Starting phenix.real_space_refine on Thu Nov 14 19:35:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxo_45007/11_2024/9bxo_45007.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxo_45007/11_2024/9bxo_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxo_45007/11_2024/9bxo_45007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxo_45007/11_2024/9bxo_45007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxo_45007/11_2024/9bxo_45007.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxo_45007/11_2024/9bxo_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-5513/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: 4.08, per 1000 atoms: 0.57 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: 1.74 Conformation dependent library (CDL) restraints added in 635.5 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: 0.73 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: 2.43 Time building geometry restraints manager: 2.08 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: 0.870 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.550 Find NCS groups from input model: 0.180 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:14.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.410 ------------------------------------------------------------------------------- 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 : 0.621 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: 3.3138 time to fit residues: 413.2322 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 : 0.631 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7809 (tt0) cc_final: 0.7563 (mt0) REVERT: B 317 LYS cc_start: 0.8529 (ptmt) cc_final: 0.8139 (ptpt) REVERT: B 321 LYS cc_start: 0.8487 (mttt) cc_final: 0.7992 (mttp) REVERT: B 336 GLN cc_start: 0.7688 (mt0) cc_final: 0.7130 (tt0) REVERT: B 372 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7971 (mt-10) REVERT: C 369 LYS cc_start: 0.8722 (ttpp) cc_final: 0.8330 (tppt) REVERT: D 314 ASP cc_start: 0.9019 (t70) cc_final: 0.8769 (t0) REVERT: D 321 LYS cc_start: 0.8364 (mttt) cc_final: 0.8117 (mttm) REVERT: D 336 GLN cc_start: 0.7534 (mt0) cc_final: 0.6877 (tt0) REVERT: D 342 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7216 (mm-30) REVERT: D 343 LYS cc_start: 0.6758 (mttp) cc_final: 0.6285 (mtpp) REVERT: D 347 LYS cc_start: 0.6095 (mtpt) cc_final: 0.5379 (mttp) REVERT: D 379 ARG cc_start: 0.7309 (mmm-85) cc_final: 0.7103 (mmm-85) REVERT: E 338 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6927 (mm-30) REVERT: E 340 LYS cc_start: 0.6907 (mttt) cc_final: 0.6209 (pptt) REVERT: E 347 LYS cc_start: 0.7487 (mtpt) cc_final: 0.6405 (pptt) REVERT: E 349 ARG cc_start: 0.6846 (mtt90) cc_final: 0.5677 (ttp80) REVERT: E 350 VAL cc_start: 0.7012 (p) cc_final: 0.6739 (m) REVERT: E 353 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7410 (ttmm) REVERT: F 321 LYS cc_start: 0.8450 (mttt) cc_final: 0.7659 (mptt) REVERT: F 342 GLU cc_start: 0.7141 (mt-10) cc_final: 0.5708 (pm20) REVERT: F 345 ASP cc_start: 0.6997 (m-30) cc_final: 0.6586 (t0) REVERT: F 347 LYS cc_start: 0.7524 (mtpt) cc_final: 0.6750 (mtmm) REVERT: F 369 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8273 (mtpt) outliers start: 5 outliers final: 1 residues processed: 85 average time/residue: 3.6769 time to fit residues: 319.1472 Evaluate side-chains 75 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 31 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3582 Z= 0.215 Angle : 0.531 4.927 4794 Z= 0.284 Chirality : 0.051 0.136 534 Planarity : 0.003 0.028 618 Dihedral : 8.989 67.551 480 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.99 % Allowed : 9.95 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.99 (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 0.005 0.001 HIS A 330 PHE 0.008 0.002 PHE B 378 TYR 0.012 0.002 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: 8 poor density : 72 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7773 (tt0) cc_final: 0.7527 (mt0) REVERT: B 311 LYS cc_start: 0.8421 (tmmt) cc_final: 0.8195 (mtmm) REVERT: B 317 LYS cc_start: 0.8502 (ptmt) cc_final: 0.8136 (ptpt) REVERT: B 321 