Starting phenix.real_space_refine on Tue Jan 14 19:05:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxo_45007/01_2025/9bxo_45007.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxo_45007/01_2025/9bxo_45007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bxo_45007/01_2025/9bxo_45007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxo_45007/01_2025/9bxo_45007.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxo_45007/01_2025/9bxo_45007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxo_45007/01_2025/9bxo_45007.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2202 2.51 5 N 648 2.21 5 O 672 1.98 5 H 3654 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7182 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1197 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1197 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1197 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1197 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1197 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1197 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 4.25, per 1000 atoms: 0.59 Number of scatterers: 7182 At special positions: 0 Unit cell: (135.942, 105.918, 37.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 672 8.00 N 648 7.00 C 2202 6.00 H 3654 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 767.2 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.746A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.646A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS C 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N SER E 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR C 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N CYS E 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS C 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.706A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN C 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ILE E 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS C 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 360 removed outlier: 6.352A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP C 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 377 removed outlier: 6.649A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU E 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 306 through 310 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.731A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 317 through 324 removed outlier: 6.421A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS D 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N SER F 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR D 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N CYS F 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS D 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N SER F 324 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY D 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 328 through 330 Processing sheet with id=AB5, first strand: chain 'B' and resid 336 through 340 Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 346 removed outlier: 6.822A pdb=" N LYS B 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N PHE D 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS D 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N PHE F 346 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP D 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.764A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN D 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ILE F 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS D 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.368A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP D 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR F 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE D 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 372 removed outlier: 6.606A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS D 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLU F 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE D 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 46 hydrogen bonds defined for protein. 