Starting phenix.real_space_refine on Tue Aug 4 14:13:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28lp_56600/08_2026/28lp_56600.cif Found real_map, /net/cci-nas-00/data/ceres_data/28lp_56600/08_2026/28lp_56600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/28lp_56600/08_2026/28lp_56600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28lp_56600/08_2026/28lp_56600.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28lp_56600/08_2026/28lp_56600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28lp_56600/08_2026/28lp_56600.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 2305 2.51 5 N 690 2.21 5 O 690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3690 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 738 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.68, per 1000 atoms: 0.18 Number of scatterers: 3690 At special positions: 0 Unit cell: (111.51, 83.426, 49.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 690 8.00 N 690 7.00 C 2305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 128.5 milliseconds 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 840 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 86.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 253 through 260 removed outlier: 6.694A pdb=" N LEU A 253 " --> pdb=" O LYS E 254 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL E 256 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN A 255 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N SER E 258 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS A 257 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE E 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 259 " --> pdb=" O ILE E 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.781A pdb=" N THR B 263 " --> pdb=" O GLU C 264 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LEU C 266 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN B 265 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N HIS C 268 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS B 267 " --> pdb=" O HIS C 268 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR A 263 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N LEU B 266 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN A 265 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N HIS B 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS A 267 " --> pdb=" O HIS B 268 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR D 263 " --> pdb=" O GLU E 264 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N LEU E 266 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN D 265 " --> pdb=" O LEU E 266 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N HIS E 268 " --> pdb=" O ASN D 265 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS D 267 " --> pdb=" O HIS E 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 274 through 310 removed outlier: 6.295A pdb=" N LYS A 274 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE E 308 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.790A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 317 through 321 removed outlier: 6.425A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS B 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER A 320 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL D 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS E 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER D 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.466A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 336 through 354 removed outlier: 6.593A pdb=" N VAL B 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LYS C 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL B 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLU C 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N SER B 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU C 344 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N LYS B 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N PHE C 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N ASP B 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N ASP C 348 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N LYS B 347 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N VAL C 350 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ARG B 349 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N SER C 352 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N GLN B 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N ILE C 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N LYS B 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLU B 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N SER A 341 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N LYS A 343 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N PHE B 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N ASP B 348 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N LYS A 347 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N VAL B 350 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ARG A 349 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N SER B 352 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS E 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 344 