Starting phenix.real_space_refine on Sat Aug 23 05:47:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7t_18233/08_2025/8q7t_18233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7t_18233/08_2025/8q7t_18233.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/8q7t_18233/08_2025/8q7t_18233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7t_18233/08_2025/8q7t_18233.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7t_18233/08_2025/8q7t_18233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7t_18233/08_2025/8q7t_18233.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 9 5.16 5 C 3102 2.51 5 N 903 2.21 5 O 933 1.98 5 H 5136 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s 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: 10083 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "A" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "G" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "H" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "I" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.50, per 1000 atoms: 0.15 Number of scatterers: 10083 At special positions: 0 Unit cell: (161.394, 145.4, 47.982, 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 9 16.00 O 933 8.00 N 903 7.00 C 3102 6.00 H 5136 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: 0.59 Conformation dependent library (CDL) restraints added in 318.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1134 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 25 sheets defined 0.0% alpha, 54.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.488A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.859A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.324A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.603A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 337 through 346 removed outlier: 6.569A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER D 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS B 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LYS D 343 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLU B 342 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASP D 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU F 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP B 345 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE F 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 362 removed outlier: 6.899A pdb=" N GLN D 351 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER B 352 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS D 353 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY D 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLN B 351 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N SER F 352 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 353 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE F 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY B 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER F 356 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.462A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 309 through 310 removed outlier: 6.542A pdb=" N VAL E 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.796A pdb=" N VAL E 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.468A pdb=" N VAL C 318 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LYS H 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER C 320 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLY H 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N CYS C 322 " --> pdb=" O GLY H 323 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU H 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER C 324 " --> pdb=" O LEU H 325 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS E 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N SER H 320 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR E 319 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N CYS H 322 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS E 321 " --> pdb=" O CYS H 322 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N SER H 324 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY E 323 " --> pdb=" O SER H 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.461A pdb=" N ILE E 328 " --> pdb=" O HIS H 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.576A pdb=" N GLU E 338 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER H 341 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS E 340 " --> pdb=" O SER H 341 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.538A pdb=" N ASP E 345 " --> pdb=" O PHE H 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.512A pdb=" N GLN E 351 " --> pdb=" O