Starting phenix.real_space_refine on Fri Feb 14 10:09:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7t_18233/02_2025/8q7t_18233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7t_18233/02_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_18233/02_2025/8q7t_18233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7t_18233/02_2025/8q7t_18233.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7t_18233/02_2025/8q7t_18233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7t_18233/02_2025/8q7t_18233.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 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.33, per 1000 atoms: 0.63 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: 2.51 Conformation dependent library (CDL) restraints added in 727.6 milliseconds 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: 0.97 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: 3.34 Time building geometry restraints manager: 3.02 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: 0.01 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: 4.200 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: 0.140 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.530 Find NCS groups from input model: 0.360 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:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.930 ------------------------------------------------------------------------------- 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= 0.738 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 (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: -1.65 (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 HIS 0.012 0.003 HIS E 374 PHE 0.071 0.019 PHE C 346 TYR 0.123 0.015 TYR E 310 ARG 0.009 0.002 ARG B 349 *********************** 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 : 0.750 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: symmetry clash REVERT: B 368 ASN cc_start: 0.5745 (m-40) cc_final: 0.5432 (m110) REVERT: D 368 ASN cc_start: 0.4983 (m-40) cc_final: 0.4758 (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: 0.7812 (tt0) REVERT: C 347 LYS cc_start: 0.8162 (mttt) cc_final: 0.7478 (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: 0.7414 (tttm) REVERT: E 311 LYS cc_start: 0.7720 (mtmt) cc_final: 0.6994 (mmtm) REVERT: E 347 LYS cc_start: 0.8054 (mttt) cc_final: 0.7608 (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 340 LYS cc_start: 0.7485 (mttt) cc_final: 0.7134 (mtmp) REVERT: H 347 LYS cc_start: 0.8031 (mttt) cc_final: 0.7218 (tttp) 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: 0.6581 (ttmm) outliers start: 1 outliers final: 2 residues processed: 167 average time/residue: 2.5436 time to fit residues: 440.8793 Evaluate side-chains 97 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 50 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 A 327 ASN G 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.203110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.150674 restraints weight = 17060.992| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.45 r_work: 0.3996 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5025 Z= 0.373 Angle : 0.641 4.691 6723 Z= 0.329 Chirality : 0.050 0.147 756 Planarity : 0.004 0.024 855 Dihedral : 6.786 37.158 667 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.17 % Allowed : 13.23 % Favored : 83.60 % 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: -1.28 (0.29), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 374 PHE 0.007 0.001 PHE A 346 TYR 0.011 0.002 TYR A 310 ARG 0.004 0.001 ARG F 349 *********************** 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 126 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4140 (t0) cc_final: 0.3929 (t70) REVERT: B 353 LYS cc_start: 0.5978 (tttt) cc_final: 0.5751 (tmtm) REVERT: B 368 ASN cc_start: 0.5869 (m-40) cc_final: 0.5568 (m110) REVERT: D 321 LYS cc_start: 0.3208 (pptt) cc_final: 0.2559 (pmtt) REVERT: D 368 ASN cc_start: 0.5076 (m-40) cc_final: 0.4730 (m110) REVERT: F 325 LEU cc_start: 0.3864 (mt) cc_final: 0.3451 (mt) REVERT: F 358 ASP cc_start: 0.6956 (p0) cc_final: 0.6501 (t0) REVERT: F 368 ASN cc_start: 0.4760 (OUTLIER) cc_final: 0.4543 (m110) REVERT: C 338 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8287 (tt0) REVERT: C 347 LYS cc_start: 0.8352 (mttt) cc_final: 0.8080 (pmtt) REVERT: C 369 