Starting phenix.real_space_refine on Fri Aug 22 19:16:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxo_45007/08_2025/9bxo_45007.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxo_45007/08_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_45007/08_2025/9bxo_45007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxo_45007/08_2025/9bxo_45007.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxo_45007/08_2025/9bxo_45007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxo_45007/08_2025/9bxo_45007.cif" } resolution = 3.0 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= 0.003 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.48, per 1000 atoms: 0.21 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: 0.62 Conformation dependent library (CDL) restraints added in 417.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.25 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: 1.60 Time building geometry restraints manager: 0.90 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: 0.00 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: 1.930 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: 0.050 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.090 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.390 ------------------------------------------------------------------------------- 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= 0.683 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 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: -1.64 (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 ARG 0.002 0.000 ARG D 379 TYR 0.027 0.011 TYR E 310 PHE 0.014 0.006 PHE E 346 HIS 0.010 0.003 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.01099 ( 3582) covalent geometry : angle 1.74122 ( 4794) hydrogen bonds : bond 0.13897 ( 46) hydrogen bonds : angle 8.39086 ( 138) *********************** 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 : 0.222 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: 0.8189 (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: 0.8030 (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: 0.7813 (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: 0.6689 (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: 0.8382 (mtpt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 1.7267 time to fit residues: 214.8685 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 : 0.213 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS B 330 HIS ** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 336 GLN D 330 HIS F 307 GLN F 336 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.159345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.118056 restraints weight = 11664.470| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.91 r_work: 0.3505 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3582 Z= 0.110 Angle : 0.553 3.893 4794 Z= 0.294 Chirality : 0.049 0.128 534 Planarity : 0.003 0.033 618 Dihedral : 9.884 75.005 480 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.24 % Allowed : 7.96 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.30), 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 ARG 0.004 0.001 ARG D 349 TYR 0.010 0.002 TYR F 310 PHE 0.013 0.002 PHE C 346 HIS 0.004 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 3582) covalent geometry : angle 0.55295 ( 4794) hydrogen bonds : bond 0.02983 ( 46) hydrogen bonds : angle 5.96212 ( 138) *********************** 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 90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7833 (tt0) cc_final: 0.7621 (mt0) REVERT: B 317 LYS cc_start: 0.8577 (ptmt) cc_final: 0.8328 (ptpt) REVERT: B 321 LYS cc_start: 0.8773 (mttt) cc_final: 0.8461 (mttp) REVERT: B 336 GLN cc_start: 0.8109 (mt0) cc_final: 0.7855 (tt0) REVERT: B 372 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7925 (mt-10) REVERT: D 336 GLN cc_start: 0.8098 (mt0) cc_final: 0.7696 (tt0) REVERT: D 342 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7767 (mm-30) REVERT: D 343 LYS cc_start: 0.7757 (mttp) cc_final: 0.7237 (mtpp) REVERT: D 347 LYS cc_start: 0.7302 (mtpt) cc_final: 0.6557 (mttp) REVERT: E 338 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7013 (mm-30) REVERT: E 340 LYS cc_start: 0.6914 (mttt) cc_final: 0.6300 (pptt) REVERT: E 347 LYS cc_start: 0.7552 (mtpt) cc_final: 0.6473 (pptt) REVERT: E 349 ARG cc_start: 0.6817 (mtt90) cc_final: 0.5677 (ttp80) REVERT: E 350 VAL cc_start: 0.7066 (p) cc_final: 0.6826 (m) REVERT: E 353 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7431 (ttmm) REVERT: F 321 LYS cc_start: 0.8599 (mttt) cc_final: 0.8077 (mptt) REVERT: F 342 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6307 (pm20) REVERT: F 347 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7646 (mtmm) REVERT: F 358 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7947 (m-30) REVERT: F 369 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8478 (mtmt) outliers start: 5 outliers final: 1 residues processed: 86 average time/residue: 1.8839 time to fit residues: 164.9492 Evaluate side-chains 76 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS 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 336 GLN F 362 HIS F 374 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.160040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.118258 restraints weight = 11522.439| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.86 r_work: 0.3487 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3582 Z= 0.098 Angle : 0.499 4.554 4794 Z= 0.264 Chirality : 0.051 0.136 534 Planarity : 0.003 0.036 618 Dihedral : 8.909 67.351 480 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.99 % Allowed : 9.70 % 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 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: -1.94 (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 ARG 0.004 0.001 ARG D 379 TYR 0.011 0.002 TYR F 310 PHE 0.006 0.001 PHE C 378 HIS 0.006 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 3582) covalent geometry : angle 0.49879 ( 4794) hydrogen bonds : bond 0.02041 ( 46) hydrogen bonds : angle 4.93618 ( 138) *********************** 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 82 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.8439 (tmmt) cc_final: 0.8195 (mtmm) REVERT: B 317 LYS cc_start: 0.8602 (ptmt) cc_final: 0.8355 (ptpt) REVERT: B 321 LYS cc_start: 0.8756 (mttt) cc_final: 0.8463 (mttp) REVERT: B 336 GLN cc_start: 0.8237 (mt0) cc_final: 0.7782 (tt0) REVERT: B 353 LYS cc_start: 0.7510 (ttmt) cc_final: 0.7287 (ttmt) REVERT: B 372 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7996 (mm-30) REVERT: D 342 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7690 (mm-30) REVERT: D 343 LYS cc_start: 0.7801 (mttp) cc_final: 0.7281 (mtpp) REVERT: D 347 LYS cc_start: 0.7336 (mtpt) cc_final: 0.6524 (mttp) REVERT: D 379 ARG cc_start: 0.7399 (mmm-85) cc_final: 0.7172 (tpp80) REVERT: E 338 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6817 (mm-30) REVERT: E 340 LYS cc_start: 0.6965 (mttt) cc_final: 0.6211 (pptt) REVERT: E 347 LYS cc_start: 0.7451 (mtpt) cc_final: 0.6343 (pptt) REVERT: E 349 ARG cc_start: 0.6852 (mtt90) cc_final: 0.6475 (mtp-110) REVERT: E 350 VAL cc_start: 0.7154 (p) cc_final: 0.6948 (m) REVERT: E 353 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7583 (ttmm) REVERT: F 321 LYS cc_start: 0.8478 (mttt) cc_final: 0.7927 (mptt) REVERT: F 342 GLU cc_start: 0.7630 (mt-10) cc_final: 0.6467 (pm20) REVERT: F 347 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7620 (mtmm) REVERT: F 369 LYS cc_start: 0.8732 (mtpp) cc_final: 0.8463 (mtpt) outliers start: 8 outliers final: 4 residues processed: 77 average time/residue: 1.9960 time to fit residues: 156.5743 Evaluate side-chains 72 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 356 SER 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 0 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.150222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107773 restraints weight = 11787.412| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.92 r_work: 0.3407 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3582 Z= 0.166 Angle : 0.550 5.119 4794 Z= 0.294 Chirality : 0.051 0.137 534 Planarity : 0.003 0.032 618 Dihedral : 8.856 68.647 480 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.74 % Allowed : 11.19 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 379 TYR 0.012 0.002 TYR F 310 PHE 0.010 0.002 PHE B 378 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 3582) covalent geometry : angle 0.55032 ( 4794) hydrogen bonds : bond 0.02096 ( 46) hydrogen bonds : angle 4.78246 ( 138) *********************** 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 75 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.8460 (tmmt) cc_final: 0.8240 (mtmm) REVERT: B 317 LYS cc_start: 0.8595 (ptmt) cc_final: 0.8318 (ptpt) REVERT: B 321 LYS cc_start: 0.8833 (mttt) cc_final: 0.8505 (mttp) REVERT: B 372 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8017 (mt-10) REVERT: D 342 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7626 (mm-30) REVERT: D 343 LYS cc_start: 0.7838 (mttp) cc_final: 0.7267 (mtpp) REVERT: D 347 LYS cc_start: 0.7326 (mtpt) cc_final: 0.6447 (mttp) REVERT: D 379 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.7187 (tpp80) REVERT: E 338 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6816 (mm-30) REVERT: E 340 LYS cc_start: 0.7055 (mttt) cc_final: 0.6198 (pptt) REVERT: E 347 LYS cc_start: 0.7293 (mtpt) cc_final: 0.6192 (pptt) REVERT: E 349 ARG cc_start: 0.6859 (mtt90) cc_final: 0.6462 (mtp-110) REVERT: E 350 VAL cc_start: 0.7163 (p) cc_final: 0.6923 (m) REVERT: E 353 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7624 (ttmm) REVERT: F 342 GLU cc_start: 0.7774 (mt-10) cc_final: 0.6544 (pm20) REVERT: F 369 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8534 (mtpt) outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 2.0167 time to fit residues: 143.8807 Evaluate side-chains 69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 30 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.156409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.114408 restraints weight = 11661.512| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.88 r_work: 0.3437 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4856 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= 0.121 Angle : 0.493 3.890 4794 Z= 0.258 Chirality : 0.050 0.132 534 Planarity : 0.003 0.032 618 Dihedral : 8.688 67.263 480 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.49 % Allowed : 11.19 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.07 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.009 0.002 TYR F 310 PHE 0.006 0.001 PHE B 378 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3582) covalent geometry : angle 0.49308 ( 4794) hydrogen bonds : bond 0.01772 ( 46) hydrogen bonds : angle 4.56058 ( 138) *********************** 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 80 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8591 (ptmt) cc_final: 0.8323 (ptpt) REVERT: B 321 LYS cc_start: 0.8807 (mttt) cc_final: 0.8471 (mttp) REVERT: B 372 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7979 (mt-10) REVERT: D 342 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7701 (mm-30) REVERT: D 343 LYS cc_start: 0.7883 (mttp) cc_final: 0.7331 (mtpp) REVERT: D 347 LYS cc_start: 0.7336 (mtpt) cc_final: 0.6442 (mttp) REVERT: D 356 SER cc_start: 0.9235 (p) cc_final: 0.9031 (p) REVERT: D 379 ARG cc_start: 0.7414 (mmm-85) cc_final: 0.7193 (tpp80) REVERT: E 338 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6766 (mm-30) REVERT: E 340 LYS cc_start: 0.7080 (mttt) cc_final: 0.6132 (pptt) REVERT: E 342 GLU cc_start: 0.4925 (pm20) cc_final: 0.4708 (pm20) REVERT: E 347 LYS cc_start: 0.7247 (mtpt) cc_final: 0.6178 (pptt) REVERT: E 349 ARG cc_start: 0.6710 (mtt90) cc_final: 0.6289 (mtp-110) REVERT: E 350 VAL cc_start: 0.7133 (p) cc_final: 0.6909 (m) REVERT: E 353 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7654 (ttmm) REVERT: F 342 GLU cc_start: 0.7788 (mt-10) cc_final: 0.6547 (pm20) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 1.8832 time to fit residues: 146.0089 Evaluate side-chains 69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 341 SER 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 32 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.0670 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.156521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114627 restraints weight = 11699.799| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.88 r_work: 0.3442 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3582 Z= 0.109 Angle : 0.491 5.435 4794 Z= 0.253 Chirality : 0.050 0.131 534 Planarity : 0.003 0.034 618 Dihedral : 8.517 66.502 480 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.24 % Allowed : 11.94 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.11 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 379 TYR 0.008 0.002 TYR F 310 PHE 0.005 0.001 PHE B 378 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3582) covalent geometry : angle 0.49143 ( 4794) hydrogen bonds : bond 0.01662 ( 46) hydrogen bonds : angle 4.40052 ( 138) *********************** 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 69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8588 (ptmt) cc_final: 0.8304 (ptpt) REVERT: B 321 LYS cc_start: 0.8787 (mttt) cc_final: 0.8452 (mttp) REVERT: B 353 LYS cc_start: 0.7520 (ttmt) cc_final: 0.7222 (ttmt) REVERT: B 372 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8019 (mt-10) REVERT: D 343 LYS cc_start: 0.7882 (mttp) cc_final: 0.7328 (mtpp) REVERT: D 347 LYS cc_start: 0.7320 (mtpt) cc_final: 0.6411 (mttp) REVERT: D 356 SER cc_start: 0.9185 (p) cc_final: 0.8978 (p) REVERT: D 379 ARG cc_start: 0.7428 (mmm-85) cc_final: 0.7212 (tpp80) REVERT: E 338 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6738 (mm-30) REVERT: E 340 LYS cc_start: 0.7143 (mttt) cc_final: 0.6145 (pptt) REVERT: E 342 GLU cc_start: 0.4992 (pm20) cc_final: 0.4691 (pm20) REVERT: E 349 ARG cc_start: 0.6721 (mtt90) cc_final: 0.6301 (mtp-110) REVERT: E 350 VAL cc_start: 0.7193 (p) cc_final: 0.6957 (m) REVERT: E 353 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7634 (ttmm) REVERT: F 342 GLU cc_start: 0.7824 (mt-10) cc_final: 0.6498 (pm20) outliers start: 5 outliers final: 5 residues processed: 65 average time/residue: 2.0881 time to fit residues: 