138 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: 2.31 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3648 1.12 - 1.29: 600 1.29 - 1.46: 963 1.46 - 1.63: 2019 1.63 - 1.80: 6 Bond restraints: 7236 Sorted by residual: bond pdb=" ND2 ASN E 327 " pdb="HD21 ASN E 327 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" CD2 HIS D 330 " pdb=" HD2 HIS D 330 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N VAL C 350 " pdb=" H VAL C 350 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NE2 GLN D 336 " pdb="HE22 GLN D 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N LYS D 375 " pdb=" H LYS D 375 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 7231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 11166 2.47 - 4.94: 1542 4.94 - 7.41: 453 7.41 - 9.89: 21 9.89 - 12.36: 6 Bond angle restraints: 13188 Sorted by residual: angle pdb=" CB HIS E 330 " pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 131.20 124.69 6.51 1.30e+00 5.92e-01 2.51e+01 angle pdb=" CB HIS C 330 " pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 131.20 124.71 6.49 1.30e+00 5.92e-01 2.49e+01 angle pdb=" CB HIS A 330 " pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 131.20 124.72 6.48 1.30e+00 5.92e-01 2.48e+01 angle pdb=" CB HIS F 330 " pdb=" CG HIS F 330 " pdb=" CD2 HIS F 330 " ideal model delta sigma weight residual 131.20 124.73 6.47 1.30e+00 5.92e-01 2.48e+01 angle pdb=" CB HIS B 330 " pdb=" CG HIS B 330 " pdb=" CD2 HIS B 330 " ideal model delta sigma weight residual 131.20 124.74 6.46 1.30e+00 5.92e-01 2.47e+01 ... (remaining 13183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 3012 17.00 - 34.00: 135 34.00 - 51.00: 78 51.00 - 67.99: 93 67.99 - 84.99: 6 Dihedral angle restraints: 3324 sinusoidal: 1902 harmonic: 1422 Sorted by residual: dihedral pdb=" CA SER F 320 " pdb=" C SER F 320 " pdb=" N LYS F 321 " pdb=" CA LYS F 321 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER B 320 " pdb=" C SER B 320 " pdb=" N LYS B 321 " pdb=" CA LYS B 321 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA SER D 320 " pdb=" C SER D 320 " pdb=" N LYS D 321 " pdb=" CA LYS D 321 " ideal model delta harmonic sigma weight residual 180.00 161.12 18.88 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 3321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 269 0.057 - 0.114: 170 0.114 - 0.171: 74 0.171 - 0.228: 13 0.228 - 0.285: 8 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA GLU E 380 " pdb=" N GLU E 380 " pdb=" C GLU E 380 " pdb=" CB GLU E 380 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA GLU A 380 " pdb=" N GLU A 380 " pdb=" C GLU A 380 " pdb=" CB GLU A 380 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA GLU C 380 " pdb=" N GLU C 380 " pdb=" C GLU C 380 " pdb=" CB GLU C 380 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 531 not shown) Planarity restraints: 1056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 375 " -0.021 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" N LEU D 376 " 0.066 2.00e-02 2.50e+03 pdb=" CA LEU D 376 " -0.019 2.00e-02 2.50e+03 pdb=" H LEU D 376 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 375 " -0.021 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" N LEU B 376 " 0.066 2.00e-02 2.50e+03 pdb=" CA LEU B 376 " -0.019 2.00e-02 2.50e+03 pdb=" H LEU B 376 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 375 " -0.021 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" N LEU F 376 " 0.066 2.00e-02 2.50e+03 pdb=" CA LEU F 376 " -0.019 2.00e-02 2.50e+03 pdb=" H LEU F 376 " -0.026 2.00e-02 2.50e+03 ... (remaining 1053 not shown) Histogram of nonbonded interaction distances: 0.82 - 1.58: 38 1.58 - 2.33: 1422 2.33 - 3.09: 21448 3.09 - 3.84: 26900 3.84 - 4.60: 41780 Warning: very small nonbonded interaction distances. Nonbonded interactions: 91588 Sorted by model distance: nonbonded pdb=" HE1 PHE C 346 " pdb=" HD2 PHE E 346 " model vdw 0.820 2.100 nonbonded pdb=" HE1 PHE A 346 " pdb=" HD2 PHE C 346 " model vdw 0.821 2.100 nonbonded pdb=" HD2 HIS A 330 " pdb=" OG1 THR C 361 " model vdw 1.012 2.450 nonbonded pdb=" HD2 HIS C 330 " pdb=" OG1 THR E 361 " model vdw 1.030 2.450 nonbonded pdb=" HA LEU D 325 " pdb="HD11 LEU F 325 " model vdw 1.165 2.440 ... (remaining 91583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.650 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: 0.110 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.000 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 0.040 3582 Z= 0.751 Angle : 1.741 6.507 4794 Z= 1.146 Chirality : 0.085 0.285 534 Planarity : 0.007 0.039 618 Dihedral : 12.754 84.993 1380 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 23.