 (mttt) cc_final: 0.7386 (pttp) REVERT: I 358 ASP cc_start: 0.7969 (m-30) cc_final: 0.7553 (t0) outliers start: 9 outliers final: 7 residues processed: 104 average time/residue: 0.4603 time to fit residues: 58.1890 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 : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER 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 7 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 0.0030 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 overall best weight: 4.7998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.196786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.175263 restraints weight = 17332.775| |-----------------------------------------------------------------------------| r_work (start): 0.4544 rms_B_bonded: 2.59 r_work: 0.4483 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4409 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5382 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= 0.338 Angle : 0.591 5.022 6381 Z= 0.316 Chirality : 0.050 0.149 720 Planarity : 0.004 0.038 810 Dihedral : 6.016 19.188 630 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.59 % Allowed : 17.59 % Favored : 79.81 % 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: -2.90 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (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 C 346 TYR 0.020 0.005 TYR F 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 103 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8161 (m-80) cc_final: 0.7871 (m-80) REVERT: B 347 LYS cc_start: 0.7940 (mttt) cc_final: 0.7265 (tmtt) REVERT: A 347 LYS cc_start: 0.8019 (mttt) cc_final: 0.7207 (tmtt) REVERT: A 358 ASP cc_start: 0.8173 (m-30) cc_final: 0.7753 (t0) REVERT: C 347 LYS cc_start: 0.8031 (mttt) cc_final: 0.7210 (tmtt) REVERT: C 358 ASP cc_start: 0.8150 (m-30) cc_final: 0.7685 (t0) REVERT: C 376 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8263 (mt) REVERT: D 311 LYS cc_start: 0.8652 (pttt) cc_final: 0.8233 (mmtm) REVERT: D 343 LYS cc_start: 0.8508 (mttt) cc_final: 0.7386 (mmpt) REVERT: D 347 LYS cc_start: 0.7819 (mttt) cc_final: 0.7510 (tmtt) REVERT: E 311 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8141 (mmtm) REVERT: E 327 ASN cc_start: 0.7535 (m-40) cc_final: 0.7109 (t0) REVERT: E 343 LYS cc_start: 0.8573 (mttt) cc_final: 0.7460 (mmpt) REVERT: E 347 LYS cc_start: 0.7947 (mttt) cc_final: 0.7583 (tmtt) REVERT: F 311 LYS cc_start: 0.8683 (ttmt) cc_final: 0.7968 (mmtm) REVERT: F 347 LYS cc_start: 0.8114 (mttt) cc_final: 0.7507 (tmtt) REVERT: F 351 GLN cc_start: 0.8018 (mp10) cc_final: 0.7409 (tt0) REVERT: G 347 LYS cc_start: 0.8323 (mttt) cc_final: 0.7588 (pttm) REVERT: H 311 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8058 (ttpt) REVERT: H 347 LYS cc_start: 0.8117 (mttt) cc_final: 0.7391 (pttp) REVERT: H 358 ASP cc_start: 0.8149 (m-30) cc_final: 0.7662 (t0) REVERT: H 376 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8264 (mt) REVERT: I 347 LYS cc_start: 0.7970 (mttt) cc_final: 0.7261 (pttp) REVERT: I 358 ASP cc_start: 0.8027 (m-30) cc_final: 0.7630 (t0) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 0.4456 time to fit residues: 53.0029 Evaluate side-chains 97 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain A residue 325 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 H residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 ** 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 = 0.4758 r_free = 0.4758 target = 0.202264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.180625 restraints weight = 17324.270| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 2.62 r_work: 0.4536 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4460 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4770 Z= 0.196 Angle : 0.528 4.348 6381 Z= 0.280 Chirality : 0.049 0.153 720 Planarity : 0.004 0.043 810 Dihedral : 5.555 17.646 630 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.22 % Allowed : 