SER H 352 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE H 354 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS E 353 " --> pdb=" O ILE H 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.523A pdb=" N ASN C 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N HIS H 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR C 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 368 through 374 Processing sheet with id=AB8, first strand: chain 'G' and resid 305 through 310 removed outlier: 6.571A pdb=" N VAL A 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL I 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 313 through 314 removed outlier: 6.919A pdb=" N VAL A 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 317 through 325 removed outlier: 6.491A pdb=" N VAL A 318 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS I 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N SER A 320 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLY I 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N CYS A 322 " --> pdb=" O GLY I 323 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU I 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 324 " --> pdb=" O LEU I 325 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 328 through 330 removed outlier: 6.696A pdb=" N ILE A 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 333 through 334 removed outlier: 6.854A pdb=" N GLY A 333 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 337 through 346 removed outlier: 6.403A pdb=" N GLU A 338 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N SER G 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS A 340 " --> pdb=" O SER G 341 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LYS G 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N GLU A 342 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ASP G 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N LEU A 344 " --> pdb=" O ASP G 345 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LYS I 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU I 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER A 341 " --> pdb=" O GLU I 342 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU I 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS A 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N PHE I 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N ASP A 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 350 through 358 removed outlier: 6.406A pdb=" N GLN A 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE G 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS A 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N SER G 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N GLY A 355 " --> pdb=" O SER G 356 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP G 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N LEU A 357 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 350 " --> pdb=" O GLN I 351 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LYS I 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER A 352 " --> pdb=" O LYS I 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.320A pdb=" N THR A 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 368 through 377 removed outlier: 6.478A pdb=" N LYS A 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLU G 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N HIS G 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR A 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU G 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS A 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) 98 hydrogen bonds defined for protein. 294 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: 1.40 Time building geometry restraints manager: 0.86 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: 5127 1.12 - 1.29: 834 1.29 - 1.47: 1711 1.47 - 1.64: 2480 1.64 - 1.82: 9 Bond restraints: 10161 Sorted by residual: bond pdb=" NE2 HIS F 329 " pdb=" HE2 HIS F 329 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN F 327 " pdb="HD22 ASN F 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS D 353 " pdb=" H LYS D 353 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NE2 HIS D 362 " pdb=" HE2 HIS D 362 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ASP E 345 " pdb=" H ASP E 345 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 10156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 15834 2.57 - 5.15: 2071 5.15 - 7.72: 613 7.72 - 10.29: 10 10.29 - 12.87: 6 Bond angle restraints: 18534 Sorted by residual: angle pdb=" CA GLY I 355 " pdb=" C GLY I 355 " pdb=" N SER I 356 " ideal model delta sigma