Starting phenix.real_space_refine on Sat Nov 16 01:32:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/11_2024/8q7t_18233.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/11_2024/8q7t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/11_2024/8q7t_18233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/11_2024/8q7t_18233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/11_2024/8q7t_18233.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/11_2024/8q7t_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-5513/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: 6.74, per 1000 atoms: 0.67 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: 2.70 Conformation dependent library (CDL) restraints added in 718.7 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: 1.10 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: 3.14 Time building geometry restraints manager: 3.32 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: 5.680 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: 0.190 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.500 Find NCS groups from input model: 0.330 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.580 ------------------------------------------------------------------------------- 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 : 0.895 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: 2.5487 time to fit residues: 441.9888 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 : 0.992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 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 : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 321 LYS cc_start: 0.3408 (pptt) cc_final: 0.2737 (pmtt) REVERT: D 368 ASN cc_start: 0.5331 (m-40) cc_final: 0.5097 (m110) REVERT: F 325 LEU cc_start: 0.4540 (mt) cc_final: 0.4152 (mt) REVERT: F 358 ASP cc_start: 0.6832 (p0) cc_final: 0.6354 (t0) REVERT: C 317 LYS cc_start: 0.8063 (mttt) cc_final: 0.7817 (mttm) REVERT: C 338 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7833 (tt0) REVERT: C 347 LYS cc_start: 0.8294 (mttt) cc_final: 0.7815 (pmtt) REVERT: C 369 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7452 (mtmt) REVERT: A 311 LYS cc_start: 0.7896 (mttt) cc_final: 0.7479 (tttm) REVERT: A 338 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7312 (tt0) REVERT: A 360 ILE cc_start: 0.7949 (mt) cc_final: 0.7516 (mm) REVERT: E 311 LYS cc_start: 0.7803 (mtmt) cc_final: 0.6990 (mmtm) REVERT: E 347 LYS cc_start: 0.8208 (mttt) cc_final: 0.7805 (tttt) REVERT: E 369 LYS cc_start: 0.7650 (ttmt) cc_final: 0.7019 (tttm) REVERT: G 311 LYS cc_start: 0.8201 (mttt) cc_final: 0.7678 (tttm) REVERT: G 349 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6895 (mtm180) REVERT: G 360 ILE cc_start: 0.8476 (mt) cc_final: 0.8211 (mp) REVERT: H 340 LYS cc_start: 0.7343 (mttt) cc_final: 0.6976 (mtmm) REVERT: H 347 LYS cc_start: 0.8108 (mttt) cc_final: 0.7778 (mttp) REVERT: H 369 LYS cc_start: 0.7613 (ttmt) cc_final: 0.6852 (mtmt) REVERT: I 311 LYS cc_start: 0.7728 (mttt) cc_final: 0.6971 (mmtm) REVERT: I 338 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7420 (mm-30) REVERT: I 360 ILE cc_start: 0.8186 (mt) cc_final: 0.7707 (mm) REVERT: I 375 LYS cc_start: 0.7274 (tttt) cc_final: 0.6662 (ttmm) outliers start: 18 outliers final: 11 residues processed: 119 average time/residue: 2.5305 time to fit residues: 313.8849 Evaluate side-chains 101 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5025 Z= 0.223 Angle : 0.577 7.954 6723 Z= 0.294 Chirality : 0.052 0.142 756 Planarity : 0.003 0.020 855 Dihedral : 5.825 30.057 665 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.35 % Allowed : 14.64 % Favored : 82.01 % 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: -1.35 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 