18.52 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.003 0.001 PHE C 346 TYR 0.011 0.002 TYR F 310 ARG 0.001 0.000 ARG B 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 104 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8192 (m-80) cc_final: 0.7934 (m-80) REVERT: B 347 LYS cc_start: 0.7939 (mttt) cc_final: 0.7250 (tmtt) REVERT: A 347 LYS cc_start: 0.8087 (mttt) cc_final: 0.7419 (tmtt) REVERT: A 358 ASP cc_start: 0.8118 (m-30) cc_final: 0.7693 (t0) REVERT: C 347 LYS cc_start: 0.7989 (mttt) cc_final: 0.7177 (tmtt) REVERT: C 358 ASP cc_start: 0.8088 (m-30) cc_final: 0.7630 (t0) REVERT: C 376 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8213 (mt) REVERT: D 311 LYS cc_start: 0.8618 (pttt) cc_final: 0.8190 (mmtm) REVERT: D 343 LYS cc_start: 0.8272 (mttt) cc_final: 0.7339 (mmpt) REVERT: D 347 LYS cc_start: 0.7862 (mttt) cc_final: 0.7510 (tmtt) REVERT: D 351 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7314 (mt0) REVERT: E 311 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8134 (mmtm) REVERT: E 327 ASN cc_start: 0.7475 (m-40) cc_final: 0.7078 (t0) REVERT: E 343 LYS cc_start: 0.8559 (mttt) cc_final: 0.7405 (mmpt) REVERT: E 347 LYS cc_start: 0.8021 (mttt) cc_final: 0.7603 (tmtt) REVERT: F 311 LYS cc_start: 0.8649 (ttmt) cc_final: 0.7919 (mmtm) REVERT: F 347 LYS cc_start: 0.8094 (mttt) cc_final: 0.7539 (tmtt) REVERT: F 351 GLN cc_start: 0.7981 (mp10) cc_final: 0.7414 (tt0) REVERT: G 347 LYS cc_start: 0.8316 (mttt) cc_final: 0.7601 (pttm) REVERT: H 311 LYS cc_start: 0.8721 (ttmt) cc_final: 0.8012 (ttpt) REVERT: H 347 LYS cc_start: 0.8130 (mttt) cc_final: 0.7441 (pttp) REVERT: H 358 ASP cc_start: 0.8134 (m-30) cc_final: 0.7616 (t0) REVERT: H 376 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8235 (mt) REVERT: I 347 LYS cc_start: 0.8030 (mttt) cc_final: 0.7285 (pttp) REVERT: I 358 ASP cc_start: 0.8013 (m-30) cc_final: 0.7562 (t0) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 0.4510 time to fit residues: 54.5244 Evaluate side-chains 98 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain A residue 325 LEU 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 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 H residue 376 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.198251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.176558 restraints weight = 17557.464| |-----------------------------------------------------------------------------| r_work (start): 0.4558 rms_B_bonded: 2.62 r_work: 0.4496 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4420 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4770 Z= 0.284 Angle : 0.554 4.781 6381 Z= 0.297 Chirality : 0.050 0.154 720 Planarity : 0.004 0.042 810 Dihedral : 5.737 18.610 630 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.15 % Allowed : 18.33 % Favored : 78.52 % 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: -2.97 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.004 0.001 PHE C 346 TYR 0.016 0.004 TYR F 310 ARG 0.001 0.000 ARG G 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 103 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8164 (m-80) cc_final: 0.7883 (m-80) REVERT: B 347 LYS cc_start: 0.7956 (mttt) cc_final: 0.7258 (tmtt) REVERT: A 347 LYS cc_start: 0.8049 (mttt) cc_final: 0.7390 (tmtt) REVERT: A 358 ASP cc_start: 0.8153 (m-30) cc_final: 0.7763 (t0) REVERT: C 347 LYS cc_start: 0.7982 (mttt) cc_final: 0.7199 (tmtt) REVERT: C 358 ASP cc_start: 0.8200 (m-30) cc_final: 0.7688 (t0) REVERT: C 376 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8252 (mt) REVERT: D 311 LYS cc_start: 0.8673 (pttt) cc_final: 0.8223 (mmtm) REVERT: D 343 LYS cc_start: 0.8550 (mttt) cc_final: 0.7435 (mmpt) REVERT: D 347 LYS cc_start: 0.7903 (mttt) cc_final: 0.7518 (tmtt) REVERT: D 351 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7276 (mt0) REVERT: E 311 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8148 (mmtm) REVERT: E 327 ASN cc_start: 0.7521 (m-40) cc_final: 0.7076 (t0) REVERT: E 343 LYS cc_start: 0.8587 (mttt) cc_final: 0.7442 (mmpt) REVERT: E 347 LYS cc_start: 0.7999 (mttt) cc_final: 0.7582 (tmtt) REVERT: F 311 LYS cc_start: 0.8669 (ttmt) cc_final: 0.7947 (mmtm) REVERT: F 347 LYS cc_start: 0.8142 (mttt) cc_final: 0.7521 (tmtt) REVERT: F 351 GLN cc_start: 0.7990 (mp10) cc_final: 0.7426 (tt0) REVERT: G 325 LEU cc_start: 0.8608 (tt) cc_final: 0.8404 (tp) REVERT: G 347 LYS cc_start: 0.8308 (mttt) cc_final: 0.7596 (pttm) REVERT: H 311 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8050 (ttpt) REVERT: H 347 LYS cc_start: 0.8117 (mttt) cc_final: 0.7422 (pttp) REVERT: H 358 ASP cc_start: 0.8166 (m-30) cc_final: 0.7652 (t0) REVERT: H 376 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8287 (mt) REVERT: I 347 LYS cc_start: 0.8001 (mttt) cc_final: 0.7299 (pttp) REVERT: I 358 ASP cc_start: 0.7995 (m-30) cc_final: 0.7606 (t0) outliers start: 17 outliers final: 10 residues processed: 98 average time/residue: 0.4527 time to fit residues: 54.0836 Evaluate side-chains 99 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 356 SER 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 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 H residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 0.0040 chunk 2 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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** F 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.204432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.182489 restraints weight = 17030.902| |-----------------------------------------------------------------------------| r_work (start): 0.4612 rms_B_bonded: 2.65 r_work: 0.4551 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4474 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4770 Z= 0.146 Angle : 0.510 4.143 6381 Z= 0.271 Chirality : 0.049 0.151 720 Planarity : 0.004 0.050 810 Dihedral : 5.238 16.447 630 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.78 % Allowed : 18.52 % 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: -2.90 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.002 0.001 PHE C 346 TYR 0.010 0.002 TYR D 310 ARG 0.001 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 112 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8197 (m-80) cc_final: 0.7949 (m-80) REVERT: B 347 LYS cc_start: 0.7956 (mttt) cc_final: 0.7252 (tmtt) REVERT: A 347 LYS cc_start: 0.8075 (mttt) cc_final: 0.7435 (tmtt) REVERT: A 358 ASP cc_start: 0.8250 (m-30) cc_final: 0.7771 (t0) REVERT: A 375 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8280 (mtpt) REVERT: C 347 LYS cc_start: 0.7998 (mttt) cc_final: 0.7177 (tmtt) REVERT: C 376 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8200 (mt) REVERT: D 311 LYS cc_start: 0.8640 (pttt) cc_final: 0.8131 (mmtm) REVERT: D 343 LYS cc_start: 0.8287 (mttt) cc_final: 0.7345 (mmpt) REVERT: D 347 LYS cc_start: 0.7888 (mttt) cc_final: 0.7528 (tmtt) REVERT: D 351 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7314 (mt0) REVERT: E 311 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8144 (mmtm) REVERT: E 327 ASN cc_start: 0.7416 (m-40) cc_final: 0.7073 (t0) REVERT: E 343 LYS cc_start: 0.8554 (mttt) cc_final: 0.7366 (mmpt) REVERT: E 347 LYS cc_start: 0.8007 (mttt) cc_final: 0.7548 (tmtt) REVERT: F 347 LYS cc_start: 0.8081 (mttt) cc_final: 0.7491 (tmtt) REVERT: G 347 LYS cc_start: 0.8304 (mttt) cc_final: 0.7588 (pttm) REVERT: H 311 LYS cc_start: 0.8721 (ttmt) cc_final: 0.7996 (ttpt) REVERT: H 347 LYS cc_start: 0.8156 (mttt) cc_final: 0.7445 (pttp) REVERT: H 358 ASP cc_start: 0.8110 (m-30) cc_final: 0.7591 (t0) REVERT: H 376 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8267 (mt) REVERT: I 311 LYS cc_start: 0.8620 (ttmt) cc_final: 0.7876 (ttpt) REVERT: I 347 LYS cc_start: 0.8045 (mttt) cc_final: 0.7289 (pttp) REVERT: I 358 ASP cc_start: 0.7979 (m-30) cc_final: 0.7663 (t0) outliers start: 15 outliers final: 10 residues processed: 106 average time/residue: 0.4807 time to