Starting phenix.real_space_refine on Fri Oct 10 11:08:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8f_18253/10_2025/8q8f_18253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8f_18253/10_2025/8q8f_18253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q8f_18253/10_2025/8q8f_18253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8f_18253/10_2025/8q8f_18253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q8f_18253/10_2025/8q8f_18253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8f_18253/10_2025/8q8f_18253.map" } resolution = 2.93 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.04, per 1000 atoms: 0.30 Number of scatterers: 3468 At special positions: 0 Unit cell: (111.24, 124.424, 36.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 648 8.00 N 642 7.00 C 2172 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: 0.28 Conformation dependent library (CDL) restraints added in 101.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 47.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.520A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL E 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.853A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.441A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.441A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.302A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.614A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.267A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.409A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.357A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.379A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N LYS E 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS A 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR E 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.492A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.783A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 321 removed outlier: 6.245A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.653A pdb=" N HIS B 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 336 through 340 removed outlier: 6.410A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 343 through 348 removed outlier: 6.831A pdb=" N ASP D 348 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N LYS B 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N PHE F 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N ASP F 348 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LYS B 347 " --> pdb=" O ASP F 348 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 351 through 354 removed outlier: 6.744A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.580A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 378 removed outlier: 6.410A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 159 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: 0.45 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1030 1.33 - 1.45: 405 1.45 - 1.58: 2081 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 3522 Sorted by residual: bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.24e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.49e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.40e+00 bond pdb=" CZ ARG B 379 " pdb=" NH2 ARG B 379 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.11e+00 bond pdb=" CZ ARG D 379 " pdb=" NH2 ARG D 379 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.91e+00 ... (remaining 3517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 3406 1.92 - 3.83: 1137 3.83 - 5.75: 150 5.75 - 7.66: 12 7.66 - 9.58: 5 Bond angle restraints: 4710 Sorted by residual: angle pdb=" O CYS D 322 " pdb=" C CYS D 322 " pdb=" N GLY D 323 " ideal model delta sigma weight residual 123.25 115.67 7.58 1.14e+00 7.69e-01 4.43e+01 angle pdb=" O CYS B 322 " pdb=" C CYS B 322 " pdb=" N GLY B 323 " ideal model delta sigma weight residual 123.17 115.44 7.73 1.21e+00 6.83e-01 4.08e+01 angle pdb=" CA CYS D 322 " pdb=" C CYS D 322 " pdb=" N GLY D 323 " ideal model delta sigma weight residual 115.36 124.74 -9.38 1.48e+00 4.57e-01 4.01e+01 angle pdb=" CA CYS B 322 " pdb=" C CYS B 322 " pdb=" N GLY B 323 " ideal model delta sigma