LYS cc_start: 0.8471 (mttt) cc_final: 0.7980 (mttp) REVERT: B 336 GLN cc_start: 0.7719 (mt0) cc_final: 0.6954 (tt0) REVERT: B 372 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8069 (mt-10) REVERT: C 369 LYS cc_start: 0.8760 (ttpp) cc_final: 0.8366 (tppt) REVERT: D 314 ASP cc_start: 0.9079 (t70) cc_final: 0.8850 (t0) REVERT: D 321 LYS cc_start: 0.8401 (mttt) cc_final: 0.7986 (mttp) REVERT: D 342 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7104 (mm-30) REVERT: D 343 LYS cc_start: 0.6783 (mttp) cc_final: 0.6299 (mtpp) REVERT: D 347 LYS cc_start: 0.6041 (mtpt) cc_final: 0.5303 (mttp) REVERT: D 379 ARG cc_start: 0.7335 (mmm-85) cc_final: 0.7038 (tpp80) REVERT: E 338 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6772 (mm-30) REVERT: E 340 LYS cc_start: 0.7104 (mttt) cc_final: 0.6222 (pptt) REVERT: E 347 LYS cc_start: 0.7351 (mtpt) cc_final: 0.6234 (pptt) REVERT: E 349 ARG cc_start: 0.6854 (mtt90) cc_final: 0.6409 (mtp-110) REVERT: E 350 VAL cc_start: 0.7130 (p) cc_final: 0.6881 (m) REVERT: E 353 LYS cc_start: 0.7877 (ttmt) cc_final: 0.7570 (ttmm) REVERT: F 342 GLU cc_start: 0.7394 (mt-10) cc_final: 0.5725 (pm20) REVERT: F 345 ASP cc_start: 0.7023 (m-30) cc_final: 0.6529 (t0) REVERT: F 369 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8333 (mtpt) outliers start: 8 outliers final: 4 residues processed: 75 average time/residue: 3.6526 time to fit residues: 279.7637 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 : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 40.0000 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3582 Z= 0.261 Angle : 0.543 5.201 4794 Z= 0.288 Chirality : 0.051 0.136 534 Planarity : 0.003 0.031 618 Dihedral : 8.903 68.175 480 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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 (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: -2.07 (0.31), 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 HIS 0.004 0.001 HIS B 329 PHE 0.008 0.002 PHE B 378 TYR 0.011 0.002 TYR F 310 ARG 0.002 0.000 ARG D 349 *********************** 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 77 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7765 (tt0) cc_final: 0.7474 (mt0) REVERT: B 311 LYS cc_start: 0.8459 (tmmt) cc_final: 0.8237 (mtmm) REVERT: B 317 LYS cc_start: 0.8483 (ptmt) cc_final: 0.8096 (ptpt) REVERT: B 321 LYS cc_start: 0.8552 (mttt) cc_final: 0.8038 (mttp) REVERT: B 372 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8037 (mt-10) REVERT: C 369 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8375 (tppt) REVERT: D 314 ASP cc_start: 0.9122 (t70) cc_final: 0.8905 (t0) REVERT: D 321 LYS cc_start: 0.8411 (mttt) cc_final: 0.8118 (mttm) REVERT: D 342 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7156 (mm-30) REVERT: D 343 LYS cc_start: 0.6865 (mttp) cc_final: 0.6345 (mtpp) REVERT: D 347 LYS cc_start: 0.6003 (mtpt) cc_final: 0.5230 (mttp) REVERT: D 379 ARG cc_start: 0.7300 (mmm-85) cc_final: 0.7008 (tpp80) REVERT: E 338 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6737 (mm-30) REVERT: E 340 LYS cc_start: 0.7051 (mttt) cc_final: 0.6134 (pptt) REVERT: E 347 LYS cc_start: 0.7290 (mtpt) cc_final: 0.6190 (pptt) REVERT: E 349 ARG cc_start: 0.6929 (mtt90) cc_final: 0.6503 (mtp-110) REVERT: E 350 VAL cc_start: 0.7147 (p) cc_final: 0.6883 (m) REVERT: E 353 LYS cc_start: 0.8039 (ttmt) cc_final: 0.7624 (ttmm) REVERT: F 342 GLU cc_start: 0.7295 (mt-10) cc_final: 0.5653 (pm20) REVERT: F 345 ASP cc_start: 0.7104 (m-30) cc_final: 0.6654 (t0) outliers start: 6 outliers final: 4 residues processed: 73 average time/residue: 3.5008 time to fit residues: 261.1669 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 : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4871 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= 0.167 Angle : 0.480 3.840 4794 Z= 0.250 Chirality : 0.050 0.132 534 Planarity : 0.003 0.031 618 Dihedral : 8.667 67.059 480 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.99 % Allowed : 11.19 % 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 (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: -2.09 