374 PHE 0.005 0.001 PHE B 346 TYR 0.011 0.002 TYR A 310 ARG 0.001 0.000 ARG A 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 118 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4807 (t70) cc_final: 0.4388 (t70) REVERT: D 372 GLU cc_start: 0.4819 (mm-30) cc_final: 0.4349 (mm-30) REVERT: F 321 LYS cc_start: 0.6091 (OUTLIER) cc_final: 0.5470 (mtpp) REVERT: F 325 LEU cc_start: 0.4443 (mt) cc_final: 0.3825 (mt) REVERT: F 327 ASN cc_start: 0.3381 (m-40) cc_final: 0.3019 (m110) REVERT: C 311 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7688 (mttt) REVERT: C 338 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7827 (tt0) REVERT: C 347 LYS cc_start: 0.8272 (mttt) cc_final: 0.7768 (pmtt) REVERT: C 369 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7466 (mtmt) REVERT: A 311 LYS cc_start: 0.7913 (mttt) cc_final: 0.7523 (tttm) REVERT: A 338 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7304 (tt0) REVERT: A 349 ARG cc_start: 0.7013 (mtt180) cc_final: 0.6546 (mtm180) REVERT: A 360 ILE cc_start: 0.7989 (mt) cc_final: 0.7544 (mm) REVERT: E 311 LYS cc_start: 0.7751 (mtmt) cc_final: 0.6931 (mmtm) REVERT: E 340 LYS cc_start: 0.7565 (mttt) cc_final: 0.7263 (mtmm) REVERT: E 347 LYS cc_start: 0.8176 (mttt) cc_final: 0.7785 (tttt) REVERT: E 369 LYS cc_start: 0.7655 (ttmt) cc_final: 0.7068 (tttm) REVERT: G 311 LYS cc_start: 0.8232 (mttt) cc_final: 0.7105 (tmmt) REVERT: G 327 ASN cc_start: 0.8424 (m110) cc_final: 0.8199 (m110) REVERT: G 349 ARG cc_start: 0.7214 (mtt180) cc_final: 0.6585 (mtm-85) REVERT: G 360 ILE cc_start: 0.8493 (mt) cc_final: 0.8230 (mp) REVERT: H 340 LYS cc_start: 0.7273 (mttt) cc_final: 0.7024 (mtmm) REVERT: H 347 LYS cc_start: 0.8120 (mttt) cc_final: 0.7364 (mmtt) REVERT: H 369 LYS cc_start: 0.7622 (ttmt) cc_final: 0.6878 (mtmt) REVERT: I 311 LYS cc_start: 0.7736 (mttt) cc_final: 0.6929 (mmtm) REVERT: I 338 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7394 (mm-30) REVERT: I 360 ILE cc_start: 0.8228 (mt) cc_final: 0.7759 (mm) REVERT: I 375 LYS cc_start: 0.7321 (tttt) cc_final: 0.6670 (ttmm) outliers start: 19 outliers final: 11 residues processed: 111 average time/residue: 2.5081 time to fit residues: 289.7285 Evaluate side-chains 102 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 F residue 356 SER 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 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.5070 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= 0.294 Angle : 0.567 5.276 6723 Z= 0.289 Chirality : 0.051 0.141 756 Planarity : 0.003 0.024 855 Dihedral : 5.735 31.194 665 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.94 % Allowed : 13.76 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.22), 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 0.013 0.002 TYR C 310 ARG 0.004 0.001 ARG G 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 126 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4880 (t70) cc_final: 0.4474 (t70) REVERT: B 358 ASP cc_start: 0.7564 (p0) cc_final: 0.7313 (p0) REVERT: D 321 LYS cc_start: 0.3416 (OUTLIER) cc_final: 0.3025 (pmtt) REVERT: D 331 LYS cc_start: 0.6256 (mttt) cc_final: 0.5387 (pptt) REVERT: D 372 GLU cc_start: 0.4740 (mm-30) cc_final: 0.4239 (mm-30) REVERT: F 321 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.5721 (mtpp) REVERT: F 325 LEU cc_start: 0.4512 (mt) cc_final: 0.3795 (mt) REVERT: F 327 ASN cc_start: 0.3887 (m-40) cc_final: 0.3517 (m110) REVERT: F 358 ASP cc_start: 0.6722 (p0) cc_final: 0.6394 (t0) REVERT: C 311 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7668 (mttt) REVERT: C 338 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7870 (tt0) REVERT: C 347 LYS cc_start: 0.8306 (mttt) cc_final: 0.7612 (pmtt) REVERT: C 369 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7463 (mtmt) REVERT: A 311 LYS cc_start: 0.7914 (mttt) cc_final: 0.7535 (tttm) REVERT: A 338 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7252 (tt0) REVERT: A 349 ARG cc_start: 0.7179 (mtt180) cc_final: 0.6576 (mtp85) REVERT: A 360 ILE cc_start: 0.7964 (mt) cc_final: 0.7479 (mm) REVERT: E 311 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7029 (mmtm) REVERT: E 347 LYS cc_start: 0.8224 (mttt) cc_final: 0.7776 (tttt) REVERT: E 369 LYS cc_start: 0.7644 (ttmt) cc_final: 0.7108 (tttm) REVERT: G 311 LYS cc_start: 0.8214 (mttt) cc_final: 0.7110 (tmmt) REVERT: G 349 ARG cc_start: 0.7310 (mtt180) cc_final: 0.6826 (mtm180) REVERT: G 360 ILE cc_start: 0.8497 (mt) cc_final: 0.7998 (mm) REVERT: H 340 LYS cc_start: 0.7222 (mttt) cc_final: 0.6873 (mtmm) REVERT: H 347 LYS cc_start: 0.8125 (mttt) cc_final: 0.7380 (tttp) REVERT: H 369 LYS cc_start: 0.7645 (ttmt) cc_final: 0.6914 (ttmt) REVERT: I 311 LYS cc_start: 0.7771 (mttt) cc_final: 0.6964 (mmtm) REVERT: I 338 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7371 (mm-30) REVERT: I 375 LYS cc_start: 0.7324 (tttt) cc_final: 0.6663 (ttmm) outliers start: 28 outliers final: 13 residues processed: 119 average time/residue: 2.5284 time to fit residues: 312.7681 Evaluate side-chains 108 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 40.0000 chunk 43 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.5352 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= 0.177 Angle : 0.518 5.183 6723 Z= 0.260 Chirality : 0.051 0.156 756 Planarity : 0.003 0.027 855 Dihedral : 5.325 30.570 665 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.35 % Allowed : 15.17 % Favored : 81.48 % 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: -1.42 (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 HIS 0.002 0.001 HIS E 374 PHE 0.003 0.001 PHE A 346 TYR 0.010 0.002 TYR C 310 ARG 0.004 0.000 ARG F 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 111 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 321 LYS cc_start: 0.3212 (OUTLIER) cc_final: 0.2815 (pmtt) REVERT: D 331 LYS cc_start: 0.6355 (mttt) cc_final: 0.5483 (pptt) REVERT: D 372 GLU cc_start: 0.4407 (mm-30) cc_final: 0.3898 (mm-30) REVERT: F 321 LYS cc_start: 0.6390 (OUTLIER) cc_final: 0.6146 (mmpt) REVERT: F 325 LEU cc_start: 0.4547 (mt) cc_final: 0.3765 (mt) REVERT: F 327 ASN cc_start: 0.3730 (m-40) cc_final: 0.3372 (m110) REVERT: F 336 GLN cc_start: 0.4699 (tp40) cc_final: 0.4086 (tp40) REVERT: F 358 ASP cc_start: 0.6643 (p0) cc_final: 0.6423 (t0) REVERT: C 311 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7606 (mttt) REVERT: C 338 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7832 (tt0) REVERT: C 347 LYS cc_start: 0.8306 (mttt) cc_final: 0.7626 (pmtt) REVERT: C 369 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7784 (tttm) REVERT: C 375 LYS cc_start: 0.5108 (tmtt) cc_final: 0.4559 (tptp) REVERT: A 311 LYS cc_start: 0.7868 (mttt) cc_final: 0.7512 (tttm) REVERT: A 338 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7283 (tt0) REVERT: A 349 ARG cc_start: 0.7189 (mtt180) cc_final: 0.6571 (mtp85) REVERT: A 360 ILE cc_start: 0.7994 (mt) cc_final: 0.7511 (mm) REVERT: E 311 LYS cc_start: 0.7711 (mtmt) cc_final: 0.6957 (mmtm) REVERT: E 347 LYS cc_start: 0.8222 (mttt) cc_final: 0.7770 (tttt) REVERT: E 369 LYS cc_start: 0.7607 (ttmt) cc_final: 0.7074 (tttm) REVERT: G 311 LYS cc_start: 0.8187 (mttt) cc_final: 0.7053 (tmmt) REVERT: G 338 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7792 (tt0) REVERT: G 349 ARG cc_start: 0.7348 (mtt180) cc_final: 0.6805 (mtm180) REVERT: G 360 ILE cc_start: 0.8488 (mt) cc_final: 0.8002 (mm) REVERT: H 340 LYS cc_start: 0.7249 (mttt) cc_final: 0.6927 (mtmm) REVERT: H 347 LYS cc_start: 0.8141 (mttt) cc_final: 0.7381 (tttp) REVERT: H 369 LYS cc_start: 0.7605 (ttmt) cc_final: 0.6917 (ttmt) REVERT: I 311 LYS cc_start: 0.7749 (mttt) cc_final: 0.6892 (mmtm) REVERT: I 338 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7387 (mm-30) REVERT: I 375 LYS cc_start: 0.7320 (tttt) cc_final: 0.6660 (ttmm) outliers start: 19 outliers final: 12 residues processed: 108 average time/residue: 2.5835 time to fit residues: 290.3292 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 : 0.939 ------------------------------------------------------------------------------- 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 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 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 14 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 5025 Z= 0.379 Angle : 0.607 4.883 6723 Z= 0.311 Chirality : 0.050 0.154 756 Planarity : 0.004 0.031 855 Dihedral : 5.938 31.491 665 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.41 % Allowed : 14.11 % Favored : 81.48 % 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: -1.57 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 374 PHE 0.011 0.002 PHE D 346 TYR 0.016 0.002 TYR A 310 ARG 0.006 0.001 ARG G 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 107 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.5001 (t70) cc_final: 0.4586 (t70) REVERT: D 321 LYS cc_start: 0.3145 (OUTLIER) cc_final: 0.2763 (pmtt) REVERT: D 331 LYS cc_start: 0.6362 (mttt) cc_final: 0.5539 (pptt) REVERT: D 372 GLU cc_start: 0.4496 (mm-30) cc_final: 0.3921 (mm-30) REVERT: F 321 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.6200 (mmpt) REVERT: F 325 LEU cc_start: 0.4740 (mt) cc_final: 0.4093 (mt) REVERT: F 327 ASN cc_start: 0.4144 (m-40) cc_final: 0.3905 (m110) REVERT: C 338 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7944 (tt0) REVERT: C 342 GLU cc_start: 0.7881 (tt0) cc_final: 0.7372 (tp30) REVERT: C 347 LYS cc_start: 0.8379 (mttt) cc_final: 0.7645 (pmtt) REVERT: C 369 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7822 (tttm) REVERT: C 375 LYS cc_start: 0.5074 (tmtt) cc_final: 0.4727 (tptp) REVERT: A 311 LYS cc_start: 0.7902 (mttt) cc_final: 0.7524 (tttm) REVERT: A 360 ILE cc_start: 0.7953 (mt) cc_final: 0.7470 (mm) REVERT: E 311 LYS cc_start: 0.7848 (mtmt) cc_final: 0.6951 (mmpt) REVERT: E 347 LYS cc_start: 0.8239 (mttt) cc_final: 0.7777 (tttt) REVERT: E 369 LYS cc_start: 0.7655 (ttmt) cc_final: 0.7086 (tttm) REVERT: G 311 LYS cc_start: 0.8133 (mttt) cc_final: 0.7620 (tttm) REVERT: G 349 ARG cc_start: 0.7532 (mtt180) cc_final: 0.6845 (mtm180) REVERT: G 360 ILE cc_start: 0.8508 (mt) cc_final: 0.8027 (mm) REVERT: H 340 LYS cc_start: 0.7315 (mttt) cc_final: 0.7016 (mtmp) REVERT: H 347 LYS cc_start: 0.8131 (mttt) cc_final: 0.7359 (tttt) REVERT: H 369 LYS cc_start: 0.7656 (ttmt) cc_final: 0.6984 (ttmt) REVERT: I 311 LYS cc_start: 0.7935 (mttt) cc_final: 0.7455 (tttm) REVERT: I 338 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7263 (mm-30) REVERT: I 375 LYS cc_start: 0.7279 (tttt) cc_final: 0.6617 (ttmm) outliers start: 25 outliers final: 13 residues processed: 101 average time/residue: 2.6626 time to fit residues: 278.9579 Evaluate side-chains 94 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 321 LYS Chi-restraints excluded: chain D residue 336 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5025 Z= 0.188 Angle : 0.519 5.131 6723 Z= 0.263 Chirality : 0.051 0.155 756 Planarity : 0.003 0.032 855 Dihedral : 5.406 30.791 665 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.00 % Allowed : 15.70 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.005 0.001 PHE D 346 TYR 0.009 0.002 TYR A 310 ARG 0.002 0.000 ARG A 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 101 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.978 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: 