weight residual 114.58 119.53 -4.95 8.60e-01 1.35e+00 3.31e+01 angle pdb=" OE1 GLN I 336 " pdb=" CD GLN I 336 " pdb=" NE2 GLN I 336 " ideal model delta sigma weight residual 122.60 117.08 5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" OE1 GLN B 336 " pdb=" CD GLN B 336 " pdb=" NE2 GLN B 336 " ideal model delta sigma weight residual 122.60 117.08 5.52 1.00e+00 1.00e+00 3.04e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.95 -5.35 1.00e+00 1.00e+00 2.86e+01 angle pdb=" OE1 GLN G 336 " pdb=" CD GLN G 336 " pdb=" NE2 GLN G 336 " ideal model delta sigma weight residual 122.60 117.32 5.28 1.00e+00 1.00e+00 2.79e+01 ... (remaining 18529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 4147 16.79 - 33.58: 266 33.58 - 50.38: 119 50.38 - 67.17: 145 67.17 - 83.96: 6 Dihedral angle restraints: 4683 sinusoidal: 2676 harmonic: 2007 Sorted by residual: dihedral pdb=" CA PRO C 332 " pdb=" C PRO C 332 " pdb=" N GLY C 333 " pdb=" CA GLY C 333 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA GLY C 334 " pdb=" C GLY C 334 " pdb=" N GLY C 335 " pdb=" CA GLY C 335 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLY A 367 " pdb=" C GLY A 367 " pdb=" N ASN A 368 " pdb=" CA ASN A 368 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 4680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 508 0.081 - 0.161: 213 0.161 - 0.242: 27 0.242 - 0.322: 6 0.322 - 0.402: 2 Chirality restraints: 756 Sorted by residual: chirality pdb=" CA PRO H 332 " pdb=" N PRO H 332 " pdb=" C PRO H 332 " pdb=" CB PRO H 332 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA PRO C 332 " pdb=" N PRO C 332 " pdb=" C PRO C 332 " pdb=" CB PRO C 332 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA LYS F 347 " pdb=" N LYS F 347 " pdb=" C LYS F 347 " pdb=" CB LYS F 347 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 753 not shown) Planarity restraints: 1473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 368 " 0.110 2.00e-02 2.50e+03 1.01e-01 1.53e+02 pdb=" CG ASN A 368 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 368 " -0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN A 368 " -0.044 2.00e-02 2.50e+03 pdb="HD21 ASN A 368 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN A 368 " 0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.099 2.00e-02 2.50e+03 5.55e-02 9.25e+01 pdb=" CG TYR E 310 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.139 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " -0.033 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 368 " 0.082 2.00e-02 2.50e+03 7.83e-02 9.19e+01 pdb=" CG ASN G 368 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN G 368 " -0.073 2.00e-02 2.50e+03 pdb=" ND2 ASN G 368 " -0.029 2.00e-02 2.50e+03 pdb="HD21 ASN G 368 " -0.094 2.00e-02 2.50e+03 pdb="HD22 ASN G 368 " 0.123 2.00e-02 2.50e+03 ... (remaining 1470 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 599 2.14 - 2.75: 15950 2.75 - 3.37: 26764 3.37 - 3.98: 35994 3.98 - 4.60: 49732 Nonbonded interactions: 129039 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.520 2.450 nonbonded pdb=" OD1 ASP H 314 " pdb=" HG SER H 316 " model vdw 1.527 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.559 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.581 2.450 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.582 2.450 ... (remaining 129034 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' and resid 308 through 375) selection = (chain 'B' and resid 308 through 375) selection = chain 'C' selection = (chain 'D' and resid 308 through 375) selection = chain 'E' selection = (chain 'F' and resid 308 through 375) selection = (chain 'G' and resid 308 through 375) selection = chain 'H' selection = (chain 'I' and resid 308 through 375) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 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: 0.040 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.970 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 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 5025 Z= 0.674 Angle : 1.800 6.507 6723 Z= 1.186 Chirality : 0.085 0.402 756 Planarity : 0.009 0.066 855 Dihedral : 12.353 83.957 1920 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.18 % Allowed : 3.17 % Favored : 96.65 % 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: -1.65 (0.27), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 349 TYR 0.123 0.015 TYR E 310 PHE 0.071 0.019 PHE C 346 HIS 0.012 0.003 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.01086 ( 5025) covalent geometry : angle 1.80017 ( 6723) hydrogen bonds : bond 0.07534 ( 98) hydrogen bonds : angle 7.90665 ( 294) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 