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP E 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE A 346 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS E 347 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP A 348 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG E 349 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 350 " --> pdb=" O ARG E 349 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLN E 351 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER A 352 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS E 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE A 354 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL D 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LYS E 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL D 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLU E 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N SER D 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU E 344 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N LYS D 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N PHE E 346 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N ASP D 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N ASP E 348 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N LYS D 347 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N VAL E 350 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ARG D 349 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N SER E 352 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N GLN D 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N ILE E 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N LYS D 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.258A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.848A pdb=" N LYS B 370 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS A 370 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N PHE E 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS D 370 " --> pdb=" O LYS E 369 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.46 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 883 1.34 - 1.46: 879 1.46 - 1.57: 1978 1.57 - 1.69: 0 1.69 - 1.81: 5 Bond restraints: 3745 Sorted by residual: bond pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.25e+00 bond pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.12e+00 bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.10e+00 bond pdb=" CG HIS D 362 " pdb=" CD2 HIS D 362 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.08e+00 bond pdb=" CG HIS E 362 " pdb=" CD2 HIS E 362 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.06e+00 ... (remaining 3740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 4187 1.91 - 3.82: 683 3.82 - 5.73: 105 5.73 - 7.64: 20 7.64 - 9.54: 5 Bond angle restraints: 5000 Sorted by residual: angle pdb=" C GLU D 342 " pdb=" CA GLU D 342 " pdb=" CB GLU D 342 " ideal model delta sigma weight residual 110.42 119.96 -9.54 1.99e+00 2.53e-01 2.30e+01 angle pdb=" C GLU C 342 " pdb=" CA GLU C 342 " pdb=" CB GLU C 342 " ideal model delta sigma weight residual 110.42 119.95 -9.53 1.99e+00 2.53e-01 2.29e+01 angle pdb=" C GLU B 342 " pdb=" CA GLU B 342 " pdb=" CB GLU B 342 " ideal model delta sigma weight residual 110.42 119.95 -9.53 1.99e+00 2.53e-01 2.29e+01 angle pdb=" C GLU A 342 " pdb=" CA GLU A 342 " pdb=" CB GLU A 342 " ideal model delta sigma weight residual 110.42 119.93 -9.51 1.99e+00 2.53e-01 2.28e+01 angle pdb=" C GLU E 342 " pdb=" CA GLU E 342 " pdb=" CB GLU E 342 " ideal model delta sigma weight residual 110.42 119.91 -9.49 1.99e+00 2.53e-01 2.28e+01 ... (remaining 4995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.90: 2070 13.90 - 27.79: 195 27.79 - 41.69: 15 41.69 - 55.58: 15 55.58 - 69.48: 5 Dihedral angle restraints: 2300 sinusoidal: 975 harmonic: 1325 Sorted by residual: dihedral pdb=" CA ASP E 358 " pdb=" C ASP E 358 " pdb=" N ASN E 359 " pdb=" CA ASN E 359 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP A 358 " pdb=" C ASP A 358 " pdb=" N ASN A 359 " pdb=" CA ASN A 359 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP D 358 " pdb=" C ASP D 358 " pdb=" N ASN D 359 " pdb=" CA ASN D 359 " ideal model delta harmonic sigma weight residual -180.00 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 2297 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.059: 233 0.059 - 0.117: 203 0.117 - 0.174: 76 0.174 - 0.232: 38 0.232 - 0.289: 5 Chirality restraints: 555 Sorted by residual: chirality pdb=" CA GLU E 338 " pdb=" N GLU E 338 " pdb=" C GLU E 338 " pdb=" CB GLU E 338 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA GLU C 338 " pdb=" N GLU C 338 " pdb=" C GLU C 338 " pdb=" CB GLU C 338 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA GLU A 338 " pdb=" N GLU A 338 " pdb=" C GLU A 338 " pdb=" CB GLU A 338 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 552 not shown) Planarity restraints: 640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 265 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C ASN C 265 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN C 265 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU C 266 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 265 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C ASN E 265 