fit residues: 61.6846 Evaluate side-chains 107 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain C residue 356 SER 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 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.202396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.180753 restraints weight = 17305.047| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 2.63 r_work: 0.4529 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4454 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4770 Z= 0.207 Angle : 0.521 4.340 6381 Z= 0.277 Chirality : 0.049 0.160 720 Planarity : 0.005 0.053 810 Dihedral : 5.305 16.570 630 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.78 % Allowed : 18.33 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 329 PHE 0.003 0.001 PHE C 346 TYR 0.012 0.003 TYR F 310 ARG 0.000 0.000 ARG I 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 107 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8171 (m-80) cc_final: 0.7895 (m-80) REVERT: B 347 LYS cc_start: 0.7984 (mttt) cc_final: 0.7282 (tmtt) REVERT: A 347 LYS cc_start: 0.8066 (mttt) cc_final: 0.7434 (tmtt) REVERT: A 358 ASP cc_start: 0.8226 (m-30) cc_final: 0.7746 (t0) REVERT: A 375 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8284 (mtpt) REVERT: C 347 LYS cc_start: 0.7991 (mttt) cc_final: 0.7181 (tmtt) REVERT: C 376 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8229 (mt) REVERT: D 311 LYS cc_start: 0.8664 (pttt) cc_final: 0.8161 (mmtm) REVERT: D 343 LYS cc_start: 0.8304 (mttt) cc_final: 0.7377 (mmpt) REVERT: D 347 LYS cc_start: 0.7885 (mttt) cc_final: 0.7523 (tmtt) REVERT: D 351 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7290 (mt0) REVERT: E 311 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8162 (mmtm) REVERT: E 327 ASN cc_start: 0.7442 (m-40) cc_final: 0.7052 (t0) REVERT: E 343 LYS cc_start: 0.8571 (mttt) cc_final: 0.7399 (mmpt) REVERT: E 347 LYS cc_start: 0.7995 (mttt) cc_final: 0.7557 (tmtt) REVERT: F 342 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6906 (mt-10) REVERT: F 347 LYS cc_start: 0.8094 (mttt) cc_final: 0.7508 (tmtt) REVERT: G 325 LEU cc_start: 0.8576 (tt) cc_final: 0.8375 (tp) REVERT: G 347 LYS cc_start: 0.8278 (mttt) cc_final: 0.7564 (pttm) REVERT: H 311 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8022 (ttpt) REVERT: H 347 LYS cc_start: 0.8165 (mttt) cc_final: 0.7480 (pttp) REVERT: H 358 ASP cc_start: 0.8139 (m-30) cc_final: 0.7614 (t0) REVERT: H 376 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8295 (mt) REVERT: I 347 LYS cc_start: 0.8016 (mttt) cc_final: 0.7264 (pttp) REVERT: I 358 ASP cc_start: 0.8061 (m-30) cc_final: 0.7713 (t0) outliers start: 15 outliers final: 9 residues processed: 100 average time/residue: 0.4678 time to fit residues: 56.7306 Evaluate side-chains 102 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain C residue 356 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 8.9990 chunk 40 optimal weight: 0.0370 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7664 ------------------------------------------------------------------------------- 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 = 0.4895 r_free = 0.4895 target = 0.255711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.210871 restraints weight = 18630.869| |-----------------------------------------------------------------------------| r_work (start): 0.4732 rms_B_bonded: 2.95 r_work: 0.4726 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4658 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4770 Z= 0.127 Angle : 0.494 4.212 6381 Z= 0.259 Chirality : 0.049 0.153 720 Planarity : 0.005 0.059 810 Dihedral : 4.701 14.509 630 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.67 % Allowed : 19.26 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.002 0.001 PHE D 346 TYR 0.005 0.001 TYR D 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: 5203.10 seconds wall clock time: 92 minutes 54.48 seconds (5574.48 seconds total)