ASN cc_start: 0.5745 (m-40) cc_final: 0.5431 (m110) REVERT: D 368 ASN cc_start: 0.4983 (m-40) cc_final: 0.4759 (m110) REVERT: C 317 LYS cc_start: 0.8151 (mttt) cc_final: 0.7898 (mttm) REVERT: C 338 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7813 (tt0) REVERT: C 347 LYS cc_start: 0.8162 (mttt) cc_final: 0.7692 (pmtt) REVERT: C 369 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7439 (mtmt) REVERT: A 311 LYS cc_start: 0.7844 (mttt) cc_final: 0.7413 (tttm) REVERT: E 311 LYS cc_start: 0.7720 (mtmt) cc_final: 0.7003 (mmtm) REVERT: E 347 LYS cc_start: 0.8054 (mttt) cc_final: 0.7612 (tttt) REVERT: E 369 LYS cc_start: 0.7681 (ttmt) cc_final: 0.7048 (ttpm) REVERT: G 311 LYS cc_start: 0.8106 (mttt) cc_final: 0.7610 (tttm) REVERT: G 360 ILE cc_start: 0.8454 (mt) cc_final: 0.8228 (mp) REVERT: H 311 LYS cc_start: 0.7634 (mtmt) cc_final: 0.7351 (mtpt) REVERT: H 340 LYS cc_start: 0.7485 (mttt) cc_final: 0.7134 (mtmp) REVERT: H 347 LYS cc_start: 0.8031 (mttt) cc_final: 0.7650 (mmtm) REVERT: H 369 LYS cc_start: 0.7528 (ttmt) cc_final: 0.6759 (mtmt) REVERT: H 372 GLU cc_start: 0.7438 (tt0) cc_final: 0.7180 (tt0) REVERT: I 311 LYS cc_start: 0.7744 (mttt) cc_final: 0.6975 (mmtm) REVERT: I 360 ILE cc_start: 0.8178 (mt) cc_final: 0.7751 (mm) REVERT: I 375 LYS cc_start: 0.7171 (tttt) cc_final: 0.6582 (ttmm) outliers start: 1 outliers final: 2 residues processed: 167 average time/residue: 0.9910 time to fit residues: 171.8051 Evaluate side-chains 98 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN F 368 ASN G 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.203492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.150147 restraints weight = 17220.532| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.22 r_work: 0.4022 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5025 Z= 0.206 Angle : 0.644 4.560 6723 Z= 0.333 Chirality : 0.052 0.147 756 Planarity : 0.004 0.025 855 Dihedral : 6.790 37.401 667 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.17 % Allowed : 12.17 % Favored : 84.66 % 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: -1.25 (0.29), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 349 TYR 0.013 0.002 TYR A 310 PHE 0.010 0.001 PHE A 346 HIS 0.008 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 5025) covalent geometry : angle 0.64432 ( 6723) hydrogen bonds : bond 0.03070 ( 98) hydrogen bonds : angle 5.38156 ( 294) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 353 LYS cc_start: 0.5989 (tttt) cc_final: 0.5716 (tmtm) REVERT: B 368 ASN cc_start: 0.5833 (m-40) cc_final: 0.5541 (m110) REVERT: D 321 LYS cc_start: 0.3289 (pptt) cc_final: 0.2647 (pmtt) REVERT: D 368 ASN cc_start: 0.5012 (m-40) cc_final: 0.4674 (m110) REVERT: F 325 LEU cc_start: 0.3810 (mt) cc_final: 0.3383 (mt) REVERT: F 358 ASP cc_start: 0.6928 (p0) cc_final: 0.6596 (t0) REVERT: F 368 ASN cc_start: 0.4776 (OUTLIER) cc_final: 0.4554 (m110) REVERT: C 338 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8236 (tt0) REVERT: C 347 LYS cc_start: 0.8401 (mttt) cc_final: 0.7960 (pmtt) REVERT: C 369 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8009 (mtmt) REVERT: A 360 ILE cc_start: 0.8950 (mt) cc_final: 0.8675 (mm) REVERT: E 311 LYS cc_start: 0.8001 (mtmt) cc_final: 0.7212 (mmtm) REVERT: E 347 LYS cc_start: 0.8321 (mttt) cc_final: 0.8059 (tttt) REVERT: E 369 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8068 (ttpt) REVERT: H 347 LYS cc_start: 0.8236 (mttt) cc_final: 0.7703 (tttp) REVERT: H 369 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7811 (mtmt) REVERT: I 311 LYS cc_start: 0.8069 (mttt) cc_final: 0.7598 (mmtm) REVERT: I 360 ILE cc_start: 0.8955 (mt) cc_final: 0.8671 (mm) REVERT: I 375 LYS cc_start: 0.8123 (tttt) cc_final: 0.7788 (ttmm) outliers start: 18 outliers final: 11 residues processed: 121 average time/residue: 1.3363 time to fit residues: 167.6163 Evaluate side-chains 100 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.202276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.148383 restraints weight = 17250.303| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.21 r_work: 0.3989 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5025 Z= 0.211 Angle : 0.611 6.276 6723 Z= 0.314 Chirality : 0.052 0.188 756 Planarity : 0.003 0.026 855 Dihedral : 6.109 30.993 665 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.06 % Allowed : 14.99 % Favored : 80.95 % 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: -1.41 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.012 0.002 TYR A 310 PHE 0.007 0.001 PHE A 346 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 5025) covalent geometry : angle 0.61100 ( 6723) hydrogen bonds : bond 0.02688 ( 