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN E 265 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU E 266 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 265 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C ASN B 265 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN B 265 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 266 " -0.011 2.00e-02 2.50e+03 ... (remaining 637 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 1821 3.01 - 3.48: 3178 3.48 - 3.95: 5898 3.95 - 4.43: 6335 4.43 - 4.90: 13157 Nonbonded interactions: 30389 Sorted by model distance: nonbonded pdb=" OG1 THR C 361 " pdb=" OG1 THR C 373 " model vdw 2.534 3.040 nonbonded pdb=" OG1 THR B 361 " pdb=" OG1 THR B 373 " model vdw 2.534 3.040 nonbonded pdb=" OG1 THR D 361 " pdb=" OG1 THR D 373 " model vdw 2.534 3.040 nonbonded pdb=" OG1 THR A 361 " pdb=" OG1 THR A 373 " model vdw 2.534 3.040 nonbonded pdb=" OG1 THR E 361 " pdb=" OG1 THR E 373 " model vdw 2.534 3.040 ... (remaining 30384 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' } 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: 5.610 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.890 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 3745 Z= 0.581 Angle : 1.519 9.544 5000 Z= 0.961 Chirality : 0.096 0.289 555 Planarity : 0.006 0.019 640 Dihedral : 11.726 69.480 1460 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.38 % Allowed : 2.38 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.28), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.22), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 349 TYR 0.017 0.009 TYR D 310 PHE 0.013 0.003 PHE E 346 HIS 0.005 0.002 HIS E 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00919 / 0.58 ( 3745) covalent geometry : angle 1.51926 / 0.96 ( 5000) hydrogen bonds : bond 0.07384 / 4.87 ( 86) hydrogen bonds : angle 6.34183 / 4.39 ( 258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.089 Fit side-chains REVERT: C 266 LEU cc_start: 0.8307 (mp) cc_final: 0.7978 (tp) REVERT: C 311 LYS cc_start: 0.8722 (pttm) cc_final: 0.8275 (tppp) REVERT: D 379 ARG cc_start: 0.7348 (ptp-170) cc_final: 0.7137 (pmt-80) REVERT: E 266 LEU cc_start: 0.8305 (mp) cc_final: 0.8065 (tp) REVERT: E 316 SER cc_start: 0.9216 (p) cc_final: 0.9009 (p) outliers start: 10 outliers final: 6 residues processed: 106 average time/residue: 0.4504 time to fit residues: 49.2092 Evaluate side-chains 81 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN A 374 HIS B 374 HIS C 351 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS D 336 GLN D 374 HIS E 336 GLN E 374 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.115762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.098995 restraints weight = 4516.107| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.34 r_work: 0.4080 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3983 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3745 Z= 0.176 Angle : 0.749 6.212 5000 Z= 0.363 Chirality : 0.053 0.130 555 Planarity : 0.003 0.022 640 Dihedral : 7.106 48.217 509 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.57 % Allowed : 10.24 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.31), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.23), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 379 TYR 0.007 0.002 TYR C 310 PHE 0.010 0.002 PHE C 378 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 3745) covalent geometry : angle 0.74887 / 0.36 ( 5000) hydrogen bonds : bond 0.02397 / 1.64 ( 86) hydrogen bonds : angle 5.53116 / 3.88 ( 258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.147 Fit side-chains REVERT: A 264 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: A 369 LYS cc_start: 0.8175 (mttt) cc_final: 0.7823 (mtpt) REVERT: B 266 LEU cc_start: 0.8291 (mp) cc_final: 0.7808 (tp) REVERT: C 266 LEU cc_start: 0.8285 (mp) cc_final: 0.7856 (tp) REVERT: E 266 LEU cc_start: 0.8239 (mp) cc_final: 0.7882 (tp) REVERT: E 267 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8317 (mttp) REVERT: E 314 ASP cc_start: 0.8682 (t0) cc_final: 0.8475 (t0) REVERT: E 316 SER cc_start: 0.9041 (p) cc_final: 0.8791 (p) outliers start: 15 outliers final: 8 residues processed: 92 average time/residue: 0.4622 time to fit residues: 43.9472 Evaluate side-chains 91 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 31 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 336 GLN E 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.110907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.094460 restraints weight = 4629.519| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.33 r_work: 0.4001 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 3745 Z= 0.284 Angle : 0.798 7.380 5000 Z= 0.387 Chirality : 0.057 0.136 555 Planarity : 0.004 0.036 640 Dihedral : 6.728 42.340 505 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 6.90 % Allowed : 9.29 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.31), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.23), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 379 TYR 0.007 0.003 TYR C 310 PHE 0.011 0.002 PHE A 378 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.28 ( 3745) covalent geometry : angle 0.79767 / 0.39 ( 5000) hydrogen bonds : bond 0.02650 / 1.82 ( 86) hydrogen bonds : angle 5.45006 / 3.79 ( 258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.152 Fit side-chains REVERT: A 264 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: A 369 LYS cc_start: 0.8237 (mttt) cc_final: 0.7856 (mtpt) REVERT: B 266 LEU cc_start: 0.8266 (mp) cc_final: 0.7956 (tt) REVERT: C 266 LEU cc_start: 0.8243 (mp) cc_final: 0.7902 (tt) REVERT: D 314 ASP cc_start: 0.8761 (t0) cc_final: 0.8295 (t0) REVERT: D 316 SER cc_start: 0.9075 (p) cc_final: 0.8779 (p) REVERT: E 266 LEU cc_start: 0.8276 (mp) cc_final: 0.7881 (tp) REVERT: E 267 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8407 (mttp) outliers start: 29 outliers final: 20 residues processed: 87 average time/residue: 0.4930 time to fit residues: 44.2444 Evaluate side-chains 100 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN A 336 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.113550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.096919 restraints weight = 4519.923| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.33 r_work: 0.4050 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3745 Z= 0.164 Angle : 0.649 5.140 5000 Z= 0.316 Chirality : 0.051 0.128 555 Planarity : 0.003 0.022 640 Dihedral : 6.527 42.520 505 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 6.43 % Allowed : 10.48 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.31), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.006 0.002 TYR C 310 PHE 0.007 0.001 PHE A 346 HIS 0.001 0.000 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 3745) covalent geometry : angle 0.64917 / 0.32 ( 5000) hydrogen bonds : bond 0.02150 / 1.51 ( 86) hydrogen bonds : angle 5.12677 / 3.59 ( 258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.154 Fit side-chains REVERT: A 264 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: A 369 LYS cc_start: 0.8216 (mttt) cc_final: 0.7846 (mtpt) REVERT: B 266 LEU cc_start: 0.8221 (mp) cc_final: 0.7922 (tt) REVERT: C 266 LEU cc_start: 0.8239 (mp) cc_final: 0.7902 (tt) REVERT: C 359 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6393 (t0) REVERT: D 314 ASP cc_start: 0.8753 (t0) cc_final: 0.8313 (t0) REVERT: D 316 SER cc_start: 0.9068 (p) cc_final: 0.8788 (p) REVERT: E 266 LEU cc_start: 0.8258 (mp) cc_final: 0.7945 (tt) outliers start: 27 outliers final: 20 residues processed: 92 average time/residue: 0.4791 time to fit residues: 45.5189 Evaluate side-chains 104 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN A 336 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.110082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.093634 restraints weight = 4527.837| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 2.27 r_work: 0.4005 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3745 Z= 0.254 Angle : 0.719 6.599 5000 Z= 0.353 Chirality : 0.055 0.132 555 Planarity : 0.004 0.029 640 Dihedral : 6.687 43.342 505 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 7.62 % Allowed : 10.71 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.31), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 349 TYR 0.007 0.003 TYR C 310 PHE 0.010 0.002 PHE C 378 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 ( 3745) covalent geometry : angle 0.71922 / 0.35 ( 5000) hydrogen bonds : bond 0.02339 / 1.64 ( 86) hydrogen bonds : angle 5.08881 / 3.55 ( 258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.210 Fit side-chains REVERT: A 264 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: A 369 LYS cc_start: 0.8233 (mttt) cc_final: 0.7897 (mtpt) REVERT: B 349 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7579 (mtt-85) REVERT: C 264 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: C 266 LEU cc_start: 0.8262 (mp) cc_final: 0.7931 (tt) REVERT: C 359 ASN cc_start: 0.7249 (OUTLIER) cc_final: 0.6594 (t0) REVERT: D 264 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: D 314 ASP cc_start: 0.8806 (t0) cc_final: 0.8379 (t0) REVERT: D 316 SER cc_start: 0.9090 (p) cc_final: 0.8802 (p) REVERT: D 325 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8719 (tm) REVERT: D 379 ARG cc_start: 0.5626 (OUTLIER) cc_final: 0.4152 (tpt90) REVERT: E 264 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: E 266 LEU cc_start: 0.8243 (mp) cc_final: 0.7940 (tt) outliers start: 32 outliers final: 20 residues processed: 86 average time/residue: 0.5489 time to fit residues: 48.7406 Evaluate side-chains 105 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.0050 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 0.0870 chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.111298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.095021 restraints weight = 4657.108| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.25 r_work: 0.4021 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3745 Z= 0.206 Angle : 0.672 7.340 5000 Z= 0.329 Chirality : 0.053 0.132 555 Planarity : 0.003 0.024 640 Dihedral : 6.629 43.347 505 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 7.86 % Allowed : 9.76 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.31), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 349 TYR 0.007 0.002 TYR C 310 PHE 0.007 0.001 PHE C 378 HIS 0.001 0.000 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 ( 3745) covalent