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS D 362 PHE 0.014 0.006 PHE E 346 TYR 0.027 0.011 TYR E 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7791 (tt0) cc_final: 0.7555 (mt0) REVERT: B 317 LYS cc_start: 0.8536 (ptmt) cc_final: 0.8188 (ptpt) REVERT: B 321 LYS cc_start: 0.8436 (mttt) cc_final: 0.7971 (mttp) REVERT: B 336 GLN cc_start: 0.7550 (mt0) cc_final: 0.7293 (tt0) REVERT: C 369 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8451 (ttpt) REVERT: D 317 LYS cc_start: 0.8584 (ptmt) cc_final: 0.8164 (ptpt) REVERT: D 321 LYS cc_start: 0.8332 (mttt) cc_final: 0.8027 (mttm) REVERT: D 336 GLN cc_start: 0.7572 (mt0) cc_final: 0.6900 (tt0) REVERT: D 343 LYS cc_start: 0.6808 (mttp) cc_final: 0.6418 (mtpp) REVERT: D 345 ASP cc_start: 0.6258 (m-30) cc_final: 0.5431 (t70) REVERT: D 347 LYS cc_start: 0.6455 (mtpt) cc_final: 0.5717 (mttp) REVERT: E 338 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7145 (mm-30) REVERT: E 340 LYS cc_start: 0.7031 (mttt) cc_final: 0.6365 (pptt) REVERT: E 347 LYS cc_start: 0.7436 (mtpt) cc_final: 0.6651 (pptt) REVERT: E 349 ARG cc_start: 0.6836 (mtt90) cc_final: 0.5870 (ttp-170) REVERT: E 350 VAL cc_start: 0.7436 (p) cc_final: 0.7107 (m) REVERT: E 353 LYS cc_start: 0.7876 (ttmt) cc_final: 0.7291 (ttmm) REVERT: F 317 LYS cc_start: 0.8853 (ptmt) cc_final: 0.8544 (ptpp) REVERT: F 321 LYS cc_start: 0.8490 (mttt) cc_final: 0.7814 (mptt) REVERT: F 342 GLU cc_start: 0.6801 (mt-10) cc_final: 0.5514 (pm20) REVERT: F 343 LYS cc_start: 0.7588 (mttp) cc_final: 0.6688 (ttpp) REVERT: F 345 ASP cc_start: 0.7228 (m-30) cc_final: 0.6869 (t0) REVERT: F 347 LYS cc_start: 0.7672 (mtpt) cc_final: 0.6645 (mttp) REVERT: F 369 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8381 (mtpt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 3.3962 time to fit residues: 423.2715 Evaluate side-chains 78 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 374 HIS B 330 HIS ** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 336 GLN D 330 HIS D 362 HIS F 307 GLN F 336 GLN F 362 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.157538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.115906 restraints weight = 11580.046| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.91 r_work: 0.3476 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3582 Z= 0.228 Angle : 0.578 3.949 4794 Z= 0.308 Chirality : 0.050 0.128 534 Planarity : 0.003 0.033 618 Dihedral : 9.763 73.244 480 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.24 % Allowed : 8.46 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 329 PHE 0.014 0.002 PHE C 346 TYR 0.012 0.003 TYR F 310 ARG 0.003 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7816 (tt0) cc_final: 0.7591 (mt0) REVERT: B 317 LYS cc_start: 0.8612 (ptmt) cc_final: 0.8347 (ptpt) REVERT: B 321 LYS cc_start: 0.8792 (mttt) cc_final: 0.8481 (mttp) REVERT: B 336 GLN cc_start: 0.8191 (mt0) cc_final: 0.7854 (tt0) REVERT: B 372 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7932 (mt-10) REVERT: C 369 LYS cc_start: 0.8829 (ttpp) cc_final: 0.8506 (tppt) REVERT: D 314 ASP cc_start: 0.8847 (t70) cc_final: 0.8623 (t0) REVERT: D 336 GLN cc_start: 0.8141 (mt0) cc_final: 0.7718 (tt0) REVERT: D 342 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7817 (mm-30) REVERT: D 343 LYS cc_start: 0.7780 (mttp) cc_final: 0.7259 (mtpp) REVERT: D 347 LYS cc_start: 0.7289 (mtpt) cc_final: 0.6536 (mttp) REVERT: E 338 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6964 (mm-30) REVERT: E 340 LYS cc_start: 0.6946 (mttt) cc_final: 0.6258 (pptt) REVERT: E 347 LYS cc_start: 0.7521 (mtpt) cc_final: 0.6448 (pptt) REVERT: E 349 ARG cc_start: 0.6823 (mtt90) cc_final: 0.5680 (ttp80) REVERT: E 350 VAL cc_start: 0.7043 (p) cc_final: 0.6811 (m) REVERT: E 353 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7504 (ttmm) REVERT: F 321 LYS cc_start: 0.8621 (mttt) cc_final: 0.8099 (mptt) REVERT: F 342 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6306 (pm20) REVERT: F 347 LYS cc_start: 0.8298 (mtpt) cc_final: 0.7641 (mtmm) REVERT: F 369 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8465 (mtpt) outliers start: 5 outliers final: 1 residues processed: 85 average time/residue: 3.7444 time to fit residues: 324.7529 Evaluate side-chains 74 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.0040 chunk 39 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS ** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 374 HIS D 329 HIS D 374 HIS E 374 HIS F 374 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.161962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.120534 restraints weight = 11501.755| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.86 r_work: 0.3522 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3582 Z= 0.125 Angle : 0.482 5.083 4794 Z= 0.252 Chirality : 0.051 0.134 534 Planarity : 0.003 0.026 618 Dihedral : 9.077 68.744 480 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.24 % Allowed : 10.45 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.005 0.001 PHE A 346 TYR 0.008 0.001 TYR F 310 ARG 0.002 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.8445 (tmmt) cc_final: 0.8212 (mtmm) REVERT: B 317 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8343 (ptpt) REVERT: B 321 LYS cc_start: 0.8710 (mttt) cc_final: 0.8424 (mttp) REVERT: B 336 GLN cc_start: 0.8215 (mt0) cc_final: 0.7800 (tt0) REVERT: B 372 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7969 (mm-30) REVERT: C 369 LYS cc_start: 0.8807 (ttpp) cc_final: 0.8525 (tppt) REVERT: D 314 ASP cc_start: 0.8801 (t70) cc_final: 0.8574 (t0) REVERT: D 342 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7772 (mm-30) REVERT: D 343 LYS cc_start: 0.7788 (mttp) cc_final: 0.7270 (mtpp) REVERT: D 347 LYS cc_start: 0.7320 (mtpt) cc_final: 0.6509 (mttp) REVERT: E 338 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6910 (mm-30) REVERT: E 340 LYS cc_start: 0.6958 (mttt) cc_final: 0.6213 (pptt) REVERT: E 347 LYS cc_start: 0.7429 (mtpt) cc_final: 0.6332 (pptt) REVERT: E 349 ARG cc_start: 0.6846 (mtt90) cc_final: 0.6452 (mtp-110) REVERT: E 350 VAL cc_start: 0.7127 (p) cc_final: 0.6918 (m) REVERT: E 353 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7590 (ttmm) REVERT: F 321 LYS cc_start: 0.8395 (mttt) cc_final: 0.7833 (mptt) REVERT: F 342 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6431 (pm20) REVERT: F 347 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7588 (mtmm) REVERT: F 369 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8454 (mtpt) outliers start: 5 outliers final: 3 residues processed: 78 average time/residue: 3.7218 time to fit residues: 296.3662 Evaluate side-chains 72 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN D 362 HIS F 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.161384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.119561 restraints weight = 11595.961| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.88 r_work: 0.3519 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3582 Z= 0.130 Angle : 0.465 4.782 4794 Z= 0.242 Chirality : 0.050 0.132 534 Planarity : 0.003 0.032 618 Dihedral : 8.687 68.192 480 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.24 % Allowed : 10.45 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 330 PHE 0.005 0.001 PHE C 378 TYR 0.008 0.001 TYR F 310 ARG 0.003 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8603 (ptmt) cc_final: 0.8342 (ptpt) REVERT: B 321 LYS cc_start: 0.8711 (mttt) cc_final: 0.8402 (mttp) REVERT: B 336 GLN cc_start: 0.8199 (mt0) cc_final: 0.7716 (tt0) REVERT: B 372 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7970 (mm-30) REVERT: C 369 LYS cc_start: 0.8818 (ttpp) cc_final: 0.8522 (tppt) REVERT: D 314 ASP cc_start: 0.8853 (t70) cc_final: 0.8614 (t0) REVERT: D 342 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7807 (mm-30) REVERT: D 343 LYS cc_start: 0.7893 (mttp) cc_final: 0.7416 (mtpp) REVERT: D 347 LYS cc_start: 0.7317 (mtpt) cc_final: 0.6469 (mttp) REVERT: D 356 SER cc_start: 0.9309 (p) cc_final: 0.9097 (p) REVERT: E 338 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6808 (mm-30) REVERT: E 340 LYS cc_start: 0.6925 (mttt) cc_final: 0.6166 (pptt) REVERT: E 347 LYS cc_start: 0.7318 (mtpt) cc_final: 0.6184 (pptt) REVERT: E 349 ARG cc_start: 0.6822 (mtt90) cc_final: 0.6442 (mtp-110) REVERT: E 350 VAL cc_start: 0.7113 (p) cc_final: 0.6890 (m) REVERT: E 353 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7539 (ttmm) REVERT: F 321 LYS cc_start: 0.8398 (mttt) cc_final: 0.7805 (mptt) REVERT: F 342 GLU cc_start: 0.7657 (mt-10) cc_final: 0.6532 (pm20) REVERT: F 347 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7551 (mtmm) REVERT: F 369 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8479 (mtpt) outliers start: 5 outliers final: 4 residues processed: 75 average time/residue: 3.7362 time to fit residues: 285.8561 Evaluate side-chains 73 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.159948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117965 restraints weight = 11462.664| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.86 r_work: 0.3488 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3582 Z= 0.146 Angle : 0.473 4.852 4794 Z= 0.246 Chirality : 0.050 0.130 534 Planarity : 0.002 0.027 618 Dihedral : 8.435 66.783 480 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.00 % Allowed : 11.19 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.005 0.001 PHE B 378 TYR 0.006 0.002 TYR E 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8579 (ptmt) cc_final: 0.8330 (ptpt) REVERT: B 321 LYS cc_start: 0.8721 (mttt) cc_final: 0.8407 (mttp) REVERT: B 372 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7991 (mm-30) REVERT: C 369 LYS cc_start: 0.8850 (ttpp) cc_final: 0.8559 (tppt) REVERT: D 314 ASP cc_start: 0.8852 (t70) cc_final: 0.8633 (t0) REVERT: D 342 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7668 (mm-30) REVERT: D 343 LYS cc_start: 0.7867 (mttp) cc_final: 0.7317 (mtpp) REVERT: D 347 LYS cc_start: 0.7285 (mtpt) cc_final: 0.6407 (mttp) REVERT: E 338 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6813 (mm-30) REVERT: E 340 LYS cc_start: 0.6967 (mttt) cc_final: 0.6190 (pptt) REVERT: E 342 GLU cc_start: 0.4930 (pm20) cc_final: 0.4554 (pm20) REVERT: E 349 ARG cc_start: 0.6626 (mtt90) cc_final: 0.6288 (mtp-110) REVERT: E 350 VAL cc_start: 0.7122 (p) cc_final: 0.6901 (m) REVERT: E 353 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7558 (ttmm) REVERT: F 342 GLU cc_start: 0.7726 (mt-10) cc_final: 0.6537 (pm20) REVERT: F 369 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8492 (mtpt) outliers start: 4 outliers final: 3 residues processed: 71 average time/residue: 3.6126 time to fit residues: 262.1265 Evaluate side-chains 66 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 38 optimal weight: 0.0040 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN F 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.158200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115681 restraints weight = 11671.530| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.89 r_work: 0.3455 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3582 Z= 0.175 Angle : 0.485 4.068 4794 Z= 0.252 Chirality : 0.050 0.132 534 Planarity : 0.003 0.044 618 Dihedral : 8.378 66.910 480 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.00 % Allowed : 12.94 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.006 0.001 PHE C 378 TYR 0.008 0.002 TYR D 310 ARG 0.007 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8568 (ptmt) cc_final: 0.8308 (ptpt) REVERT: B 321 LYS cc_start: 0.8762 (mttt) cc_final: 0.8440 (mttp) REVERT: B 372 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8037 (mm-30) REVERT: C 369 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8565 (tppt) REVERT: D 314 ASP cc_start: 0.8893 (t70) cc_final: 0.8667 (t0) REVERT: D 342 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7803 (mm-30) REVERT: D 343 LYS cc_start: 0.7880 (mttp) cc_final: 0.7328 (mtpp) REVERT: D 347 LYS cc_start: 0.7264 (mtpt) cc_final: 0.6383 (mttp) REVERT: E 338 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6736 (mm-30) REVERT: E 340 LYS cc_start: 0.7063 (mttt) cc_final: 0.6191 (pptt) REVERT: E 342 GLU cc_start: 0.4823 (pm20) cc_final: 0.4479 (pm20) REVERT: E 349 ARG cc_start: 0.6649 (mtt90) cc_final: 0.6238 (mtp-110) REVERT: E 350 VAL cc_start: 0.7179 (p) cc_final: 0.6933 (m) REVERT: E 353 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7615 (ttmm) REVERT: F 342 GLU cc_start: 0.7830 (mt-10) cc_final: 0.6523 (pm20) REVERT: F 369 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8522 (mtpt) outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 3.9146 time to fit residues: 267.5722 Evaluate side-chains 67 