0.5070 (t70) cc_final: 0.4540 (t70) REVERT: B 339 VAL cc_start: 0.6780 (t) cc_final: 0.6252 (p) REVERT: B 358 ASP cc_start: 0.7313 (p0) cc_final: 0.7113 (p0) REVERT: D 321 LYS cc_start: 0.3113 (OUTLIER) cc_final: 0.2754 (pmtt) REVERT: D 331 LYS cc_start: 0.6380 (mttt) cc_final: 0.5553 (pptt) REVERT: D 372 GLU cc_start: 0.4481 (mm-30) cc_final: 0.4036 (mm-30) REVERT: F 321 LYS cc_start: 0.6498 (OUTLIER) cc_final: 0.6234 (mmpt) REVERT: F 325 LEU cc_start: 0.4742 (mt) cc_final: 0.4084 (mp) REVERT: F 327 ASN cc_start: 0.4044 (m-40) cc_final: 0.3760 (m110) REVERT: C 338 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7939 (tt0) REVERT: C 342 GLU cc_start: 0.7870 (tt0) cc_final: 0.7358 (tp30) REVERT: C 347 LYS cc_start: 0.8365 (mttt) cc_final: 0.7908 (pmtt) REVERT: C 369 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7826 (tttm) REVERT: C 370 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7755 (tttp) REVERT: A 311 LYS cc_start: 0.7861 (mttt) cc_final: 0.7528 (tttm) REVERT: A 338 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7292 (tt0) REVERT: E 311 LYS cc_start: 0.7791 (mtmt) cc_final: 0.7089 (mmtm) REVERT: E 347 LYS cc_start: 0.8234 (mttt) cc_final: 0.7768 (tttt) REVERT: E 369 LYS cc_start: 0.7646 (ttmt) cc_final: 0.7113 (tttm) REVERT: G 311 LYS cc_start: 0.8125 (mttt) cc_final: 0.7026 (tmmt) REVERT: G 338 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7778 (tt0) REVERT: G 349 ARG cc_start: 0.7551 (mtt180) cc_final: 0.6856 (mtm180) REVERT: H 340 LYS cc_start: 0.7251 (mttt) cc_final: 0.6963 (mtmp) REVERT: H 347 LYS cc_start: 0.8120 (mttt) cc_final: 0.7752 (mmtp) REVERT: H 369 LYS cc_start: 0.7578 (ttmt) cc_final: 0.6990 (ttmt) REVERT: I 311 LYS cc_start: 0.7909 (mttt) cc_final: 0.7446 (tttm) REVERT: I 338 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7392 (mm-30) REVERT: I 375 LYS cc_start: 0.7280 (tttt) cc_final: 0.6618 (ttmm) outliers start: 17 outliers final: 9 residues processed: 98 average time/residue: 2.6289 time to fit residues: 267.8207 Evaluate side-chains 89 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 C residue 340 LYS Chi-restraints excluded: chain C residue 370 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.0170 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.6140 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5025 Z= 0.172 Angle : 0.494 4.634 6723 Z= 0.248 Chirality : 0.050 0.156 756 Planarity : 0.003 0.032 855 Dihedral : 5.120 30.053 665 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.17 % Allowed : 15.87 % 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 (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: -1.56 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 374 PHE 0.004 0.001 PHE I 346 TYR 0.009 0.001 TYR A 310 ARG 0.001 0.000 ARG G 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 98 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 339 VAL cc_start: 0.6714 (t) cc_final: 0.6203 (p) REVERT: D 321 LYS cc_start: 0.3050 (OUTLIER) cc_final: 0.2743 (pmtt) REVERT: D 331 LYS cc_start: 0.6352 (mttt) cc_final: 0.5514 (pptt) REVERT: D 372 GLU cc_start: 0.4442 (mm-30) cc_final: 0.4005 (mm-30) REVERT: F 321 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.6244 (mmpt) REVERT: F 325 LEU cc_start: 0.4630 (mt) cc_final: 0.3930 (mp) REVERT: F 327 ASN cc_start: 0.3976 (m-40) cc_final: 0.3715 (m110) REVERT: C 338 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7948 (tt0) REVERT: C 342 GLU cc_start: 0.7878 (tt0) cc_final: 0.7343 (tp30) REVERT: C 347 LYS cc_start: 0.8322 (mttt) cc_final: 0.7845 (pmtt) REVERT: C 369 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7835 (tttm) REVERT: A 311 LYS cc_start: 0.7866 (mttt) cc_final: 0.7525 (tttm) REVERT: A 338 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7305 (tt0) REVERT: E 311 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7005 (mmtm) REVERT: E 347 LYS cc_start: 0.8212 (mttt) cc_final: 0.7770 (tttt) REVERT: E 369 LYS cc_start: 0.7663 (ttmt) cc_final: 0.7118 (tttm) REVERT: G 311 LYS cc_start: 0.8121 (mttt) cc_final: 0.7042 (tmmt) REVERT: G 338 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7764 (tt0) REVERT: G 349 ARG cc_start: 0.7564 (mtt180) cc_final: 0.6889 (mtp180) REVERT: H 340 LYS cc_start: 0.7220 (mttt) cc_final: 0.6960 (mtmp) REVERT: H 342 GLU cc_start: 0.7418 (tt0) cc_final: 0.6723 (tp30) REVERT: H 347 LYS cc_start: 0.8126 (mttt) cc_final: 0.7754 (mmtp) REVERT: H 369 LYS cc_start: 0.7597 (ttmt) cc_final: 0.7013 (ttmt) REVERT: I 311 LYS cc_start: 0.7900 (mttt) cc_final: 0.7090 (mmtm) REVERT: I 338 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7374 (mm-30) REVERT: I 375 LYS cc_start: 0.7296 (tttt) cc_final: 0.6630 (ttmm) outliers start: 18 outliers final: 11 residues processed: 93 average time/residue: 2.7070 time to fit residues: 261.3731 Evaluate side-chains 91 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 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 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 48 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5025 Z= 0.163 Angle : 0.499 5.435 6723 Z= 0.250 Chirality : 0.051 0.150 756 Planarity : 0.003 0.033 855 Dihedral : 4.935 29.151 665 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.82 % Allowed : 16.05 % Favored : 81.13 % 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: -1.54 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 374 PHE 0.003 0.001 PHE I 346 TYR 0.008 0.001 TYR C 310 ARG 0.002 0.000 ARG I 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 96 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 339 VAL cc_start: 0.6675 (t) cc_final: 0.6139 (p) REVERT: B 358 ASP cc_start: 0.7314 (p0) cc_final: 0.7066 (p0) REVERT: D 321 LYS cc_start: 0.3078 (OUTLIER) cc_final: 0.2747 (pmtt) REVERT: D 331 LYS cc_start: 0.6395 (mttt) cc_final: 0.5551 (pptt) REVERT: D 372 GLU cc_start: 0.4460 (mm-30) cc_final: 0.4030 (mm-30) REVERT: F 321 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.6254 (mmpt) REVERT: F 325 LEU cc_start: 0.4596 (mt) cc_final: 0.3882 (mp) REVERT: F 327 ASN cc_start: 0.4000 (m-40) cc_final: 0.3729 (m110) REVERT: F 358 ASP cc_start: 0.6805 (p0) cc_final: 0.6579 (t0) REVERT: C 338 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7971 (tt0) REVERT: C 342 GLU cc_start: 0.7887 (tt0) cc_final: 0.7349 (tp30) REVERT: C 347 LYS cc_start: 0.8323 (mttt) cc_final: 0.7846 (pmtt) REVERT: C 369 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7827 (tttm) REVERT: A 311 LYS cc_start: 0.7863 (mttt) cc_final: 0.7532 (tttm) REVERT: A 338 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7314 (tt0) REVERT: E 311 LYS cc_start: 0.7720 (mtmt) cc_final: 0.6982 (mmtm) REVERT: E 319 THR cc_start: 0.7900 (m) cc_final: 0.7510 (p) REVERT: E 347 LYS cc_start: 0.8217 (mttt) cc_final: 0.7778 (tttt) REVERT: E 369 LYS cc_start: 0.7642 (ttmt) cc_final: 0.7088 (tttm) REVERT: G 311 LYS cc_start: 0.8135 (mttt) cc_final: 0.7053 (tmmt) REVERT: G 338 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7737 (tt0) REVERT: G 349 ARG cc_start: 0.7567 (mtt180) cc_final: 0.6898 (mtp-110) REVERT: H 340 LYS cc_start: 0.7228 (mttt) cc_final: 0.6960 (mtmp) REVERT: H 342 GLU cc_start: 0.7402 (tt0) cc_final: 0.6750 (tp30) REVERT: H 347 LYS cc_start: 0.8136 (mttt) cc_final: 0.7756 (mmtp) REVERT: H 369 LYS cc_start: 0.7619 (ttmt) cc_final: 0.7022 (ttmt) REVERT: I 311 LYS cc_start: 0.7901 (mttt) cc_final: 0.7056 (mmtt) REVERT: I 338 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7370 (mm-30) REVERT: I 375 LYS cc_start: 0.7298 (tttt) cc_final: 0.6637 (ttmm) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 