geometry : angle 0.67244 / 0.33 ( 5000) hydrogen bonds : bond 0.02169 / 1.53 ( 86) hydrogen bonds : angle 4.97810 / 3.50 ( 258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.088 Fit side-chains REVERT: A 264 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: A 369 LYS cc_start: 0.8193 (mttt) cc_final: 0.7840 (mtpt) REVERT: B 349 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7569 (mtt-85) REVERT: B 359 ASN cc_start: 0.7730 (t0) cc_final: 0.7214 (t0) REVERT: C 266 LEU cc_start: 0.8211 (mp) cc_final: 0.7888 (tt) REVERT: C 359 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6598 (t0) REVERT: D 264 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: D 314 ASP cc_start: 0.8781 (t0) cc_final: 0.8337 (t0) REVERT: D 316 SER cc_start: 0.9074 (p) cc_final: 0.8780 (p) REVERT: D 325 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8703 (tm) REVERT: E 264 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: E 266 LEU cc_start: 0.8228 (mp) cc_final: 0.7917 (tt) REVERT: E 369 LYS cc_start: 0.8290 (mttt) cc_final: 0.7976 (mtpt) outliers start: 33 outliers final: 21 residues processed: 91 average time/residue: 0.4392 time to fit residues: 41.2459 Evaluate side-chains 106 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 0.0980 chunk 40 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.112074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.095378 restraints weight = 4615.203| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.29 r_work: 0.4042 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3745 Z= 0.165 Angle : 0.638 7.476 5000 Z= 0.309 Chirality : 0.051 0.126 555 Planarity : 0.003 0.024 640 Dihedral : 6.537 43.306 505 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 7.14 % Allowed : 10.24 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.31), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.006 0.002 TYR C 310 PHE 0.006 0.001 PHE A 346 HIS 0.001 0.000 HIS E 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 3745) covalent geometry : angle 0.63760 / 0.31 ( 5000) hydrogen bonds : bond 0.01963 / 1.38 ( 86) hydrogen bonds : angle 4.82756 / 3.41 ( 258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.089 Fit side-chains REVERT: A 264 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: A 369 LYS cc_start: 0.8201 (mttt) cc_final: 0.7865 (mtpt) REVERT: B 349 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7611 (mtt-85) REVERT: C 266 LEU cc_start: 0.8209 (mp) cc_final: 0.7920 (tt) REVERT: C 359 ASN cc_start: 0.7167 (OUTLIER) cc_final: 0.6546 (t0) REVERT: C 369 LYS cc_start: 0.8586 (mttt) cc_final: 0.8378 (mtpt) REVERT: D 264 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: D 314 ASP cc_start: 0.8791 (t0) cc_final: 0.8370 (t0) REVERT: D 316 SER cc_start: 0.9089 (p) cc_final: 0.8813 (p) REVERT: D 325 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8727 (tm) REVERT: D 379 ARG cc_start: 0.5522 (OUTLIER) cc_final: 0.3886 (tpm-80) REVERT: E 266 LEU cc_start: 0.8190 (mp) cc_final: 0.7946 (tt) REVERT: E 369 LYS cc_start: 0.8309 (mttt) cc_final: 0.8014 (mtpt) outliers start: 30 outliers final: 18 residues processed: 87 average time/residue: 0.5287 time to fit residues: 47.4035 Evaluate side-chains 103 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 41 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.110424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.093996 restraints weight = 4656.261| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 2.33 r_work: 0.4007 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3745 Z= 0.246 Angle : 0.703 7.996 5000 Z= 0.343 Chirality : 0.054 0.132 555 Planarity : 0.004 0.025 640 Dihedral : 6.668 43.941 505 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 6.90 % Allowed : 10.71 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.31), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 379 TYR 0.007 0.002 TYR C 310 PHE 0.009 0.002 PHE C 378 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.25 ( 3745) covalent geometry : angle 0.70272 / 0.34 ( 5000) hydrogen bonds : bond 0.02227 / 1.57 ( 86) hydrogen bonds : angle 4.87803 / 3.45 ( 258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.201 Fit side-chains REVERT: A 264 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: A 369 LYS cc_start: 0.8220 (mttt) cc_final: 0.7833 (mtpt) REVERT: B 349 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7562 (mtt-85) REVERT: B 359 ASN cc_start: 0.7756 (t0) cc_final: 0.7242 (t0) REVERT: C 266 LEU cc_start: 0.8224 (mp) cc_final: 0.7922 (tt) REVERT: C 359 ASN cc_start: 0.7275 (OUTLIER) cc_final: 0.6682 (t0) REVERT: C 369 LYS cc_start: 0.8606 (mttt) cc_final: 0.8375 (mtpt) REVERT: D 264 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: D 314 ASP cc_start: 0.8797 (t0) cc_final: 0.8350 (t0) REVERT: D 316 SER cc_start: 0.9076 (p) cc_final: 0.8780 (p) REVERT: D 325 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8730 (tm) REVERT: D 379 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.3871 (tpm-80) REVERT: E 264 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: E 266 LEU cc_start: 0.8198 (mp) cc_final: 0.7928 (tt) REVERT: E 369 LYS cc_start: 0.8312 (mttt) cc_final: 0.7992 (mtpt) outliers start: 29 outliers final: 20 residues processed: 86 average