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8034 (mtmt) REVERT: A 360 ILE cc_start: 0.8976 (mt) cc_final: 0.8696 (mm) REVERT: E 311 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7162 (mmtm) REVERT: E 347 LYS cc_start: 0.8339 (mttt) cc_final: 0.8085 (tttt) REVERT: E 369 LYS cc_start: 0.8397 (ttmt) cc_final: 0.8036 (tttm) REVERT: G 311 LYS cc_start: 0.8482 (mttt) cc_final: 0.8267 (tttm) REVERT: H 369 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7840 (mtmt) REVERT: I 311 LYS cc_start: 0.8097 (mttt) cc_final: 0.7629 (mmtm) REVERT: I 360 ILE cc_start: 0.8959 (mt) cc_final: 0.8666 (mm) REVERT: I 375 LYS cc_start: 0.8128 (tttt) cc_final: 0.7787 (ttmm) outliers start: 18 outliers final: 11 residues processed: 119 average time/residue: 2.5031 time to fit residues: 310.2782 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 : 0.931 ------------------------------------------------------------------------------- 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 39 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 = 0.4706 r_free = 0.4706 target = 0.205333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.152319 restraints weight = 17123.061| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.34 r_work: 0.4045 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5025 Z= 0.201 Angle : 0.576 10.687 6723 Z= 0.292 Chirality : 0.052 0.144 756 Planarity : 0.003 0.028 855 Dihedral : 5.867 29.816 665 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.17 % Allowed : 16.05 % Favored : 80.78 % 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: -1.32 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 374 PHE 0.005 0.001 PHE B 346 TYR 0.010 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** 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: 18 poor density : 98 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4223 (t0) cc_final: 0.3786 (t70) REVERT: B 353 LYS cc_start: 0.6029 (tttt) cc_final: 0.5772 (tmtm) REVERT: B 358 ASP cc_start: 0.7667 (p0) cc_final: 0.7439 (p0) REVERT: D 321 LYS cc_start: 0.3131 (pptt) cc_final: 0.2667 (pmtt) REVERT: D 368 ASN cc_start: 0.5034 (m-40) cc_final: 0.4704 (m110) REVERT: D 372 GLU cc_start: 0.5495 (mm-30) cc_final: 0.4747 (mm-30) REVERT: F 321 LYS cc_start: 0.6064 (OUTLIER) cc_final: 0.5585 (mtpp) REVERT: F 327 ASN cc_start: 0.3327 (m-40) cc_final: 0.2924 (m110) REVERT: F 358 ASP cc_start: 0.6898 (p0) cc_final: 0.6627 (t0) REVERT: C 338 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8245 (tt0) REVERT: C 347 LYS cc_start: 0.8342 (mttt) cc_final: 0.8046 (pmtt) REVERT: C 369 LYS cc_start: 0.8472 (ttmt) cc_final: 0.7997 (mtmt) REVERT: A 349 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7778 (mtm180) REVERT: A 360 ILE cc_start: 0.8954 (mt) cc_final: 0.8653 (mm) REVERT: E 311 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7060 (mmtm) REVERT: E 347 LYS cc_start: 0.8336 (mttt) cc_final: 0.8038 (tttt) REVERT: E 369 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8037 (tttm) REVERT: G 311 LYS cc_start: 0.8409 (mttt) cc_final: 0.7695 (tmmt) REVERT: H 338 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8124 (tt0) REVERT: H 369 LYS cc_start: 0.8372 (ttmt) cc_final: 0.7804 (mtmt) REVERT: I 311 LYS cc_start: 0.8032 (mttt) cc_final: 0.7549 (mmtm) REVERT: I 375 LYS cc_start: 0.8130 (tttt) cc_final: 0.7754 (ttmm) outliers start: 18 outliers final: 10 residues processed: 109 average time/residue: 2.4632 time to fit residues: 279.6539 Evaluate side-chains 98 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE 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 C residue 340 LYS 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 55 optimal weight: 0.0470 chunk 12 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN A 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.205008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.150934 restraints weight = 16917.912| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.23 r_work: 0.4042 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5025 Z= 0.215 Angle : 0.532 4.826 6723 Z= 0.266 Chirality : 0.051 0.156 756 Planarity : 0.003 0.031 855 Dihedral : 5.519 30.289 665 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.59 % Allowed : 15.52 % 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 (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: -1.33 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 