weight residual 115.36 124.94 -9.58 1.53e+00 4.27e-01 3.92e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.35 -5.55 1.00e+00 1.00e+00 3.08e+01 ... (remaining 4705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.81: 1899 12.81 - 25.62: 176 25.62 - 38.43: 42 38.43 - 51.24: 12 51.24 - 64.05: 13 Dihedral angle restraints: 2142 sinusoidal: 894 harmonic: 1248 Sorted by residual: dihedral pdb=" CA SER A 341 " pdb=" C SER A 341 " pdb=" N GLU A 342 " pdb=" CA GLU A 342 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA SER C 341 " pdb=" C SER C 341 " pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA LEU C 325 " pdb=" C LEU C 325 " pdb=" N GLY C 326 " pdb=" CA GLY C 326 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 2139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 275 0.061 - 0.122: 188 0.122 - 0.183: 52 0.183 - 0.243: 9 0.243 - 0.304: 4 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS B 347 " pdb=" N LYS B 347 " pdb=" C LYS B 347 " pdb=" CB LYS B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA LYS F 331 " pdb=" N LYS F 331 " pdb=" C LYS F 331 " pdb=" CB LYS F 331 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 525 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.161 2.00e-02 2.50e+03 9.29e-02 1.73e+02 pdb=" CG TYR E 310 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.075 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.064 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.059 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.112 2.00e-02 2.50e+03 6.20e-02 7.69e+01 pdb=" CG TYR A 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.085 2.00e-02 2.50e+03 4.92e-02 4.84e+01 pdb=" CG TYR B 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.081 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1592 2.98 - 3.46: 2729 3.46 - 3.94: 5654 3.94 - 4.42: 5646 4.42 - 4.90: 10814 Nonbonded interactions: 26435 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.504 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.505 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.520 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.528 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.556 3.040 ... (remaining 26430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.240 Find NCS groups from input model: 0.080 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 0.037 3522 Z= 0.691 Angle : 1.823 9.579 4710 Z= 1.219 Chirality : 0.082 0.304 528 Planarity : 0.010 0.093 600 Dihedral : 12.076 64.052 1350 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.76 % Allowed : 1.77 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 aren not related in a simple way. whole: -1.60 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 349 TYR 0.161 0.039 TYR E 310 PHE 0.032 0.011 PHE B 346 HIS 0.018 0.003 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.01087 ( 3522) covalent geometry : angle 1.82302 ( 4710) hydrogen bonds : bond 0.05670 ( 54) hydrogen bonds : angle 7.51606 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8664 (p) cc_final: 0.8446 (p) REVERT: A 321 LYS cc_start: 0.7354 (mttt) cc_final: 0.6833 (tttm) REVERT: A 338 GLU cc_start: 0.7668 (tt0) cc_final: 0.7362 (mt-10) REVERT: A 343 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7459 (mtpp) REVERT: A 375 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7600 (tttt) REVERT: B 321 LYS cc_start: 0.7366 (mttt) cc_final: 0.7128 (mttm) REVERT: B 369 LYS cc_start: 0.7593 (tttt) cc_final: 0.7187 (tttt) REVERT: C 314 ASP cc_start: 0.8341 (t0) cc_final: 0.7734 (t0) REVERT: C 321 LYS cc_start: 0.8086 (mttt) cc_final: 0.7591 (tttm) REVERT: C 375 LYS cc_start: 0.8500 (ttmt) cc_final: 0.8156 (ttmt) REVERT: D 310 TYR cc_start: 0.8866 (t80) cc_final: 0.8620 (t80) REVERT: D 316 SER cc_start: 0.8442 (p) cc_final: 0.8225 (p) REVERT: D 321 LYS cc_start: 0.7992 (mttt) cc_final: 0.7697 (mttm) REVERT: E 321 LYS cc_start: 0.7487 (mttt) cc_final: 0.6983 (tttt) REVERT: E 370 LYS cc_start: 0.8138 (tttt) cc_final: 0.7936 (tttm) REVERT: E 372 GLU cc_start: 0.8334 (tt0) cc_final: 0.8110 (tt0) REVERT: F 321 LYS cc_start: 0.7752 (mttt) cc_final: 0.7520 (mtmm) outliers start: 3 outliers final: 0 residues processed: 139 