138.2430 Evaluate side-chains 67 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 E residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 21 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 38 optimal weight: 0.0970 chunk 0 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 4 optimal weight: 50.0000 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.160806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.119552 restraints weight = 11506.257| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.86 r_work: 0.3517 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3582 Z= 0.074 Angle : 0.448 5.513 4794 Z= 0.227 Chirality : 0.049 0.129 534 Planarity : 0.003 0.033 618 Dihedral : 8.318 65.012 480 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.24 % Allowed : 12.19 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.006 0.001 TYR D 310 PHE 0.003 0.001 PHE C 346 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00170 ( 3582) covalent geometry : angle 0.44835 ( 4794) hydrogen bonds : bond 0.01426 ( 46) hydrogen bonds : angle 4.14450 ( 138) *********************** 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 72 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8584 (ptmt) cc_final: 0.8304 (ptpt) REVERT: B 321 LYS cc_start: 0.8720 (mttt) cc_final: 0.8383 (mttp) REVERT: B 353 LYS cc_start: 0.7601 (ttmt) cc_final: 0.7313 (ttmt) REVERT: B 372 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7990 (mm-30) REVERT: D 343 LYS cc_start: 0.7916 (mttp) cc_final: 0.7362 (mtpp) REVERT: D 347 LYS cc_start: 0.7399 (mtpt) cc_final: 0.6491 (mttp) REVERT: D 379 ARG cc_start: 0.7410 (mmm-85) cc_final: 0.7166 (tpp80) REVERT: E 338 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6760 (mm-30) REVERT: E 340 LYS cc_start: 0.7134 (mttt) cc_final: 0.6170 (pptt) REVERT: E 342 GLU cc_start: 0.4981 (pm20) cc_final: 0.4768 (pm20) REVERT: E 349 ARG cc_start: 0.6597 (mtt90) cc_final: 0.6240 (mtp-110) REVERT: E 350 VAL cc_start: 0.6935 (p) cc_final: 0.6703 (m) REVERT: E 353 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7627 (ttmm) outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 1.9697 time to fit residues: 136.5261 Evaluate side-chains 64 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.150870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108998 restraints weight = 11813.977| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.92 r_work: 0.3430 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.5174 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= 0.128 Angle : 0.493 3.749 4794 Z= 0.257 Chirality : 0.050 0.132 534 Planarity : 0.003 0.048 618 Dihedral : 8.352 67.167 480 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.00 % Allowed : 14.18 % 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 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: -2.11 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 379 TYR 0.009 0.002 TYR B 310 PHE 0.007 0.001 PHE B 378 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3582) covalent geometry : angle 0.49272 ( 4794) hydrogen bonds : bond 0.01699 ( 46) hydrogen bonds : angle 4.30722 ( 138) *********************** 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 67 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8588 (ptmt) cc_final: 0.8286 (ptpt) REVERT: B 321 LYS cc_start: 0.8806 (mttt) cc_final: 0.8466 (mttp) REVERT: B 353 LYS cc_start: 0.7478 (ttmt) cc_final: 0.7173 (ttmt) REVERT: B 372 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8073 (mm-30) REVERT: D 343 LYS cc_start: 0.7880 (mttp) cc_final: 0.7328 (mtpp) REVERT: D 347 LYS cc_start: 0.7322 (mtpt) cc_final: 0.6413 (mttp) REVERT: D 379 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.6807 (tpp80) REVERT: E 338 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6798 (mm-30) REVERT: E 340 LYS cc_start: 0.7130 (mttt) cc_final: 0.6055 (pptt) REVERT: E 342 GLU cc_start: 0.4919 (pm20) cc_final: 0.4646 (pm20) REVERT: E 349 ARG cc_start: 0.6579 (mtt90) cc_final: 0.6194 (mtp-110) REVERT: E 350 VAL cc_start: 0.7066 (p) cc_final: 0.6811 (m) REVERT: E 353 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7615 (ttmm) REVERT: F 342 GLU cc_start: 0.7770 (mt-10) cc_final: 0.6389 (pm20) REVERT: F 379 ARG cc_start: 0.7716 (mmm-85) cc_final: 0.6749 (mmt-90) outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 2.0812 time to fit residues: 137.7522 Evaluate side-chains 62 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.157126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.116125 restraints weight = 11733.052| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.92 r_work: 0.3466 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3582 Z= 0.091 Angle : 0.464 4.053 4794 Z= 0.239 Chirality : 0.049 0.129 534 Planarity : 0.003 0.048 618 Dihedral : 8.295 65.614 480 