Starting phenix.real_space_refine on Thu Mar 14 23:11:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/03_2024/8q7t_18233.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/03_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_18233/03_2024/8q7t_18233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/03_2024/8q7t_18233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/03_2024/8q7t_18233.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/03_2024/8q7t_18233.pdb" } 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 Residue "C ASP 314": "OD1" <-> "OD2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "E ASP 314": "OD1" <-> "OD2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 348": "OD1" <-> "OD2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 358": "OD1" <-> "OD2" Residue "G GLU 372": "OE1" <-> "OE2" Residue "H ASP 314": "OD1" <-> "OD2" Residue "H GLU 338": "OE1" <-> "OE2" Residue "H PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 348": "OD1" <-> "OD2" Residue "I PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 358": "OD1" <-> "OD2" Residue "I GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.65, per 1000 atoms: 0.46 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 - 3.50 Amino acid : False - 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: 7.45 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.92 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: 3.11 Time building geometry restraints manager: 7.75 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: 96.13 - 103.07: 31 103.07 - 110.00: 9630 110.00 - 116.93: 3930 116.93 - 123.86: 4283 123.86 - 130.80: 660 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 1.850 nonbonded pdb=" OD1 ASP H 314 " pdb=" HG SER H 316 " model vdw 1.527 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.559 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.581 1.850 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.582 1.850 ... (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 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: 2.270 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: 0.150 Extract box with map and model: 11.880 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 32.970 Find NCS groups from input model: 0.510 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:10.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.470 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 0.839 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: 2.3684 time to fit residues: 410.8028 Evaluate side-chains 97 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 6.9990 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: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN F 368 ASN G 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5025 Z= 0.319 Angle : 0.643 4.682 6723 Z= 0.331 Chirality : 0.052 0.144 756 Planarity : 0.004 0.025 855 Dihedral : 6.778 36.407 667 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.17 % Allowed : 12.52 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.29), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 374 PHE 0.009 0.002 PHE A 346 TYR 0.013 0.002 TYR A 310 ARG 0.003 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 130 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 ASN cc_start: 0.5954 (m-40) cc_final: 0.5751 (m110) REVERT: D 321 LYS cc_start: 0.3405 (pptt) cc_final: 0.2879 (pmtt) REVERT: D 368 ASN cc_start: 0.5422 (m-40) cc_final: 0.5180 (m110) REVERT: F 325 LEU cc_start: 0.4341 (mt) cc_final: 0.3962 (mt) REVERT: F 358 ASP cc_start: 0.6790 (p0) cc_final: 0.6484 (t0) REVERT: C 311 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7592 (mttt) REVERT: C 317 LYS cc_start: 0.8091 (mttt) cc_final: 0.7835 (mttm) REVERT: C 338 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7787 (tt0) REVERT: C 347 LYS cc_start: 0.8320 (mttt) cc_final: 0.7670 (pmtt) REVERT: C 369 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7452 (mtmt) REVERT: A 311 LYS cc_start: 0.7873 (mttt) cc_final: 0.7439 (tttm) REVERT: A 338 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7293 (tt0) REVERT: A 360 ILE cc_start: 0.7928 (mt) cc_final: 0.7528 (mm) REVERT: E 311 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7013 (mmtm) REVERT: E 315 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8449 (mt) REVERT: E 340 LYS cc_start: 0.7491 (mttt) cc_final: 0.7139 (mtmm) REVERT: E 347 LYS cc_start: 0.8207 (mttt) cc_final: 0.7789 (tttt) REVERT: E 369 LYS cc_start: 0.7609 (ttmt) cc_final: 0.6967 (tttm) REVERT: G 311 LYS cc_start: 0.8187 (mttt) cc_final: 0.7685 (tttm) REVERT: G 327 ASN cc_start: 0.8157 (m110) cc_final: 0.7922 (m-40) REVERT: G 360 ILE cc_start: 0.8513 (mt) cc_final: 0.8061 (mm) REVERT: H 340 LYS cc_start: 0.7364 (mttt) cc_final: 0.7111 (mtmm) REVERT: H 347 LYS cc_start: 0.8095 (mttt) cc_final: 0.7368 (tttp) REVERT: H 369 LYS cc_start: 0.7632 (ttmt) cc_final: 0.6896 (mtmt) REVERT: I 311 LYS cc_start: 0.7747 (mttt) cc_final: 0.6993 (mmtm) REVERT: I 338 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7344 (mm-30) REVERT: I 360 ILE cc_start: 0.8134 (mt) cc_final: 0.7689 (mm) REVERT: I 375 LYS cc_start: 0.7230 (tttt) cc_final: 0.6622 (ttmm) outliers start: 18 outliers final: 11 residues processed: 123 average time/residue: 2.3038 time to fit residues: 295.4386 Evaluate side-chains 107 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain D residue 328 ILE 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 E residue 315 LEU Chi-restraints excluded: chain G residue 320 SER 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: 7.9990 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5025 Z= 0.260 Angle : 0.591 5.467 6723 Z= 0.305 Chirality : 0.053 0.421 756 Planarity : 0.003 0.024 855 Dihedral : 5.893 30.167 665 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.88 % Allowed : 13.76 % Favored : 82.36 % 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: -1.36 (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 0.006 0.001 HIS E 374 PHE 0.006 0.001 PHE A 346 TYR 0.011 0.002 TYR A 310 ARG 0.002 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 124 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4820 (t70) cc_final: 0.4489 (t70) REVERT: B 358 ASP cc_start: 0.7455 (p0) cc_final: 0.7221 (p0) REVERT: D 331 LYS cc_start: 0.6162 (mttt) cc_final: 0.5312 (pptt) REVERT: D 368 ASN cc_start: 0.5547 (m-40) cc_final: 0.5324 (m110) REVERT: D 372 GLU cc_start: 0.4984 (mm-30) cc_final: 0.4467 (mm-30) REVERT: F 321 LYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5471 (mtpp) REVERT: F 325 LEU cc_start: 0.4370 (mt) cc_final: 0.3770 (mt) REVERT: F 327 ASN cc_start: 0.4029 (m-40) cc_final: 0.3680 (m110) REVERT: F 358 ASP cc_start: 0.6734 (p0) cc_final: 0.6480 (t0) REVERT: C 311 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7623 (mttt) REVERT: C 338 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7861 (tt0) REVERT: C 347 LYS cc_start: 0.8282 (mttt) cc_final: 0.7645 (pmtt) REVERT: C 369 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7481 (mtmt) REVERT: A 311 LYS cc_start: 0.7875 (mttt) cc_final: 0.7468 (tttm) REVERT: A 338 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7318 (tt0) REVERT: A 360 ILE cc_start: 0.7900 (mt) cc_final: 0.7527 (mm) REVERT: E 311 LYS cc_start: 0.7798 (mtmt) cc_final: 0.6988 (mmtm) REVERT: E 340 LYS cc_start: 0.7484 (mttt) cc_final: 0.7183 (mtmm) REVERT: E 347 LYS cc_start: 0.8175 (mttt) cc_final: 