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.005 0.001 PHE A 378 TYR 0.007 0.002 TYR F 310 ARG 0.003 0.000 ARG B 379 *********************** 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 77 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7755 (tt0) cc_final: 0.7458 (mt0) REVERT: B 317 LYS cc_start: 0.8459 (ptmt) cc_final: 0.8085 (ptpt) REVERT: B 321 LYS cc_start: 0.8547 (mttt) cc_final: 0.8024 (mttp) REVERT: B 372 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8059 (mt-10) REVERT: C 369 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8359 (tppt) REVERT: D 314 ASP cc_start: 0.9096 (t70) cc_final: 0.8880 (t0) REVERT: D 321 LYS cc_start: 0.8428 (mttt) cc_final: 0.8120 (mttm) REVERT: D 343 LYS cc_start: 0.6899 (mttp) cc_final: 0.6379 (mtpp) REVERT: D 347 LYS cc_start: 0.6028 (mtpt) cc_final: 0.5213 (mttp) REVERT: D 356 SER cc_start: 0.8920 (p) cc_final: 0.8672 (p) REVERT: D 379 ARG cc_start: 0.7266 (mmm-85) cc_final: 0.6968 (tpp80) REVERT: E 338 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6705 (mm-30) REVERT: E 340 LYS cc_start: 0.7057 (mttt) cc_final: 0.6075 (pptt) REVERT: E 342 GLU cc_start: 0.4789 (pm20) cc_final: 0.4586 (pm20) REVERT: E 349 ARG cc_start: 0.6728 (mtt90) cc_final: 0.6271 (mtp-110) REVERT: E 350 VAL cc_start: 0.7104 (p) cc_final: 0.6846 (m) REVERT: E 353 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7566 (ttmm) REVERT: F 342 GLU cc_start: 0.7288 (mt-10) cc_final: 0.5636 (pm20) outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 3.3467 time to fit residues: 242.5742 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 : 0.395 ------------------------------------------------------------------------------- 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 E residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 0.0470 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4956 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= 0.194 Angle : 0.504 5.360 4794 Z= 0.261 Chirality : 0.050 0.132 534 Planarity : 0.003 0.034 618 Dihedral : 8.567 66.975 480 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.99 % Allowed : 11.94 % 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: -2.13 (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 HIS 0.003 0.001 HIS F 330 PHE 0.007 0.001 PHE B 378 TYR 0.009 0.002 TYR F 310 ARG 0.002 0.000 ARG B 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 76 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7748 (tt0) cc_final: 0.7461 (mt0) REVERT: B 317 LYS cc_start: 0.8438 (ptmt) cc_final: 0.8054 (ptpt) REVERT: B 321 LYS cc_start: 0.8570 (mttt) cc_final: 0.8044 (mttp) REVERT: B 372 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8037 (mm-30) REVERT: C 369 LYS cc_start: 0.8767 (ttpp) cc_final: 0.8376 (tppt) REVERT: D 314 ASP cc_start: 0.9100 (t70) cc_final: 0.8885 (t0) REVERT: D 321 LYS cc_start: 0.8432 (mttt) cc_final: 0.8115 (mttm) REVERT: D 343 LYS cc_start: 0.6882 (mttp) cc_final: 0.6362 (mtpp) REVERT: D 347 LYS cc_start: 0.5992 (mtpt) cc_final: 0.5172 (mttp) REVERT: D 356 SER cc_start: 0.8853 (p) cc_final: 0.8651 (p) REVERT: D 379 ARG cc_start: 0.7220 (mmm-85) cc_final: 0.6927 (tpp80) REVERT: E 338 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6699 (mm-30) REVERT: E 340 LYS cc_start: 0.7121 (mttt) cc_final: 0.6073 (pptt) REVERT: E 342 GLU cc_start: 0.4804 (pm20) cc_final: 0.4511 (pm20) REVERT: E 349 ARG cc_start: 0.6723 (mtt90) cc_final: 0.6291 (mtp-110) REVERT: E 350 VAL cc_start: 0.7159 (p) cc_final: 0.6886 (m) REVERT: E 353 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7599 (ttmm) REVERT: F 342 GLU cc_start: 0.7194 (mt-10) cc_final: 0.5606 (pm20) outliers start: 8 outliers final: 3 residues processed: 70 average time/residue: 3.2387 time to fit residues: 231.3891 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 : 0.393 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3582 Z= 0.165 Angle : 0.474 3.738 4794 Z= 0.245 Chirality : 0.049 0.131 534 Planarity : 0.003 0.036 618 Dihedral : 8.473 66.417 480 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.49 % Allowed : 12.19 % Favored : 86.32 % 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: -2.13 (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 HIS 0.003 0.001 HIS A 362 PHE 0.005 0.001 PHE B 378 TYR 0.008 0.002 TYR B 310 ARG 0.002 0.000 ARG F 349 *********************** 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: 6 poor density : 66 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7739 (tt0) cc_final: 0.7461 (mt0) REVERT: B 317 LYS cc_start: 0.8476 (ptmt) cc_final: 0.8090 (ptpt) REVERT: B 321 LYS cc_start: 0.8557 (mttt) cc_final: 0.8021 (mttp) REVERT: B 353 LYS cc_start: 0.6551 (ttmt) cc_final: 0.6242 (ttmt) REVERT: B 372 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8041 (mm-30) REVERT: C 369 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8409 (tppt) REVERT: D 321 LYS cc_start: 0.8437 (mttt) cc_final: 0.8109 (mttm) REVERT: D 343 LYS cc_start: 0.6855 (mttp) cc_final: 0.6340 (mtpp) REVERT: D 347 LYS cc_start: 0.6033 (mtpt) cc_final: 0.5211 (mttp) REVERT: D 379 ARG cc_start: 0.7195 (mmm-85) cc_final: 0.6897 (tpp80) REVERT: E 338 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6687 (mm-30) REVERT: E 340 LYS cc_start: 0.7128 (mttt) cc_final: 0.6026 (pptt) REVERT: E 342 GLU cc_start: 0.4767 (pm20) cc_final: 0.4492 (pm20) REVERT: E 349 ARG cc_start: 0.6621 (mtt90) cc_final: 0.6224 (mtp-110) REVERT: E 350 VAL cc_start: 0.7185 (p) cc_final: 0.6916 (m) REVERT: E 353 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7592 (ttmm) REVERT: F 342 GLU cc_start: 0.7246 (mt-10) cc_final: 0.5666 (pm20) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 3.8152 time to fit residues: 264.7712 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 : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 SER 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 3 optimal weight: 9.9990 chunk 31 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5137 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= 0.130 Angle : 0.455 4.637 4794 Z= 0.233 Chirality : 0.049 0.129 534 Planarity : 0.003 0.035 618 Dihedral : 8.356 65.827 480 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.24 % Allowed : 12.69 % 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: -2.13 (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 HIS 0.004 0.001 HIS A 362 PHE 0.004 0.001 PHE B 378 TYR 0.007 0.001 TYR F 310 ARG 0.001 0.000 ARG F 349 *********************** 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: 5 poor density : 63 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7741 (tt0) cc_final: 0.7477 (mt0) REVERT: B 317 LYS cc_start: 0.8502 (ptmt) cc_final: 0.8097 (ptpt) REVERT: B 321 LYS cc_start: 0.8530 (mttt) cc_final: 0.7988 (mttp) REVERT: B 353 LYS cc_start: 0.6602 (ttmt) cc_final: 0.6293 (ttmt) REVERT: B 372 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8065 (mm-30) REVERT: C 369 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8412 (tppt) REVERT: D 321 LYS cc_start: 0.8372 (mttt) cc_final: 0.8045 (mttm) REVERT: D 343 LYS cc_start: 0.6882 (mttp) cc_final: 0.6364 (mtpp) REVERT: D 347 LYS cc_start: 0.6025 (mtpt) cc_final: 0.5200 (mttp) REVERT: D 379 ARG cc_start: 0.7154 (mmm-85) cc_final: 0.6854 (tpp80) REVERT: E 338 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6696 (mm-30) REVERT: E 340 LYS cc_start: 0.7169 (mttt) cc_final: 0.6055 (pptt) REVERT: E 342 GLU cc_start: 0.4736 (pm20) cc_final: 0.4483 (pm20) REVERT: E 349 ARG cc_start: 0.6575 (mtt90) cc_final: 0.6162 (mtp-110) REVERT: E 350 VAL cc_start: 0.6839 (p) cc_final: 0.6560 (m) REVERT: E 353 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7557 (ttmm) REVERT: F 342 GLU cc_start: 0.7286 (mt-10) cc_final: 0.5700 (pm20) outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 3.8221 time to fit residues: 253.6835 Evaluate side-chains 65 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3582 Z= 0.284 Angle : 0.524 4.644 4794 Z= 0.277 Chirality : 0.050 0.134 534 Planarity : 0.003 0.034 618 Dihedral : 8.544 68.400 480 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -2.21 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.008 0.002 PHE B 378 TYR 0.011 0.002 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** 