average time/residue: 0.6468 time to fit residues: 91.9261 Evaluate side-chains 109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 336 GLN C 359 ASN C 362 HIS E 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.129638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.110150 restraints weight = 4601.260| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.91 r_work: 0.3579 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3522 Z= 0.139 Angle : 0.656 6.961 4710 Z= 0.323 Chirality : 0.050 0.149 528 Planarity : 0.003 0.029 600 Dihedral : 6.024 20.686 468 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.52 % Allowed : 15.66 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 aren not related in a simple way. whole: -1.67 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.020 0.003 TYR F 310 PHE 0.015 0.002 PHE E 378 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 3522) covalent geometry : angle 0.65562 ( 4710) hydrogen bonds : bond 0.01721 ( 54) hydrogen bonds : angle 5.31770 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8244 (mttt) cc_final: 0.7958 (tttm) REVERT: A 343 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7838 (tttt) REVERT: A 379 ARG cc_start: 0.7328 (mmm-85) cc_final: 0.7089 (mmt90) REVERT: B 321 LYS cc_start: 0.8445 (mttt) cc_final: 0.8215 (mttm) REVERT: B 342 GLU cc_start: 0.5975 (pm20) cc_final: 0.5443 (tp30) REVERT: B 369 LYS cc_start: 0.8569 (tttt) cc_final: 0.8326 (tttp) REVERT: C 343 LYS cc_start: 0.8425 (mtpp) cc_final: 0.8047 (tttt) REVERT: D 321 LYS cc_start: 0.8567 (mttt) cc_final: 0.8352 (mttm) REVERT: E 321 LYS cc_start: 0.8239 (mttt) cc_final: 0.8020 (tttt) REVERT: E 343 LYS cc_start: 0.8224 (mtpp) cc_final: 0.7857 (tttt) REVERT: E 349 ARG cc_start: 0.7322 (mtm180) cc_final: 0.6791 (mpt90) REVERT: E 369 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8316 (mttt) REVERT: E 379 ARG cc_start: 0.7120 (mtt180) cc_final: 0.6330 (mmp80) outliers start: 6 outliers final: 1 residues processed: 115 average time/residue: 0.7248 time to fit residues: 85.0451 Evaluate side-chains 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 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 = 0.3891 r_free = 0.3891 target = 0.129054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.108551 restraints weight = 4659.474| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.92 r_work: 0.3552 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3522 Z= 0.161 Angle : 0.638 7.964 4710 Z= 0.310 Chirality : 0.049 0.123 528 Planarity : 0.003 0.026 600 Dihedral : 5.580 19.315 468 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.03 % Allowed : 21.21 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 aren not related in a simple way. whole: -1.67 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.016 0.003 TYR A 310 PHE 0.011 0.002 PHE E 378 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3522) covalent geometry : angle 0.63796 ( 4710) hydrogen bonds : bond 0.01665 ( 54) hydrogen bonds : angle 4.65436 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8222 (mttt) cc_final: 0.7875 (tttt) REVERT: A 343 LYS cc_start: 0.8249 (mtmt) cc_final: 0.7926 (tttt) REVERT: B 342 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5707 (tp30) REVERT: B 369 LYS cc_start: 0.8698 (tttt) cc_final: 0.8400 (tppt) REVERT: C 321 LYS cc_start: 0.8568 (mttt) cc_final: 0.8267 (tttm) REVERT: C 343 LYS cc_start: 0.8294 (mtpp) cc_final: 0.8031 (tttt) REVERT: D 321 LYS cc_start: 0.8770 (mttt) cc_final: 0.8534 (mttm) REVERT: D 379 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.4530 (mtm180) REVERT: E 321 LYS cc_start: 0.8221 (mttt) cc_final: 0.7976 (tttm) REVERT: E 343 LYS cc_start: 0.8320 (mtpp) cc_final: 0.7994 (tttt) REVERT: E 348 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7797 (p0) REVERT: E 349 ARG cc_start: 0.7339 (mtm180) cc_final: 0.6896 (mpt180) REVERT: E 369 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8413 (mttt) REVERT: E 379 ARG cc_start: 0.7540 (mtt180) cc_final: 0.6873 (mmp80) outliers start: 12 outliers final: 4 residues processed: 103 average time/residue: 0.7095 time to fit residues: 74.6096 Evaluate side-chains 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 