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain E residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.157275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.115240 restraints weight = 11569.265| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.86 r_work: 0.3449 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3582 Z= 0.179 Angle : 0.479 3.784 4794 Z= 0.249 Chirality : 0.050 0.130 534 Planarity : 0.003 0.044 618 Dihedral : 8.329 66.167 480 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.00 % Allowed : 12.94 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.006 0.001 PHE B 378 TYR 0.008 0.002 TYR D 310 ARG 0.007 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8546 (ptmt) cc_final: 0.8292 (ptpt) REVERT: B 321 LYS cc_start: 0.8762 (mttt) cc_final: 0.8434 (mttp) REVERT: B 372 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7979 (mm-30) REVERT: C 369 LYS cc_start: 0.8873 (ttpp) cc_final: 0.8589 (tppt) REVERT: D 314 ASP cc_start: 0.8896 (t70) cc_final: 0.8646 (t0) REVERT: D 342 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7784 (mm-30) REVERT: D 343 LYS cc_start: 0.7886 (mttp) cc_final: 0.7332 (mtpp) REVERT: D 347 LYS cc_start: 0.7311 (mtpt) cc_final: 0.6418 (mttp) REVERT: E 338 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6763 (mm-30) REVERT: E 340 LYS cc_start: 0.7132 (mttt) cc_final: 0.6129 (pptt) REVERT: E 342 GLU cc_start: 0.4741 (pm20) cc_final: 0.4481 (pm20) REVERT: E 349 ARG cc_start: 0.6649 (mtt90) cc_final: 0.6244 (mtp-110) REVERT: E 350 VAL cc_start: 0.7216 (p) cc_final: 0.6968 (m) REVERT: E 353 LYS cc_start: 0.8064 (ttmt) cc_final: 0.7616 (ttmm) REVERT: F 342 GLU cc_start: 0.7789 (mt-10) cc_final: 0.6487 (pm20) outliers start: 4 outliers final: 4 residues processed: 67 average time/residue: 3.8180 time to fit residues: 260.9428 Evaluate side-chains 68 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 0.0980 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 0.0470 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.161059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119641 restraints weight = 11588.062| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.87 r_work: 0.3518 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3582 Z= 0.118 Angle : 0.460 7.021 4794 Z= 0.230 Chirality : 0.049 0.128 534 Planarity : 0.003 0.055 618 Dihedral : 8.187 64.229 480 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.49 % Allowed : 12.69 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.003 0.001 PHE C 346 TYR 0.006 0.001 TYR D 310 ARG 0.008 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8520 (ptmt) cc_final: 0.8266 (ptpt) REVERT: B 321 LYS cc_start: 0.8697 (mttt) cc_final: 0.8398 (mttp) REVERT: B 372 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7983 (mm-30) REVERT: C 369 LYS cc_start: 0.8836 (ttpp) cc_final: 0.8542 (tppt) REVERT: D 314 ASP cc_start: 0.8859 (t70) cc_final: 0.8619 (t0) REVERT: D 342 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7708 (mm-30) REVERT: D 343 LYS cc_start: 0.7828 (mttp) cc_final: 0.7296 (mtpp) REVERT: D 347 LYS cc_start: 0.7314 (mtpt) cc_final: 0.6403 (mttp) REVERT: E 338 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6784 (mm-30) REVERT: E 340 LYS cc_start: 0.7111 (mttt) cc_final: 0.6125 (pptt) REVERT: E 342 GLU cc_start: 0.4817 (pm20) cc_final: 0.4551 (pm20) REVERT: E 349 ARG cc_start: 0.6516 (mtt90) cc_final: 0.6188 (mtp-110) REVERT: E 353 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7593 (ttmm) REVERT: F 342 GLU cc_start: 0.7787 (mt-10) cc_final: 0.6522 (pm20) REVERT: F 369 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8468 (mtpt) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 3.7122 time to fit residues: 242.6582 Evaluate side-chains 67 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.0050 chunk 5 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.160323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.118723 restraints weight = 11526.337| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.87 r_work: 0.3504 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3582 Z= 0.127 Angle : 0.453 3.913 4794 Z= 0.231 Chirality : 0.049 0.128 534 Planarity : 0.003 0.055 618 Dihedral : 8.081 64.461 480 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.49 % Allowed : 13.68 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.004 