time/residue: 0.5401 time to fit residues: 47.9422 Evaluate side-chains 106 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.112203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.095649 restraints weight = 4599.967| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.29 r_work: 0.4048 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3952 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3745 Z= 0.157 Angle : 0.627 7.828 5000 Z= 0.303 Chirality : 0.051 0.128 555 Planarity : 0.003 0.023 640 Dihedral : 6.501 43.565 505 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 7.14 % Allowed : 10.95 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.32), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.006 0.002 TYR C 310 PHE 0.009 0.001 PHE A 346 HIS 0.001 0.000 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 3745) covalent geometry : angle 0.62722 / 0.30 ( 5000) hydrogen bonds : bond 0.01969 / 1.39 ( 86) hydrogen bonds : angle 4.74114 / 3.38 ( 258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.148 Fit side-chains REVERT: A 264 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: A 369 LYS cc_start: 0.8183 (mttt) cc_final: 0.7788 (mtpt) REVERT: B 349 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7589 (mtt-85) REVERT: B 359 ASN cc_start: 0.7697 (t0) cc_final: 0.7062 (t0) REVERT: B 369 LYS cc_start: 0.8354 (mttt) cc_final: 0.8004 (mtpt) REVERT: C 266 LEU cc_start: 0.8211 (mp) cc_final: 0.7905 (tt) REVERT: C 359 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6537 (t0) REVERT: C 369 LYS cc_start: 0.8589 (mttt) cc_final: 0.8363 (mtpt) REVERT: D 264 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: D 314 ASP cc_start: 0.8781 (t0) cc_final: 0.8364 (t0) REVERT: D 316 SER cc_start: 0.9088 (p) cc_final: 0.8810 (p) REVERT: D 325 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8720 (tm) REVERT: D 379 ARG cc_start: 0.5519 (OUTLIER) cc_final: 0.3814 (tpm-80) REVERT: E 266 LEU cc_start: 0.8191 (mp) cc_final: 0.7938 (tt) REVERT: E 314 ASP cc_start: 0.8453 (t0) cc_final: 0.8020 (t70) REVERT: E 369 LYS cc_start: 0.8302 (mttt) cc_final: 0.7991 (mtpt) outliers start: 30 outliers final: 20 residues processed: 89 average time/residue: 0.5516 time to fit residues: 50.6495 Evaluate side-chains 106 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.115720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.098912 restraints weight = 4537.770| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.34 r_work: 0.4089 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3995 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3745 Z= 0.104 Angle : 0.592 7.699 5000 Z= 0.280 Chirality : 0.050 0.125 555 Planarity : 0.003 0.026 640 Dihedral : 6.279 43.357 505 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.24 % Allowed : 12.86 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.32), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.005 0.001 TYR B 310 PHE 0.004 0.001 PHE A 378 HIS 0.001 0.000 HIS E 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.10 ( 3745) covalent geometry : angle 0.59197 / 0.28 ( 5000) hydrogen bonds : bond 0.01627 / 1.16 ( 86) hydrogen bonds : angle 4.50802 / 3.22 ( 258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.153 Fit side-chains REVERT: A 369 LYS cc_start: 0.8140 (mttt) cc_final: 0.7786 (mtpt) REVERT: B 349 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7612 (mtt-85) REVERT: B 359 ASN cc_start: 0.7553 (t0) cc_final: 0.6967 (t0) REVERT: B 369 LYS cc_start: 0.8351 (mttt) cc_final: 0.8001 (mtpt) REVERT: C 258 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8678 (t) REVERT: C 359 ASN cc_start: 0.6683 (OUTLIER) cc_final: 0.6090 (t0) REVERT: C 369 LYS cc_start: 0.8579 (mttt) cc_final: 0.8362 (mtpt) REVERT: D 314 ASP cc_start: 0.8808 (t0) cc_final: 0.8535 (t0) REVERT: D 325 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8726 (tm) REVERT: D 379 ARG cc_start: 0.5467 (OUTLIER) cc_final: 0.3803 (tpm-80) REVERT: E 266 LEU cc_start: 0.8170 (mp) cc_final: 0.7915 (tt) REVERT: E 314 ASP cc_start: 0.8400 (t0) cc_final: 0.7956 (t70) REVERT: E 369 LYS cc_start: 0.8306 (mttt) cc_final: 0.8001 (mtpt) outliers start: 22 outliers final: 11 residues processed: 87 average time/residue: 0.5286 time to fit residues: 47.4739 Evaluate side-chains 94 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.109958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.093606 restraints weight = 4587.978| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.30 r_work: 0.4005 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3745 Z= 0.267 Angle : 0.733 8.151 5000 Z= 0.356 Chirality : 0.054 0.128 555 Planarity : 0.004 0.027 640 Dihedral : 6.625 44.802 505 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.48 % Allowed : 13.33 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.32), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 379 TYR 0.008 0.003 TYR C 310 PHE 0.010 0.002 PHE C 378 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.27 ( 3745) covalent geometry : angle 0.73333 / 0.36 ( 5000) hydrogen bonds : bond 0.02197 / 1.54 ( 86) hydrogen bonds : angle 4.77638 / 3.39 ( 258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2286.74 seconds wall clock time: 39 minutes 47.81 seconds (2387.81 seconds total)