373 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 330 HIS ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN F 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.124653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104989 restraints weight = 4703.049| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.88 r_work: 0.3502 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3522 Z= 0.192 Angle : 0.644 9.232 4710 Z= 0.311 Chirality : 0.048 0.126 528 Planarity : 0.003 0.027 600 Dihedral : 5.513 21.405 468 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.55 % Allowed : 22.22 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 aren not related in a simple way. whole: -1.82 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.017 0.003 TYR A 310 PHE 0.008 0.002 PHE E 378 HIS 0.005 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 3522) covalent geometry : angle 0.64383 ( 4710) hydrogen bonds : bond 0.01564 ( 54) hydrogen bonds : angle 4.43974 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.111 Fit side-chains REVERT: A 321 LYS cc_start: 0.8399 (mttt) cc_final: 0.7981 (tttm) REVERT: A 343 LYS cc_start: 0.8346 (mtmt) cc_final: 0.7882 (tttt) REVERT: B 369 LYS cc_start: 0.8678 (tttt) cc_final: 0.8465 (tppt) REVERT: C 321 LYS cc_start: 0.8578 (mttt) cc_final: 0.8210 (tttm) REVERT: C 343 LYS cc_start: 0.8359 (mtpp) cc_final: 0.8098 (tttt) REVERT: D 349 ARG cc_start: 0.7605 (mtm-85) cc_final: 0.7127 (mtp85) REVERT: D 379 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.5007 (mtm180) REVERT: E 321 LYS cc_start: 0.8286 (mttt) cc_final: 0.8022 (tttm) REVERT: E 343 LYS cc_start: 0.8336 (mtpp) cc_final: 0.8038 (tttt) REVERT: E 348 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7854 (p0) REVERT: E 349 ARG cc_start: 0.7433 (mtm180) cc_final: 0.6981 (mpt90) REVERT: E 369 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8403 (mttt) REVERT: E 379 ARG cc_start: 0.7814 (mtt180) cc_final: 0.6900 (tpm170) outliers start: 18 outliers final: 6 residues processed: 100 average time/residue: 0.7546 time to fit residues: 76.9640 Evaluate side-chains 97 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.128655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.109150 restraints weight = 4554.659| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.81 r_work: 0.3542 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3522 Z= 0.144 Angle : 0.600 9.467 4710 Z= 0.288 Chirality : 0.048 0.117 528 Planarity : 0.003 0.022 600 Dihedral : 5.213 18.297 468 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.79 % Allowed : 22.47 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 aren not related in a simple way. whole: -1.87 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.013 0.002 TYR A 310 PHE 0.007 0.001 PHE E 378 HIS 0.003 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3522) covalent geometry : angle 0.60023 ( 4710) hydrogen bonds : bond 0.01348 ( 54) hydrogen bonds : angle 4.21028 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.160 Fit side-chains REVERT: A 321 LYS cc_start: 0.8380 (mttt) cc_final: 0.7981 (tttt) REVERT: A 343 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7922 (tttt) REVERT: B 351 GLN cc_start: 0.8040 (tt0) cc_final: 0.7182 (mp10) REVERT: B 369 LYS cc_start: 0.8703 (tttt) cc_final: 0.8493 (ttmt) REVERT: C 321 LYS cc_start: 0.8508 (mttt) cc_final: 0.8160 (tttm) REVERT: C 343 LYS cc_start: 0.8331 (mtpp) cc_final: 0.8102 (tttt) REVERT: D 321 LYS cc_start: 0.8728 (mttt) cc_final: 0.8466 (mttm) REVERT: D 349 ARG cc_start: 0.7593 (mtm-85) cc_final: 0.7139 (mtp85) REVERT: D 379 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.5527 (mtm-85) REVERT: E 321 LYS cc_start: 0.8271 (mttt) cc_final: 0.8025 (tttm) REVERT: E 343 LYS cc_start: 0.8329 (mtpp) cc_final: 0.8043 (tttt) REVERT: E 348 ASP cc_start: 0.8048 (p0) cc_final: 0.7827 (p0) REVERT: E 349 ARG cc_start: 0.7364 (mtm180) cc_final: 0.6918 (mpt90) REVERT: E 369 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8431 (mttt) REVERT: E 379 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7373 (mmp80) REVERT: F 379 ARG cc_start: 0.5856 (OUTLIER) cc_final: 0.4127 (mmp-170) outliers start: 15 