98) hydrogen bonds : angle 5.02423 ( 294) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4522 (t70) cc_final: 0.4057 (t70) REVERT: B 353 LYS cc_start: 0.6070 (tttt) cc_final: 0.5843 (tmtm) REVERT: D 368 ASN cc_start: 0.5211 (m-40) cc_final: 0.4895 (m110) REVERT: D 372 GLU cc_start: 0.5417 (mm-30) cc_final: 0.4691 (mm-30) REVERT: F 321 LYS cc_start: 0.6192 (OUTLIER) cc_final: 0.5679 (mtpp) REVERT: F 325 LEU cc_start: 0.3824 (mt) cc_final: 0.3165 (mt) REVERT: F 327 ASN cc_start: 0.3604 (m-40) cc_final: 0.3119 (m110) REVERT: C 311 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7859 (mttt) REVERT: C 338 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8240 (tt0) REVERT: C 347 LYS cc_start: 0.8352 (mttt) cc_final: 0.7964 (pmtt) REVERT: C 369 LYS cc_start: 0.8523 (ttmt) cc_final: 0.8066 (mtmt) REVERT: A 360 ILE cc_start: 0.8963 (mt) cc_final: 0.8658 (mm) REVERT: E 311 LYS cc_start: 0.7959 (mtmt) cc_final: 0.7165 (mmtm) REVERT: E 347 LYS cc_start: 0.8350 (mttt) cc_final: 0.8068 (tttt) REVERT: E 369 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8069 (tttm) REVERT: H 347 LYS cc_start: 0.8245 (mttt) cc_final: 0.7693 (tttp) REVERT: H 369 LYS cc_start: 0.8393 (ttmt) cc_final: 0.7838 (mtmt) REVERT: I 311 LYS cc_start: 0.8122 (mttt) cc_final: 0.7650 (mmtm) REVERT: I 360 ILE cc_start: 0.8988 (mt) cc_final: 0.8699 (mm) REVERT: I 375 LYS cc_start: 0.8163 (tttt) cc_final: 0.7805 (ttmm) outliers start: 23 outliers final: 13 residues processed: 108 average time/residue: 1.2819 time to fit residues: 144.0615 Evaluate side-chains 103 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.204062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.150172 restraints weight = 17153.916| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.17 r_work: 0.4026 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3944 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5025 Z= 0.118 Angle : 0.528 4.439 6723 Z= 0.266 Chirality : 0.051 0.148 756 Planarity : 0.003 0.035 855 Dihedral : 5.545 31.181 665 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.70 % Allowed : 16.75 % Favored : 79.54 % 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: -1.43 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 349 TYR 0.009 0.001 TYR A 310 PHE 0.004 0.001 PHE B 346 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 5025) covalent geometry : angle 0.52800 ( 6723) hydrogen bonds : bond 0.02343 ( 98) hydrogen bonds : angle 4.62245 ( 294) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4607 (t70) cc_final: 0.4193 (t70) REVERT: B 358 ASP cc_start: 0.7660 (p0) cc_final: 0.7424 (p0) REVERT: D 321 LYS cc_start: 0.3356 (OUTLIER) cc_final: 0.2929 (pmtt) REVERT: D 331 LYS cc_start: 0.6120 (mttt) cc_final: 0.5207 (pptt) REVERT: D 368 ASN cc_start: 0.5207 (m-40) cc_final: 0.4940 (m110) REVERT: D 372 GLU cc_start: 0.5308 (mm-30) cc_final: 0.4640 (mm-30) REVERT: F 321 LYS cc_start: 0.6265 (OUTLIER) cc_final: 0.5734 (mtpp) REVERT: F 325 LEU cc_start: 0.3710 (mt) cc_final: 0.2967 (mt) REVERT: F 327 ASN cc_start: 0.3686 (m-40) cc_final: 0.3235 (m110) REVERT: F 358 ASP cc_start: 0.6922 (p0) cc_final: 0.6578 (t0) REVERT: C 311 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7873 (mttt) REVERT: C 338 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8232 (tt0) REVERT: C 347 LYS cc_start: 0.8354 (mttt) cc_final: 0.8068 (pmtt) REVERT: A 349 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7741 (mtp85) REVERT: A 360 ILE cc_start: 0.8972 (mt) cc_final: 0.8678 (mm) REVERT: E 311 LYS cc_start: 0.7898 (mtmt) cc_final: 0.7083 (mmtm) REVERT: E 347 LYS cc_start: 0.8345 (mttt) cc_final: 0.8050 (tttt) REVERT: E 369 LYS cc_start: 0.8328 (ttmt) cc_final: 0.8050 (tttm) REVERT: H 347 LYS cc_start: 0.8223 (mttt) cc_final: 0.7950 (mmtp) REVERT: H 369 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7844 (mtmt) REVERT: I 311 LYS cc_start: 0.8077 (mttt) cc_final: 0.7576 (mmtm) REVERT: I 375 LYS cc_start: 0.8180 (tttt) cc_final: 0.7799 (ttmm) outliers start: 21 outliers final: 10 residues processed: 110 average time/residue: 1.3366 time to fit residues: 152.4753 Evaluate side-chains 99 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.203688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.149758 restraints weight = 17089.892| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.08 r_work: 0.4048 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5025 Z= 0.124 Angle : 0.511 5.405 6723 Z= 0.257 Chirality : 0.050 0.156 756 Planarity : 0.003 0.037 855 Dihedral : 5.311 30.863 665 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.88 % Allowed : 16.05 % Favored : 80.07 % 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: -1.44 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.013 0.002 TYR C 310 PHE 0.004 0.001 PHE A 346 HIS 0.002 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5025) covalent geometry : angle 0.51132 ( 6723) hydrogen bonds : bond 0.02380 ( 98) hydrogen bonds : angle 4.40689 ( 294) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 321 LYS cc_start: 0.2954 (OUTLIER) cc_final: 0.2556 (pmtt) REVERT: D 331 LYS cc_start: 0.6149 (mttt) cc_final: 0.5244 (pptt) REVERT: D 368 ASN cc_start: 0.5303 (m-40) cc_final: 0.5050 (m110) REVERT: D 372 GLU cc_start: 0.4861 (mm-30) cc_final: 0.4143 (mm-30) REVERT: F 321 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.6018 (mmpt) REVERT: F 325 LEU cc_start: 0.3923 (mt) cc_final: 0.3153 (mt) REVERT: F 327 ASN cc_start: 0.3926 (m-40) cc_final: 0.3437 (m110) REVERT: C 311 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7790 (mttt) REVERT: C 338 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8230 (tt0) REVERT: C 347 LYS cc_start: 0.8340 (mttt) cc_final: 0.7918 (pmtt) REVERT: C 375 LYS cc_start: 0.5509 (tmtt) cc_final: 0.4933 (tptp) REVERT: A 360 ILE cc_start: 0.9000 (mt) cc_final: 0.8687 (mm) REVERT: E 311 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7092 (mmtm) REVERT: E 347 LYS cc_start: 0.8349 (mttt) cc_final: 0.8054 (tttt) REVERT: E 369 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8036 (tttm) REVERT: H 347 LYS cc_start: 0.8227 (mttt) cc_final: 0.7745 (tttp) REVERT: H 369 LYS cc_start: 0.8388 (ttmt) cc_final: 0.7894 (ttmt) REVERT: I 311 LYS cc_start: 0.8058 (mttt) cc_final: 0.7555 (mmtm) REVERT: I 375 LYS cc_start: 0.8146 (tttt) cc_final: 0.7775 (ttmm) outliers start: 22 outliers final: 15 residues processed: 103 average time/residue: 1.3163 time to fit residues: 140.7286 Evaluate side-chains 98 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 50 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4709 r_free = 0.4709 target = 0.205464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.154317 restraints weight = 17332.592| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.19 r_work: 0.4071 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3989 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5025 Z= 0.098 Angle : 0.501 6.026 6723 Z= 0.250 Chirality : 0.051 0.150 756 Planarity : 0.003 0.039 855 Dihedral : 5.033 29.986 665 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.35 % Allowed : 16.23 % Favored : 80.42 % 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: -1.43 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.011 0.001 TYR C 310 PHE 0.003 0.001 PHE A 346 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5025) covalent geometry : angle 0.50121 ( 6723) hydrogen bonds : bond 0.02045 ( 98) hydrogen bonds : angle 4.16913 ( 294) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 357 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7264 (tp) REVERT: B 358 ASP cc_start: 0.7718 (p0) cc_final: 0.7354 (p0) REVERT: D 321 LYS cc_start: 0.2846 (OUTLIER) cc_final: 0.2476 (pmtt) REVERT: D 331 LYS cc_start: 0.6227 (mttt) cc_final: 0.5333 (pptt) REVERT: D 368 ASN cc_start: 0.5360 (m-40) cc_final: 0.5131 (m110) REVERT: D 372 GLU cc_start: 0.4812 (mm-30) cc_final: 0.4038 (mm-30) REVERT: F 321 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.6024 (mmpt) REVERT: F 325 LEU cc_start: 0.3937 (mt) cc_final: 0.3144 (mp) REVERT: F 327 ASN cc_start: 0.3912 (m-40) cc_final: 0.3424 (m110) REVERT: F 358 ASP cc_start: 0.6902 (p0) cc_final: 0.6672 (t0) REVERT: C 311 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7844 (mttt) REVERT: C 338 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8260 (tt0) REVERT: C 342 GLU cc_start: 0.7979 (tt0) cc_final: 0.7725 (tp30) REVERT: C 347 LYS cc_start: 0.8321 (mttt) cc_final: 0.8094 (pmtt) REVERT: C 375 LYS cc_start: 0.5485 (tmtt) cc_final: 0.4997 (tptp) REVERT: A 360 ILE cc_start: 0.9007 (mt) cc_final: 0.8707 (mm) REVERT: E 311 LYS cc_start: 0.7824 (mtmt) cc_final: 0.7049 (mmtm) REVERT: E 347 LYS cc_start: 0.8355 (mttt) cc_final: 0.8092 (tttt) REVERT: E 369 LYS cc_start: 0.8362 (ttmt) cc_final: 0.8100 (tttm) REVERT: H 369 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7905 (ttmt) REVERT: I 311 LYS cc_start: 0.8064 (mttt) cc_final: 0.7584 (mmtm) REVERT: I 375 LYS cc_start: 0.8185 (tttt) cc_final: 0.7856 (ttmm) outliers start: 19 outliers final: 14 residues processed: 97 average time/residue: 1.3864 time to fit residues: 139.5646 Evaluate side-chains 96 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 30.0000 chunk 34 optimal weight: 0.0270 chunk 26 optimal weight: 0.1980 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.3640 ------------------------------------------------------------------------------- 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 = 0.4715 r_free = 0.4715 target = 0.205600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.154454 restraints weight = 17214.550| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 2.05 r_work: 0.4065 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3980 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5025 Z= 0.098 Angle : 0.494 5.003 6723 Z= 0.244 Chirality : 0.050 0.150 756 Planarity : 0.003 0.040 855 Dihedral : 4.855 29.060 665 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.17 % Allowed : 16.75 % Favored : 80.07 % 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: -1.42 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.010 0.001 TYR C 310 PHE 0.003 0.001 PHE E 346 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5025) covalent geometry : angle 0.49445 ( 6723) hydrogen bonds : bond 0.02072 ( 98) hydrogen bonds : angle 4.02891 ( 294) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 321 LYS cc_start: 0.3031 (OUTLIER) cc_final: 0.2713 (pmtt) REVERT: D 331 LYS cc_start: 0.6226 (mttt) cc_final: 0.5339 (pptt) REVERT: D 368 ASN cc_start: 0.5396 (m-40) cc_final: 0.5181 (m110) REVERT: D 372 GLU cc_start: 0.4848 (mm-30) cc_final: 0.4111 (mm-30) REVERT: F 321 LYS cc_start: 0.6323 (OUTLIER) cc_final: 0.6039 (mmpt) REVERT: F 325 LEU cc_start: 0.3880 (mt) cc_final: 0.3022 (mp) REVERT: F 327 ASN cc_start: 0.3896 (m-40) cc_final: 0.3377 (m110) REVERT: C 311 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7850 (mttt) REVERT: C 342 GLU cc_start: 0.8018 (tt0) cc_final: 0.7788 (tp30) REVERT: A 360 ILE cc_start: 0.9021 (mt) cc_final: 0.8700 (mm) REVERT: E 311 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7040 (mmtm) REVERT: E 369 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8139 (tttm) REVERT: H 347 LYS cc_start: 0.8307 (mmtp) cc_final: 0.7652 (mmtt) REVERT: H 369 LYS cc_start: 0.8389 (ttmt) cc_final: 0.7923 (ttmt) REVERT: I 311 LYS cc_start: 0.8087 (mttt) cc_final: 0.7601 (mmtm) REVERT: I 375 LYS cc_start: 0.8197 (tttt) cc_final: 0.7879 (ttmm) outliers start: 18 outliers final: 14 residues processed: 98 average time/residue: 1.3379 time to fit residues: 136.0883 Evaluate side-chains 91 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.4632 r_free = 0.4632 target = 0.198931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.146244 restraints weight = 17516.246| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.26 r_work: 0.3982 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3903 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5025 Z= 0.203 Angle : 0.558 6.260 6723 Z= 0.284 Chirality : 0.050 0.157 756 Planarity : 0.004 0.039 855 Dihedral : 5.435 29.720 665 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.53 % Allowed : 16.23 % Favored : 80.25 % 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: -1.51 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.012 0.002 TYR A 310 PHE 0.009 0.002 PHE D 346 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 5025) covalent geometry : angle 0.55776 ( 6723) hydrogen bonds : bond 0.02383 ( 98) hydrogen bonds : angle 4.14210 ( 294) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4709 (t70) cc_final: 0.4064 (t70) REVERT: D 321 LYS cc_start: 0.2866 (OUTLIER) cc_final: 0.2590 (pmtt) REVERT: D 331 LYS cc_start: 0.6183 (mttt) cc_final: 0.5327 (pptt) REVERT: D 368 ASN cc_start: 0.5291 (m-40) cc_final: 0.5075 (m110) REVERT: D 372 GLU cc_start: 0.4898 (mm-30) cc_final: 0.4254 (mm-30) REVERT: F 321 LYS cc_start: 0.6343 (OUTLIER) cc_final: 0.6112 (mmpt) REVERT: F 327 ASN cc_start: 0.3984 (m-40) cc_final: 0.3613 (m110) REVERT: C 342 GLU cc_start: 0.8077 (tt0) cc_final: 0.7787 (tp30) REVERT: E 311 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7236 (mmtm) REVERT: E 369 LYS cc_start: 0.8356 (ttmt) cc_final: 0.8039 (tttm) REVERT: H 342 GLU cc_start: 0.7863 (tt0) cc_final: 0.7444 (tp30) REVERT: H 369 LYS cc_start: 0.8376 (ttmt) cc_final: 0.7946 (ttmt) REVERT: I 311 LYS cc_start: 0.8208 (mttt) cc_final: 0.7779 (mmtm) REVERT: I 375 LYS cc_start: 0.8140 (tttt) cc_final: 0.7735 (ttmm) outliers start: 20 outliers final: 14 residues processed: 91 average time/residue: 1.2764 time to fit residues: 120.7585 Evaluate side-chains 86 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4640 r_free = 0.4640 target = 0.199410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.147555 restraints weight = 17386.923| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 2.36 r_work: 0.3980 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.6467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5025 