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 : 0.763 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7754 (tt0) cc_final: 0.7466 (mt0) REVERT: A 311 LYS cc_start: 0.8547 (mttt) cc_final: 0.8235 (mttp) REVERT: B 317 LYS cc_start: 0.8477 (ptmt) cc_final: 0.8061 (ptpt) REVERT: B 321 LYS cc_start: 0.8596 (mttt) cc_final: 0.8067 (mttp) REVERT: B 372 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8108 (mt-10) REVERT: C 369 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8409 (tppt) REVERT: D 321 LYS cc_start: 0.8441 (mttt) cc_final: 0.8112 (mttm) REVERT: D 343 LYS cc_start: 0.6855 (mttp) cc_final: 0.6343 (mtpp) REVERT: D 347 LYS cc_start: 0.5972 (mtpt) cc_final: 0.5153 (mttp) REVERT: D 379 ARG cc_start: 0.7197 (mmm-85) cc_final: 0.6902 (tpp80) REVERT: E 338 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6713 (mm-30) REVERT: E 340 LYS cc_start: 0.7240 (mttt) cc_final: 0.5977 (pptt) REVERT: E 342 GLU cc_start: 0.4813 (pm20) cc_final: 0.4509 (pm20) REVERT: E 349 ARG cc_start: 0.6667 (mtt90) cc_final: 0.6238 (mtp-110) REVERT: E 350 VAL cc_start: 0.7192 (p) cc_final: 0.6905 (m) REVERT: E 353 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7626 (ttmm) REVERT: F 342 GLU cc_start: 0.7247 (mt-10) cc_final: 0.5645 (pm20) outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 3.9726 time to fit residues: 267.5891 Evaluate side-chains 66 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3582 Z= 0.151 Angle : 0.462 3.839 4794 Z= 0.239 Chirality : 0.049 0.130 534 Planarity : 0.003 0.032 618 Dihedral : 8.430 66.508 480 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.75 % Allowed : 13.93 % Favored : 85.32 % 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: -2.20 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (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 378 TYR 0.009 0.002 TYR B 310 ARG 0.002 0.000 ARG F 349 ********************** 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 66 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7740 (tt0) cc_final: 0.7450 (mt0) REVERT: B 317 LYS cc_start: 0.8498 (ptmt) cc_final: 0.8082 (ptpt) REVERT: B 321 LYS cc_start: 0.8560 (mttt) cc_final: 0.8014 (mttp) REVERT: B 353 LYS cc_start: 0.6541 (ttmt) cc_final: 0.6247 (ttmt) REVERT: B 372 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8062 (mm-30) REVERT: C 369 LYS cc_start: 0.8787 (ttpp) cc_final: 0.8407 (tppt) REVERT: D 321 LYS cc_start: 0.8420 (mttt) cc_final: 0.8013 (mttp) REVERT: D 343 LYS cc_start: 0.6862 (mttp) cc_final: 0.6367 (mtpp) REVERT: D 347 LYS cc_start: 0.6026 (mtpt) cc_final: 0.5195 (mttp) REVERT: D 379 ARG cc_start: 0.7162 (mmm-85) cc_final: 0.6854 (tpp80) REVERT: E 338 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6698 (mm-30) REVERT: E 340 LYS cc_start: 0.7237 (mttt) cc_final: 0.5992 (pptt) REVERT: E 342 GLU cc_start: 0.4652 (pm20) cc_final: 0.4416 (pm20) REVERT: E 349 ARG cc_start: 0.6619 (mtt90) cc_final: 0.6184 (mtp-110) REVERT: E 350 VAL cc_start: 0.6863 (p) cc_final: 0.6583 (m) REVERT: E 353 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7566 (ttmm) REVERT: F 342 GLU cc_start: 0.7237 (mt-10) cc_final: 0.5666 (pm20) outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 3.9083 time to fit residues: 255.1504 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 : 0.597 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.150724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.109609 restraints weight = 11650.956| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.89 r_work: 0.3440 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3582 Z= 0.156 Angle : 0.465 3.773 4794 Z= 0.241 Chirality : 0.050 0.130 534 Planarity : 0.003 0.030 618 Dihedral : 8.372 66.465 480 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 : 0.75 % Allowed : 13.93 % Favored : 85.32 % 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: -2.14 (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 HIS 0.004 0.001 HIS A 362 PHE 0.004 0.001 PHE C 378 TYR 0.008 0.002 TYR F 310 ARG 0.004 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5190.93 seconds wall clock time: 92 minutes 10.79 seconds (5530.79 seconds total)