374 PHE 0.005 0.001 PHE A 346 TYR 0.013 0.002 TYR C 310 ARG 0.002 0.000 ARG A 349 *********************** 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 119 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4445 (t0) cc_final: 0.4132 (t70) REVERT: B 353 LYS cc_start: 0.6056 (tttt) cc_final: 0.5821 (tmtm) REVERT: D 321 LYS cc_start: 0.3322 (pptt) cc_final: 0.2896 (pmtt) REVERT: D 331 LYS cc_start: 0.6102 (mttt) cc_final: 0.5200 (pptt) REVERT: D 368 ASN cc_start: 0.5150 (m-40) cc_final: 0.4885 (m110) REVERT: D 372 GLU cc_start: 0.5375 (mm-30) cc_final: 0.4686 (mm-30) REVERT: F 321 LYS cc_start: 0.6126 (OUTLIER) cc_final: 0.5609 (mtpp) REVERT: F 325 LEU cc_start: 0.3745 (mt) cc_final: 0.3030 (mt) REVERT: F 327 ASN cc_start: 0.3516 (m-40) cc_final: 0.3116 (m110) REVERT: C 311 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7790 (mttt) REVERT: C 338 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8243 (tt0) REVERT: C 347 LYS cc_start: 0.8344 (mttt) cc_final: 0.8087 (pmtt) REVERT: A 349 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7826 (mtm180) REVERT: A 360 ILE cc_start: 0.9009 (mt) cc_final: 0.8706 (mm) REVERT: E 311 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7078 (mmtm) REVERT: E 347 LYS cc_start: 0.8335 (mttt) cc_final: 0.8056 (tttt) REVERT: E 369 LYS cc_start: 0.8341 (ttmt) cc_final: 0.8066 (tttm) REVERT: G 311 LYS cc_start: 0.8402 (mttt) cc_final: 0.7699 (tmmt) REVERT: H 369 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7839 (mtmt) REVERT: I 311 LYS cc_start: 0.8011 (mttt) cc_final: 0.7542 (mmtm) REVERT: I 375 LYS cc_start: 0.8160 (tttt) cc_final: 0.7782 (ttmm) outliers start: 26 outliers final: 16 residues processed: 113 average time/residue: 2.5186 time to fit residues: 296.0760 Evaluate side-chains 102 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ILE 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 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 338 GLU 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 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 34 optimal weight: 0.3980 chunk 3 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.200965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.149018 restraints weight = 17149.028| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.27 r_work: 0.4005 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3926 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5025 Z= 0.287 Angle : 0.566 5.281 6723 Z= 0.288 Chirality : 0.050 0.166 756 Planarity : 0.004 0.035 855 Dihedral : 5.598 30.926 665 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.23 % Allowed : 15.70 % 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 (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: -1.45 (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 HIS 0.004 0.001 HIS E 374 PHE 0.006 0.001 PHE A 346 TYR 0.011 0.002 TYR C 310 ARG 0.003 0.001 ARG A 349 *********************** 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 107 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.875 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: B 314 ASP cc_start: 0.4667 (t0) cc_final: 0.4167 (t70) REVERT: B 358 ASP cc_start: 0.7641 (p0) cc_final: 0.7389 (p0) REVERT: D 321 LYS cc_start: 0.2897 (OUTLIER) cc_final: 0.2613 (pmtt) REVERT: D 331 LYS cc_start: 0.6151 (mttt) cc_final: 0.5249 (pptt) REVERT: D 368 ASN cc_start: 0.5300 (m-40) cc_final: 0.5060 (m110) REVERT: D 372 GLU cc_start: 0.4936 (mm-30) cc_final: 0.4205 (mm-30) REVERT: F 321 LYS cc_start: 0.6308 (OUTLIER) cc_final: 0.5753 (mtpp) REVERT: F 325 LEU cc_start: 0.4059 (mt) cc_final: 0.3347 (mt) REVERT: F 327 ASN cc_start: 0.4088 (m-40) cc_final: 0.3565 (m110) REVERT: F 358 ASP cc_start: 0.7029 (p0) cc_final: 0.6660 (t0) REVERT: C 338 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8281 (tt0) REVERT: C 347 LYS cc_start: 0.8315 (mttt) cc_final: 0.8104 (pmtt) REVERT: A 349 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7807 (mtp85) REVERT: A 360 ILE cc_start: 0.9031 (mt) cc_final: 0.8702 (mm) REVERT: E 311 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7233 (mmtm) REVERT: E 347 LYS cc_start: 0.8362 (mttt) cc_final: 0.8070 (tttt) REVERT: E 369 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8068 (tttm) REVERT: G 311 LYS cc_start: 0.8397 (mttt) cc_final: 0.7775 (tmmt) REVERT: H 369 LYS cc_start: 0.8426 (ttmt) cc_final: 0.7941 (ttmt) REVERT: I 311 LYS cc_start: 0.8096 (mttt) cc_final: 0.7633 (mmtm) REVERT: I 375 LYS cc_start: 0.8175 (tttt) cc_final: 0.7815 (ttmm) outliers start: 24 outliers final: 15 residues processed: 103 average time/residue: 2.5094 time to fit residues: 269.2001 Evaluate side-chains 97 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 368 ASN 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 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 19 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.201710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.149888 restraints weight = 17162.616| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.39 r_work: 0.4013 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5803 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= 0.225 Angle : 0.522 4.838 6723 Z= 0.264 Chirality : 0.050 0.152 756 Planarity : 0.003 0.038 855 Dihedral : 5.352 30.606 665 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.53 % Allowed : 16.58 % 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 (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: -1.49 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.005 0.001 PHE D 346 TYR 0.009 0.002 TYR A 310 ARG 0.003 0.001 ARG A 349 *********************** 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 104 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4768 (t0) cc_final: 0.4237 (t70) REVERT: B 353 LYS cc_start: 0.6086 (tttt) cc_final: 0.5863 (tttm) REVERT: D 321 LYS cc_start: 0.3012 (OUTLIER) cc_final: 0.2631 (pmtt) REVERT: D 331 LYS cc_start: 0.6202 (mttt) cc_final: 0.5338 (pptt) REVERT: D 368 ASN cc_start: 0.5369 (m-40) cc_final: 0.5151 (m110) REVERT: D 372 GLU cc_start: 0.4905 (mm-30) cc_final: 0.4159 (mm-30) REVERT: F 321 LYS cc_start: 0.6332 (OUTLIER) cc_final: 0.6032 (mmpt) REVERT: F 325 LEU cc_start: 0.3975 (mt) cc_final: 0.3290 (mt) REVERT: F 327 ASN cc_start: 0.4173 (m-40) cc_final: 0.3802 (m110) REVERT: C 338 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8242 (tt0) REVERT: C 342 GLU cc_start: 0.8055 (tt0) cc_final: 0.7792 (tp30) REVERT: C 375 LYS cc_start: 0.5572 (tmtt) cc_final: 0.4996 (tptp) REVERT: A 360 ILE cc_start: 0.9035 (mt) cc_final: 0.8708 (mm) REVERT: E 311 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7247 (mmtm) REVERT: E 347 LYS cc_start: 0.8377 (mttt) cc_final: 0.8103 (tttt) REVERT: E 369 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8108 (tttm) REVERT: H 369 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8020 (ttmt) REVERT: I 311 LYS cc_start: 0.8177 (mttt) cc_final: 0.7747 (mmtm) REVERT: I 375 LYS cc_start: 0.8207 (tttt) cc_final: 0.7860 (ttmm) outliers start: 20 outliers final: 12 residues processed: 100 average time/residue: 2.5226 time to fit residues: 262.5101 Evaluate side-chains 92 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 336 GLN 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 356 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 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 = 0.4644 r_free = 0.4644 target = 0.200520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.147676 restraints weight = 17391.531| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.28 r_work: 0.3985 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5025 Z= 0.284 Angle : 0.537 5.225 6723 Z= 0.275 Chirality : 0.049 0.158 756 Planarity : 0.004 0.039 855 Dihedral : 5.436 30.549 665 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.82 % Allowed : 17.99 % 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 (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: -1.52 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.007 0.001 PHE D 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG H 349 *********************** 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 95 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4719 (t0) cc_final: 0.4149 (t70) REVERT: B 354 ILE cc_start: 0.5848 (mt) cc_final: 0.5644 (mt) REVERT: D 321 LYS cc_start: 0.2938 (OUTLIER) cc_final: 0.2574 (pmtt) REVERT: D 331 LYS cc_start: 0.6193 (mttt) cc_final: 0.5318 (pptt) REVERT: D 368 ASN cc_start: 0.5351 (m-40) cc_final: 0.5142 (m110) REVERT: D 372 GLU cc_start: 0.4861 (mm-30) cc_final: 0.4219 (mm-30) REVERT: F 321 LYS cc_start: 0.6325 (OUTLIER) cc_final: 0.6046 (mmpt) REVERT: F 325 LEU cc_start: 0.4005 (mt) cc_final: 0.3349 (mt) REVERT: F 327 ASN cc_start: 0.3964 (m-40) cc_final: 0.3565 (m110) REVERT: C 338 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8261 (tt0) REVERT: C 342 GLU cc_start: 0.8083 (tt0) cc_final: 0.7797 (tp30) REVERT: C 375 LYS cc_start: 0.5559 (tmtt) cc_final: 0.5006 (tptp) REVERT: A 360 ILE cc_start: 0.9042 (mt) cc_final: 0.8711 (mm) REVERT: E 311 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7236 (mmtm) REVERT: E 347 LYS cc_start: 0.8370 (mttt) cc_final: 0.8035 (tttt) REVERT: E 369 LYS cc_start: 0.8372 (ttmt) cc_final: 0.8054 (tttm) REVERT: H 369 LYS cc_start: 0.8391 (ttmt) cc_final: 0.7961 (ttmt) REVERT: I 311 LYS cc_start: 0.8200 (mttt) cc_final: 0.7781 (mmtm) REVERT: I 375 LYS cc_start: 0.8151 (tttt) cc_final: 0.7736 (ttmm) outliers start: 16 outliers final: 11 residues processed: 92 average time/residue: 2.4032 time to fit residues: 230.5979 Evaluate side-chains 90 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 353 LYS Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 356 SER 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 38 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 0.0870 chunk 19 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- 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 = 0.4637 r_free = 0.4637 target = 0.198868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.148080 restraints weight = 17528.234| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.19 r_work: 0.3982 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.6411 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= 0.271 Angle : 0.540 4.448 6723 Z= 0.275 Chirality : 0.050 0.158 756 Planarity : 0.004 0.041 855 Dihedral : 5.445 29.980 665 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.88 % Allowed : 17.28 % Favored : 78.84 % 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: -1.67 (0.27), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 374 PHE 0.008 0.001 PHE D 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG H 349 *********************** 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 100 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4880 (t0) cc_final: 0.4353 (t70) REVERT: D 321 LYS cc_start: 0.2983 (OUTLIER) cc_final: 0.2670 (pmtt) REVERT: D 372 GLU cc_start: 0.4962 (mm-30) cc_final: 0.4335 (mm-30) REVERT: F 321 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.6142 (mmpt) REVERT: F 325 LEU cc_start: 0.3969 (mt) cc_final: 0.3388 (mt) REVERT: F 375 LYS cc_start: 0.4147 (OUTLIER) cc_final: 0.3878 (mtpm) REVERT: C 338 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8210 (tt0) REVERT: C 342 GLU cc_start: 0.8100 (tt0) cc_final: 0.7837 (tp30) REVERT: E 311 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7280 (mmtm) REVERT: E 347 LYS cc_start: 0.8364 (mttt) cc_final: 0.8088 (tttt) REVERT: E 369 LYS cc_start: 0.8381 (ttmt) cc_final: 0.8075 (tttm) REVERT: E 372 GLU cc_start: 0.8117 (tt0) cc_final: 0.7773 (tt0) REVERT: H 369 LYS cc_start: 0.8408 (ttmt) cc_final: 0.8094 (tttm) REVERT: I 375 LYS cc_start: 0.8161 (tttt) cc_final: 0.7764 (ttmm) outliers start: 22 outliers final: 13 residues processed: 94 average time/residue: 2.3333 time to fit residues: 230.2419 Evaluate side-chains 87 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 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 375 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 315 LEU 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 3 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.199794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.148942 restraints weight = 17498.296| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.24 r_work: 0.3989 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5025 Z= 0.225 Angle : 0.524 5.191 6723 Z= 0.264 Chirality : 0.050 0.158 756 Planarity : 0.004 0.044 855 Dihedral : 5.282 29.256 665 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.17 % Allowed : 18.69 % Favored : 78.13 % 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: -1.74 (0.27), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.006 0.001 PHE D 346 TYR 0.008 0.001 TYR A 310 ARG 0.002 0.000 ARG D 349 *********************** 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: 18 poor density : 73 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4853 (t0) cc_final: 0.4275 (t70) REVERT: D 372 GLU cc_start: 0.4925 (mm-30) cc_final: 0.4311 (mm-30) REVERT: F 321 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6193 (mmpt) REVERT: F 325 LEU cc_start: 0.3950 (mt) cc_final: 0.3409 (mt) REVERT: F 375 LYS cc_start: 0.4201 (mmtp) cc_final: 0.3839 (mtpm) REVERT: C 338 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8248 (tt0) REVERT: C 342 GLU cc_start: 0.8127 (tt0) cc_final: 0.7874 (tp30) REVERT: E 311 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7267 (mmtm) REVERT: E 347 LYS cc_start: 0.8364 (mttt) cc_final: 0.8079 (tttt) REVERT: E 369 LYS cc_start: 0.8377 (ttmt) cc_final: 0.8071 (tttm) REVERT: E 372 GLU cc_start: 0.8143 (tt0) cc_final: 0.7796 (tt0) REVERT: H 342 GLU cc_start: 0.7912 (tt0) cc_final: 0.7544 (tp30) REVERT: H 369 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8112 (tttm) REVERT: I 375 LYS cc_start: 0.8178 (tttt) cc_final: 0.7781 (ttmm) outliers start: 18 outliers final: 13 residues processed: 87 average time/residue: 2.3360 time to fit residues: 212.2891 Evaluate side-chains 86 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 356 SER 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 315 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 352 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 43 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.198991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.148391 restraints weight = 17520.603| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.31 r_work: 0.3989 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5025 Z= 0.276 Angle : 0.546 5.577 6723 Z= 0.277 Chirality : 0.050 0.155 756 Planarity : 0.004 0.041 855 Dihedral : 5.372 29.232 665 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.17 % Allowed : 19.40 % Favored : 77.43 % 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: -1.80 (0.27), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 329 PHE 0.010 0.001 PHE F 346 TYR 0.012 0.002 TYR I 310 ARG 0.001 0.000 ARG H 349 ********************** 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 90 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4877 (t0) cc_final: 0.4320 (t70) REVERT: D 331 LYS cc_start: 0.6314 (mttt) cc_final: 0.5447 (pptt) REVERT: D 372 GLU cc_start: 0.4970 (mm-30) cc_final: 0.4406 (mm-30) REVERT: F 321 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.6186 (mtpt) REVERT: F 325 LEU cc_start: 0.3935 (mt) cc_final: 0.3417 (mp) REVERT: F 375 LYS cc_start: 0.4235 (mmtp) cc_final: 0.3885 (mtpm) REVERT: C 338 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8225 (tt0) REVERT: C 342 GLU cc_start: 0.8134 (tt0) cc_final: 0.7889 (tp30) REVERT: E 311 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7154 (mmpt) REVERT: E 347 LYS cc_start: 0.8360 (mttt) cc_final: 0.8091 (tttt) REVERT: E 369 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8064 (tttm) REVERT: E 372 GLU cc_start: 0.8147 (tt0) cc_final: 0.7797 (tt0) REVERT: H 314 ASP cc_start: 0.7860 (t0) cc_final: 0.7612 (t0) REVERT: H 342 GLU cc_start: 0.7908 (tt0) cc_final: 0.7542 (tp30) REVERT: H 369 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8119 (tttm) REVERT: I 375 LYS cc_start: 0.8164 (tttt) cc_final: 0.7777 (ttmm) outliers start: 18 outliers final: 14 residues processed: 88 average time/residue: 2.2990 time to fit residues: 211.4973 Evaluate side-chains 85 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 339 VAL Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 339 VAL 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 348 ASP 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 Chi-restraints excluded: chain I residue 352 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.201456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.151203 restraints weight = 17421.852| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.96 r_work: 0.4003 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.6911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5025 Z= 0.222 Angle : 0.529 5.508 6723 Z= 0.267 Chirality : 0.050 0.156 756 Planarity : 0.004 0.042 855 Dihedral : 5.070 20.963 663 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.00 % Allowed : 19.75 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.83 (0.27), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.006 0.001 PHE D 346 TYR 0.008 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8524.21 seconds wall clock time: 150 minutes 17.07 seconds (9017.07 seconds total)