2.7882 time to fit residues: 269.4119 Evaluate side-chains 91 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 336 GLN 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 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 4 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.6187 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= 0.253 Angle : 0.534 5.293 6723 Z= 0.274 Chirality : 0.050 0.146 756 Planarity : 0.003 0.031 855 Dihedral : 5.068 29.138 665 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.94 % Allowed : 17.46 % Favored : 80.60 % 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: -1.54 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.006 0.001 PHE D 346 TYR 0.010 0.002 TYR A 310 ARG 0.003 0.000 ARG G 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: 11 poor density : 79 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 321 LYS cc_start: 0.3100 (OUTLIER) cc_final: 0.2785 (pmtt) REVERT: D 331 LYS cc_start: 0.6455 (mttt) cc_final: 0.5595 (pptt) REVERT: D 372 GLU cc_start: 0.4413 (mm-30) cc_final: 0.3982 (mm-30) REVERT: F 321 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.6291 (mmpt) REVERT: F 325 LEU cc_start: 0.4746 (mt) cc_final: 0.4132 (mp) REVERT: C 338 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7953 (tt0) REVERT: C 342 GLU cc_start: 0.7882 (tt0) cc_final: 0.7350 (tp30) REVERT: C 347 LYS cc_start: 0.8348 (mttt) cc_final: 0.7865 (pmtt) REVERT: C 369 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7843 (tttm) REVERT: A 311 LYS cc_start: 0.7894 (mttt) cc_final: 0.7576 (tttm) REVERT: A 338 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7323 (tt0) REVERT: E 311 LYS cc_start: 0.7754 (mtmt) cc_final: 0.7004 (mmtm) REVERT: E 319 THR cc_start: 0.7925 (m) cc_final: 0.7520 (p) REVERT: E 347 LYS cc_start: 0.8226 (mttt) cc_final: 0.7776 (tttt) REVERT: E 369 LYS cc_start: 0.7648 (ttmt) cc_final: 0.7096 (tttm) REVERT: E 372 GLU cc_start: 0.7928 (tt0) cc_final: 0.7438 (tt0) REVERT: G 311 LYS cc_start: 0.8148 (mttt) cc_final: 0.7090 (tmmt) REVERT: G 338 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7793 (tt0) REVERT: G 349 ARG cc_start: 0.7560 (mtt180) cc_final: 0.6872 (mtp-110) REVERT: H 340 LYS cc_start: 0.7246 (mttt) cc_final: 0.6961 (mtmp) REVERT: H 342 GLU cc_start: 0.7428 (tt0) cc_final: 0.6767 (tp30) REVERT: H 347 LYS cc_start: 0.8119 (mttt) cc_final: 0.7751 (mmtp) REVERT: H 369 LYS cc_start: 0.7642 (ttmt) cc_final: 0.7032 (ttmt) REVERT: I 311 LYS cc_start: 0.7919 (mttt) cc_final: 0.7489 (tttm) REVERT: I 338 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7361 (mm-30) REVERT: I 375 LYS cc_start: 0.7287 (tttt) cc_final: 0.6632 (ttmm) outliers start: 11 outliers final: 10 residues processed: 89 average time/residue: 2.7746 time to fit residues: 256.3204 Evaluate side-chains 89 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 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 48 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.4627 r_free = 0.4627 target = 0.197078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.146375 restraints weight = 17289.029| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.95 r_work: 0.3947 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5025 Z= 0.413 Angle : 0.608 4.850 6723 Z= 0.314 Chirality : 0.051 0.153 756 Planarity : 0.004 0.032 855 Dihedral : 5.689 29.414 665 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.00 % Allowed : 17.11 % 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: -1.70 (0.27), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 374 PHE 0.014 0.002 PHE F 346 TYR 0.014 0.002 TYR A 310 ARG 0.004 0.001 ARG G 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5786.60 seconds wall clock time: 102 minutes 51.40 seconds (6171.40 seconds total)