outliers final: 6 residues processed: 96 average time/residue: 0.7663 time to fit residues: 74.9955 Evaluate side-chains 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 359 ASN C 336 GLN D 336 GLN F 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.121576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.101625 restraints weight = 4778.933| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.89 r_work: 0.3454 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3522 Z= 0.292 Angle : 0.697 9.884 4710 Z= 0.341 Chirality : 0.048 0.137 528 Planarity : 0.004 0.049 600 Dihedral : 5.658 23.003 468 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.29 % Allowed : 22.47 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 aren not related in a simple way. whole: -2.02 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 379 TYR 0.020 0.003 TYR A 310 PHE 0.010 0.002 PHE F 378 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00677 ( 3522) covalent geometry : angle 0.69749 ( 4710) hydrogen bonds : bond 0.01809 ( 54) hydrogen bonds : angle 4.38287 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.131 Fit side-chains REVERT: A 321 LYS cc_start: 0.8428 (mttt) cc_final: 0.7989 (ttpt) REVERT: A 343 LYS cc_start: 0.8320 (mtmt) cc_final: 0.7815 (tttt) REVERT: A 379 ARG cc_start: 0.7736 (mmm-85) cc_final: 0.7367 (mmt90) REVERT: B 351 GLN cc_start: 0.8065 (tt0) cc_final: 0.7199 (mp10) REVERT: B 369 LYS cc_start: 0.8756 (tttt) cc_final: 0.8534 (ttmt) REVERT: C 321 LYS cc_start: 0.8683 (mttt) cc_final: 0.8265 (ttpp) REVERT: C 343 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8125 (tttt) REVERT: D 321 LYS cc_start: 0.8948 (mttt) cc_final: 0.8702 (mttm) REVERT: D 379 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.5372 (mtm-85) REVERT: E 321 LYS cc_start: 0.8326 (mttt) cc_final: 0.8020 (tttm) REVERT: E 343 LYS cc_start: 0.8375 (mtpp) cc_final: 0.8055 (tttt) REVERT: E 348 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7964 (p0) REVERT: E 349 ARG cc_start: 0.7580 (mtm180) cc_final: 0.6934 (mpt90) REVERT: E 369 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8466 (mttt) REVERT: E 379 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7187 (tpm170) REVERT: F 379 ARG cc_start: 0.5566 (OUTLIER) cc_final: 0.3402 (mmp-170) outliers start: 17 outliers final: 6 residues processed: 95 average time/residue: 0.7694 time to fit residues: 74.5928 Evaluate side-chains 98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.127948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.108533 restraints weight = 4542.456| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.83 r_work: 0.3546 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3522 Z= 0.123 Angle : 0.585 9.969 4710 Z= 0.278 Chirality : 0.048 0.117 528 Planarity : 0.002 0.020 600 Dihedral : 5.100 18.391 468 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.28 % Allowed : 22.73 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 aren not related in a simple way. whole: -1.97 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.010 0.002 TYR F 310 PHE 0.006 0.001 PHE E 378 HIS 0.002 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3522) covalent geometry : angle 0.58467 ( 4710) hydrogen bonds : bond 0.01322 ( 54) hydrogen bonds : angle 4.07868 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.156 Fit side-chains REVERT: A 321 LYS cc_start: 0.8367 (mttt) cc_final: 0.7960 (tttt) REVERT: A 343 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7894 (tttt) REVERT: A 379 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.7354 (mtp180) REVERT: B 351 GLN cc_start: 0.8024 (tt0) cc_final: 0.7251 (mp10) REVERT: B 353 LYS cc_start: 0.8577 (mtpt) cc_final: 0.7815 (ttpt) REVERT: B 369 LYS cc_start: 0.8730 (tttt) cc_final: 0.8521 (ttmt) REVERT: C 321 LYS cc_start: 0.8508 (mttt) cc_final: 0.8128 (tttm) REVERT: C 343 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8137 (tttt) REVERT: D 379 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.5773 (mtm-85) REVERT: E 311 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.7781 (tppt) REVERT: E 321 LYS cc_start: 0.8279 (mttt) cc_final: 0.8020 (tttm) REVERT: E 343 LYS cc_start: 0.8323 (mtpp) cc_final: 