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.75 % Allowed : 14.18 % 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 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: -2.12 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 379 TYR 0.008 0.002 TYR B 310 PHE 0.004 0.001 PHE A 378 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 3582) covalent geometry : angle 0.46405 ( 4794) hydrogen bonds : bond 0.01491 ( 46) hydrogen bonds : angle 4.21715 ( 138) *********************** 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 63 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8585 (ptmt) cc_final: 0.8298 (ptpt) REVERT: B 321 LYS cc_start: 0.8781 (mttt) cc_final: 0.8438 (mttp) REVERT: B 353 LYS cc_start: 0.7482 (ttmt) cc_final: 0.7186 (ttmt) REVERT: B 372 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8048 (mm-30) REVERT: D 343 LYS cc_start: 0.7893 (mttp) cc_final: 0.7337 (mtpp) REVERT: D 347 LYS cc_start: 0.7332 (mtpt) cc_final: 0.6427 (mttp) REVERT: D 379 ARG cc_start: 0.7393 (mmm-85) cc_final: 0.6783 (tpp80) REVERT: E 338 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6793 (mm-30) REVERT: E 340 LYS cc_start: 0.7146 (mttt) cc_final: 0.6055 (pptt) REVERT: E 342 GLU cc_start: 0.4900 (pm20) cc_final: 0.4637 (pm20) REVERT: E 349 ARG cc_start: 0.6535 (mtt90) cc_final: 0.6172 (mtp-110) REVERT: E 350 VAL cc_start: 0.6919 (p) cc_final: 0.6668 (m) REVERT: E 353 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7572 (ttmm) REVERT: E 379 ARG cc_start: 0.7507 (mpt-90) cc_final: 0.6302 (mtm-85) REVERT: F 342 GLU cc_start: 0.7744 (mt-10) cc_final: 0.6412 (pm20) REVERT: F 379 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.6781 (mmt-90) outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 2.0059 time to fit residues: 124.5680 Evaluate side-chains 62 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.155730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114468 restraints weight = 11711.968| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.93 r_work: 0.3456 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3582 Z= 0.099 Angle : 0.472 4.400 4794 Z= 0.243 Chirality : 0.050 0.129 534 Planarity : 0.003 0.047 618 Dihedral : 8.234 65.616 480 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.75 % Allowed : 14.18 % 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 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: -2.11 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 379 TYR 0.008 0.002 TYR B 310 PHE 0.004 0.001 PHE C 378 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 3582) covalent geometry : angle 0.47157 ( 4794) hydrogen bonds : bond 0.01525 ( 46) hydrogen bonds : angle 4.21825 ( 138) ********************** 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 65 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8600 (ptmt) cc_final: 0.8308 (ptpt) REVERT: B 321 LYS cc_start: 0.8798 (mttt) cc_final: 0.8455 (mttp) REVERT: B 353 LYS cc_start: 0.7480 (ttmt) cc_final: 0.7184 (ttmt) REVERT: B 372 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8085 (mm-30) REVERT: D 343 LYS cc_start: 0.7892 (mttp) cc_final: 0.7338 (mtpp) REVERT: D 347 LYS cc_start: 0.7305 (mtpt) cc_final: 0.6389 (mttp) REVERT: D 379 ARG cc_start: 0.7383 (mmm-85) cc_final: 0.6790 (tpp80) REVERT: E 338 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6776 (mm-30) REVERT: E 340 LYS cc_start: 0.7224 (mttt) cc_final: 0.6108 (pptt) REVERT: E 342 GLU cc_start: 0.4950 (pm20) cc_final: 0.4675 (pm20) REVERT: E 349 ARG cc_start: 0.6507 (mtt90) cc_final: 0.6132 (mtp-110) REVERT: E 350 VAL cc_start: 0.6753 (p) cc_final: 0.6493 (m) REVERT: E 353 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7596 (ttmm) REVERT: F 342 GLU cc_start: 0.7703 (mt-10) cc_final: 0.6340 (pm20) REVERT: F 379 ARG cc_start: 0.7755 (mmm-85) cc_final: 0.6779 (mmt-90) outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 2.0038 time to fit residues: 128.5566 Evaluate side-chains 63 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.155730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.114580 restraints weight = 11715.623| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.93 r_work: 0.3448 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3582 Z= 0.115 Angle : 0.485 4.418 4794 Z= 0.251 Chirality : 0.050 0.129 534 Planarity : 0.003 0.044 618 Dihedral : 8.281 66.094 480 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.75 % Allowed : 14.68 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 379 TYR 0.009 0.002 TYR B 310 PHE 0.005 0.001 PHE B 378 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3582) covalent geometry : angle 0.48466 ( 4794) hydrogen bonds : bond 0.01592 ( 46) hydrogen bonds : angle 4.25151 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4002.52 seconds wall clock time: 68 minutes 35.78 seconds (4115.78 seconds total)