Z= 0.177 Angle : 0.536 4.327 6723 Z= 0.272 Chirality : 0.050 0.158 756 Planarity : 0.004 0.041 855 Dihedral : 5.346 29.373 665 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.82 % Allowed : 17.28 % Favored : 79.89 % 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: -1.60 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 349 TYR 0.010 0.002 TYR A 310 PHE 0.008 0.001 PHE D 346 HIS 0.003 0.001 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 5025) covalent geometry : angle 0.53614 ( 6723) hydrogen bonds : bond 0.02363 ( 98) hydrogen bonds : angle 4.12103 ( 294) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 321 LYS cc_start: 0.2866 (OUTLIER) cc_final: 0.2525 (pmtt) REVERT: D 331 LYS cc_start: 0.6228 (mttt) cc_final: 0.5357 (pptt) REVERT: D 372 GLU cc_start: 0.4955 (mm-30) cc_final: 0.4298 (mm-30) REVERT: F 321 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.6181 (mmpt) REVERT: F 327 ASN cc_start: 0.4026 (m-40) cc_final: 0.3696 (m110) REVERT: C 342 GLU cc_start: 0.8092 (tt0) cc_final: 0.7853 (tp30) REVERT: E 311 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7275 (mmtm) REVERT: E 369 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8143 (tttm) REVERT: E 372 GLU cc_start: 0.8141 (tt0) cc_final: 0.7824 (tt0) REVERT: H 342 GLU cc_start: 0.7937 (tt0) cc_final: 0.7588 (tp30) REVERT: H 369 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8155 (tttm) REVERT: I 375 LYS cc_start: 0.8202 (tttt) cc_final: 0.7838 (ttmm) outliers start: 16 outliers final: 12 residues processed: 88 average time/residue: 1.3729 time to fit residues: 125.3194 Evaluate side-chains 84 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 55 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.4653 r_free = 0.4653 target = 0.200631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.150660 restraints weight = 17409.496| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.12 r_work: 0.3993 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5025 Z= 0.131 Angle : 0.517 4.679 6723 Z= 0.259 Chirality : 0.050 0.154 756 Planarity : 0.003 0.043 855 Dihedral : 5.132 28.669 665 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.47 % Allowed : 18.34 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.27), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.008 0.001 TYR C 310 PHE 0.006 0.001 PHE D 346 HIS 0.003 0.001 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5025) covalent geometry : angle 0.51746 ( 6723) hydrogen bonds : bond 0.02286 ( 98) hydrogen bonds : angle 4.03216 ( 294) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 339 VAL cc_start: 0.6494 (t) cc_final: 0.5960 (p) REVERT: D 321 LYS cc_start: 0.3083 (OUTLIER) cc_final: 0.2881 (pmtt) REVERT: D 331 LYS cc_start: 0.6296 (mttt) cc_final: 0.5421 (pptt) REVERT: D 372 GLU cc_start: 0.4893 (mm-30) cc_final: 0.4233 (mm-30) REVERT: F 321 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.6209 (mmpt) REVERT: F 327 ASN cc_start: 0.4092 (m-40) cc_final: 0.3791 (m110) REVERT: C 342 GLU cc_start: 0.8124 (tt0) cc_final: 0.7898 (tp30) REVERT: E 311 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7226 (mmtm) REVERT: E 319 THR cc_start: 0.8612 (m) cc_final: 0.8354 (p) REVERT: E 369 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8126 (tttm) REVERT: E 372 GLU cc_start: 0.8151 (tt0) cc_final: 0.7863 (tt0) REVERT: H 314 ASP cc_start: 0.7851 (t0) cc_final: 0.7616 (t0) REVERT: H 342 GLU cc_start: 0.7952 (tt0) cc_final: 0.7601 (tp30) REVERT: H 369 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8020 (ttmt) REVERT: I 375 LYS cc_start: 0.8196 (tttt) cc_final: 0.7817 (ttmm) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 1.3337 time to fit residues: 114.8670 Evaluate side-chains 82 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4669 r_free = 0.4669 target = 0.202058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.150644 restraints weight = 17431.420| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.93 r_work: 0.4024 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5025 Z= 0.115 Angle : 0.500 4.325 6723 Z= 0.249 Chirality : 0.050 0.146 756 Planarity : 0.003 0.043 855 Dihedral : 4.820 19.189 663 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.29 % Allowed : 18.52 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.008 0.001 TYR C 310 PHE 0.004 0.001 PHE F 346 HIS 0.002 0.001 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5025) covalent geometry : angle 0.49963 ( 6723) hydrogen bonds : bond 0.02215 ( 98) hydrogen bonds : angle 3.96268 ( 294) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4746.61 seconds wall clock time: 81 minutes 24.16 seconds (4884.16 seconds total)