0.8082 (tttt) REVERT: E 348 ASP cc_start: 0.8073 (p0) cc_final: 0.7870 (p0) REVERT: E 349 ARG cc_start: 0.7551 (mtm180) cc_final: 0.6920 (mpt90) REVERT: E 369 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8462 (mtpt) REVERT: E 379 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7464 (mmp80) REVERT: F 379 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.4154 (mmp-170) outliers start: 13 outliers final: 5 residues processed: 91 average time/residue: 0.7969 time to fit residues: 73.9751 Evaluate side-chains 94 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.4980 chunk 12 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.128516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.109181 restraints weight = 4611.822| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.81 r_work: 0.3531 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3522 Z= 0.144 Angle : 0.589 10.069 4710 Z= 0.279 Chirality : 0.047 0.115 528 Planarity : 0.002 0.021 600 Dihedral : 5.042 18.839 468 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.54 % Allowed : 23.23 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 aren not related in a simple way. whole: -1.97 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.011 0.002 TYR A 310 PHE 0.006 0.001 PHE F 378 HIS 0.003 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3522) covalent geometry : angle 0.58909 ( 4710) hydrogen bonds : bond 0.01365 ( 54) hydrogen bonds : angle 3.95539 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.150 Fit side-chains REVERT: A 321 LYS cc_start: 0.8389 (mttt) cc_final: 0.7992 (tttt) REVERT: A 343 LYS cc_start: 0.8379 (mtmt) cc_final: 0.7915 (tttt) REVERT: A 379 ARG cc_start: 0.7752 (mmm-85) cc_final: 0.7371 (mtp180) REVERT: B 351 GLN cc_start: 0.8054 (tt0) cc_final: 0.7277 (mp10) REVERT: B 353 LYS cc_start: 0.8582 (mtpt) cc_final: 0.7796 (ttpt) REVERT: B 369 LYS cc_start: 0.8754 (tttt) cc_final: 0.8547 (ttmt) REVERT: C 321 LYS cc_start: 0.8545 (mttt) cc_final: 0.8172 (tttm) REVERT: C 343 LYS cc_start: 0.8375 (mtpp) cc_final: 0.8132 (tttt) REVERT: D 379 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.5705 (mtm-85) REVERT: E 311 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.7759 (tppt) REVERT: E 321 LYS cc_start: 0.8303 (mttt) cc_final: 0.8067 (tttm) REVERT: E 343 LYS cc_start: 0.8349 (mtpp) cc_final: 0.8111 (tttt) REVERT: E 348 ASP cc_start: 0.8135 (p0) cc_final: 0.7900 (p0) REVERT: E 349 ARG cc_start: 0.7552 (mtm180) cc_final: 0.6923 (mpt90) REVERT: E 369 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8498 (mtpt) REVERT: E 379 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7431 (mmp80) REVERT: F 379 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.3770 (mmp-170) outliers start: 14 outliers final: 6 residues processed: 91 average time/residue: 0.7897 time to fit residues: 73.3310 Evaluate side-chains 95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.0370 chunk 16 optimal weight: 0.0980 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 overall best weight: 3.4264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.123312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.103302 restraints weight = 4699.169| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.91 r_work: 0.3475 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3522 Z= 0.223 Angle : 0.644 10.412 4710 Z= 0.310 Chirality : 0.048 0.120 528 Planarity : 0.003 0.037 600 Dihedral : 5.323 19.939 468 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.03 % Allowed : 24.24 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 aren not related in a simple way. whole: -2.04 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 379 TYR 0.016 0.003 TYR A 310 PHE 0.008 0.002 PHE F 378 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 3522) covalent geometry : angle 0.64417 ( 4710) hydrogen bonds : bond 0.01641 ( 54) hydrogen bonds : angle 4.13432 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.165 Fit side-chains REVERT: A 321 LYS cc_start: 0.8412 (mttt) cc_final: 0.7977 (ttpt) REVERT: A 343 LYS cc_start: 0.8451 (mtmt) cc_final: 0.7890 (tttt) REVERT: A 369 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8296 (mtmm) REVERT: A 379 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.7376 (mtp180) REVERT: B 351 GLN cc_start: 0.8055 (tt0) cc_final: 0.7259 (mp10) REVERT: B 369 LYS cc_start: 0.8765 (tttt) cc_final: 0.8544 (ttmt) REVERT: C 321 LYS cc_start: 0.8613 (mttt) cc_final: 0.8214 (ttpp) REVERT: C 343 LYS cc_start: 0.8421 (mtpp) cc_final: 0.8174 (tttt) REVERT: D 379 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.5502 (mtm-85) REVERT: E 321 LYS cc_start: 0.8381 (mttt) cc_final: 0.8082 (tttm) REVERT: E 343 LYS cc_start: 0.8397 (mtpp) cc_final: 0.8130 (tttt) REVERT: E 348 ASP cc_start: 0.8189 (p0) cc_final: 0.7951 (p0) REVERT: E 349 ARG cc_start: 0.7614 (mtm180) cc_final: 0.6891 (mpt90) REVERT: E 369 LYS cc_start: 0.8859 (mtmt) cc_final: 0.8502 (mtpt) REVERT: E 379 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7259 (tpm170) REVERT: F 379 ARG cc_start: 0.5850 (OUTLIER) cc_final: 0.3668 (mmp-170) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 0.8425 time to fit residues: 73.8253 Evaluate side-chains 93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.122910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.102862 restraints weight = 4753.849| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.92 r_work: 0.3470 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3522 Z= 0.239 Angle : 0.653 10.400 4710 Z= 0.315 Chirality : 0.047 0.124 528 Planarity : 0.003 0.040 600 Dihedral : 5.387 21.191 468 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.03 % Allowed : 24.49 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 aren not related in a simple way. whole: -2.08 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 379 TYR 0.016 0.003 TYR A 310 PHE 0.009 0.002 PHE F 378 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 3522) covalent geometry : angle 0.65297 ( 4710) hydrogen bonds : bond 0.01728 ( 54) hydrogen bonds : angle 4.24253 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.111 Fit side-chains REVERT: A 321 LYS cc_start: 0.8440 (mttt) cc_final: 0.8000 (ttpt) REVERT: A 343 LYS cc_start: 0.8431 (mtmt) cc_final: 0.7866 (tttt) REVERT: A 369 LYS cc_start: 0.8758 (mtpt) cc_final: 0.8342 (mtmm) REVERT: A 379 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7370 (mtp180) REVERT: B 351 GLN cc_start: 0.8030 (tt0) cc_final: 0.7244 (mp10) REVERT: B 369 LYS cc_start: 0.8772 (tttt) cc_final: 0.8552 (ttmt) REVERT: C 321 LYS cc_start: 0.8637 (mttt) cc_final: 0.8246 (ttpp) REVERT: C 343 LYS cc_start: 0.8470 (mtpp) cc_final: 0.8187 (tttt) REVERT: D 379 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.5529 (mtm-85) REVERT: E 321 LYS cc_start: 0.8416 (mttt) cc_final: 0.8141 (tttm) REVERT: E 343 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8092 (tttt) REVERT: E 348 ASP cc_start: 0.8163 (p0) cc_final: 0.7943 (p0) REVERT: E 349 ARG cc_start: 0.7718 (mtm180) cc_final: 0.6950 (mmt-90) REVERT: E 369 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8515 (mtpt) REVERT: E 379 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7247 (tpm170) REVERT: F 379 ARG cc_start: 0.5714 (OUTLIER) cc_final: 0.3545 (mmp-170) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.7645 time to fit residues: 68.6230 Evaluate side-chains 94 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.127287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.107821 restraints weight = 4522.701| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.83 r_work: 0.3530 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3522 Z= 0.140 Angle : 0.595 10.102 4710 Z= 0.280 Chirality : 0.047 0.118 528 Planarity : 0.002 0.021 600 Dihedral : 5.041 19.692 468 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.27 % Allowed : 25.51 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 aren not related in a simple way. whole: -2.03 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.010 0.002 TYR A 310 PHE 0.006 0.001 PHE F 378 HIS 0.003 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3522) covalent geometry : angle 0.59534 ( 4710) hydrogen bonds : bond 0.01433 ( 54) hydrogen bonds : angle 4.02599 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1927.64 seconds wall clock time: 33 minutes 37.10 seconds (2017.10 seconds total)