0.001 PHE C 346 TYR 0.008 0.002 TYR D 310 ARG 0.009 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8555 (ptmt) cc_final: 0.8291 (ptpt) REVERT: B 321 LYS cc_start: 0.8714 (mttt) cc_final: 0.8414 (mttp) REVERT: B 372 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7987 (mm-30) REVERT: C 369 LYS cc_start: 0.8850 (ttpp) cc_final: 0.8562 (tppt) REVERT: D 314 ASP cc_start: 0.8854 (t70) cc_final: 0.8637 (t0) REVERT: D 342 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7769 (mm-30) REVERT: D 343 LYS cc_start: 0.7859 (mttp) cc_final: 0.7317 (mtpp) REVERT: D 347 LYS cc_start: 0.7318 (mtpt) cc_final: 0.6430 (mttp) REVERT: E 338 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6798 (mm-30) REVERT: E 340 LYS cc_start: 0.7096 (mttt) cc_final: 0.6094 (pptt) REVERT: E 342 GLU cc_start: 0.4861 (pm20) cc_final: 0.4605 (pm20) REVERT: E 347 LYS cc_start: 0.6752 (mtpt) cc_final: 0.6234 (mptt) REVERT: E 349 ARG cc_start: 0.6545 (mtt90) cc_final: 0.6090 (mtp-110) REVERT: E 350 VAL cc_start: 0.7427 (p) cc_final: 0.7221 (m) REVERT: E 353 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7573 (ttmm) REVERT: F 342 GLU cc_start: 0.7778 (mt-10) cc_final: 0.6507 (pm20) REVERT: F 369 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8482 (mtpt) REVERT: F 379 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.6821 (mmt-90) outliers start: 6 outliers final: 6 residues processed: 66 average time/residue: 3.7726 time to fit residues: 253.9878 Evaluate side-chains 68 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 HIS F 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.159898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117882 restraints weight = 11638.105| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.88 r_work: 0.3488 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3582 Z= 0.139 Angle : 0.463 4.266 4794 Z= 0.236 Chirality : 0.049 0.128 534 Planarity : 0.003 0.054 618 Dihedral : 8.084 64.863 480 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.49 % Allowed : 13.43 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.004 0.001 PHE C 346 TYR 0.008 0.001 TYR D 310 ARG 0.009 0.001 ARG F 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.7926 (tttp) cc_final: 0.6507 (mtmt) REVERT: B 317 LYS cc_start: 0.8543 (ptmt) cc_final: 0.8285 (ptpt) REVERT: B 321 LYS cc_start: 0.8723 (mttt) cc_final: 0.8422 (mttp) REVERT: B 372 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8003 (mm-30) REVERT: C 369 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8567 (tppt) REVERT: D 314 ASP cc_start: 0.8868 (t70) cc_final: 0.8665 (t0) REVERT: D 342 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7787 (mm-30) REVERT: D 343 LYS cc_start: 0.7861 (mttp) cc_final: 0.7321 (mtpp) REVERT: D 347 LYS cc_start: 0.7328 (mtpt) cc_final: 0.6434 (mttp) REVERT: E 338 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6785 (mm-30) REVERT: E 340 LYS cc_start: 0.7119 (mttt) cc_final: 0.6069 (pptt) REVERT: E 342 GLU cc_start: 0.4786 (pm20) cc_final: 0.4556 (pm20) REVERT: E 347 LYS cc_start: 0.6700 (mtpt) cc_final: 0.6293 (mptt) REVERT: E 349 ARG cc_start: 0.6475 (mtt90) cc_final: 0.6019 (mtp-110) REVERT: E 353 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7576 (ttmm) REVERT: F 342 GLU cc_start: 0.7768 (mt-10) cc_final: 0.6493 (pm20) REVERT: F 369 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8491 (mtpt) REVERT: F 379 ARG cc_start: 0.7787 (mmm-85) cc_final: 0.6807 (mmt-90) outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 3.8613 time to fit residues: 255.9601 Evaluate side-chains 68 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.153432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.112010 restraints weight = 11675.872| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.92 r_work: 0.3427 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3582 Z= 0.234 Angle : 0.507 4.338 4794 Z= 0.264 Chirality : 0.050 0.131 534 Planarity : 0.004 0.049 618 Dihedral : 8.277 67.180 480 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.24 % Allowed : 13.68 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.006 0.001 PHE B 378 TYR 0.011 0.002 TYR B 310 ARG 0.008 0.001 ARG F 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7311.61 seconds wall clock time: 130 minutes 37.42 seconds (7837.42 seconds total)