0.7761 (tttt) REVERT: E 369 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7067 (tttm) REVERT: G 311 LYS cc_start: 0.8219 (mttt) cc_final: 0.7118 (tmmt) REVERT: G 360 ILE cc_start: 0.8522 (mt) cc_final: 0.8048 (mm) REVERT: H 338 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7420 (tt0) REVERT: H 340 LYS cc_start: 0.7304 (mttt) cc_final: 0.7046 (mtmm) REVERT: H 347 LYS cc_start: 0.8107 (mttt) cc_final: 0.7335 (tttp) REVERT: H 369 LYS cc_start: 0.7612 (ttmt) cc_final: 0.6853 (mtmt) REVERT: I 311 LYS cc_start: 0.7805 (mttt) cc_final: 0.7023 (mmtm) REVERT: I 338 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7337 (mm-30) REVERT: I 360 ILE cc_start: 0.8156 (mt) cc_final: 0.7694 (mm) REVERT: I 375 LYS cc_start: 0.7280 (tttt) cc_final: 0.6614 (ttmm) outliers start: 22 outliers final: 11 residues processed: 115 average time/residue: 2.4032 time to fit residues: 287.3645 Evaluate side-chains 103 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain 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 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 0.0000 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.6557 moved from start: 0.4921 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= 0.187 Angle : 0.519 4.300 6723 Z= 0.260 Chirality : 0.051 0.147 756 Planarity : 0.003 0.026 855 Dihedral : 5.498 27.105 665 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.35 % Allowed : 15.87 % 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: -1.38 (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 0.004 0.001 PHE A 346 TYR 0.011 0.002 TYR C 310 ARG 0.002 0.000 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 111 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.4898 (t70) cc_final: 0.4455 (t70) REVERT: B 358 ASP cc_start: 0.7443 (p0) cc_final: 0.7229 (p0) REVERT: D 331 LYS cc_start: 0.6207 (mttt) cc_final: 0.5378 (pptt) REVERT: D 372 GLU cc_start: 0.4904 (mm-30) cc_final: 0.4375 (mm-30) REVERT: F 321 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5540 (mtpp) REVERT: F 325 LEU cc_start: 0.4397 (mt) cc_final: 0.3700 (mt) REVERT: F 327 ASN cc_start: 0.3870 (m-40) cc_final: 0.3315 (m110) REVERT: F 358 ASP cc_start: 0.6786 (p0) cc_final: 0.6513 (t0) REVERT: C 311 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7587 (mttt) REVERT: C 338 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7827 (tt0) REVERT: C 347 LYS cc_start: 0.8291 (mttt) cc_final: 0.7650 (pmtt) REVERT: C 369 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7777 (tttm) REVERT: A 311 LYS cc_start: 0.7862 (mttt) cc_final: 0.7457 (tttm) REVERT: A 338 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7311 (tt0) REVERT: A 349 ARG cc_start: 0.6971 (mtt180) cc_final: 0.6536 (mtp85) REVERT: A 360 ILE cc_start: 0.7896 (mt) cc_final: 0.7515 (mm) REVERT: E 311 LYS cc_start: 0.7773 (mtmt) cc_final: 0.6975 (mmtm) REVERT: E 340 LYS cc_start: 0.7509 (mttt) cc_final: 0.7208 (mtmm) REVERT: E 347 LYS cc_start: 0.8191 (mttt) cc_final: 0.7768 (tttt) REVERT: E 369 LYS cc_start: 0.7604 (ttmt) cc_final: 0.7053 (tttm) REVERT: G 311 LYS cc_start: 0.8201 (mttt) cc_final: 0.7111 (tmmt) REVERT: G 360 ILE cc_start: 0.8529 (mt) cc_final: 0.8053 (mm) REVERT: H 338 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7358 (tt0) REVERT: H 340 LYS cc_start: 0.7272 (mttt) cc_final: 0.7015 (mtmm) REVERT: H 347 LYS cc_start: 0.8125 (mttt) cc_final: 0.7329 (tttp) REVERT: H 369 LYS cc_start: 0.7605 (ttmt) cc_final: 0.6851 (mtmt) REVERT: I 311 LYS cc_start: 0.7787 (mttt) cc_final: 0.6983 (mmtm) REVERT: I 338 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7324 (mm-30) REVERT: I 360 ILE cc_start: 0.8197 (mt) cc_final: 0.7735 (mm) REVERT: I 375 LYS cc_start: 0.7278 (tttt) cc_final: 0.6629 (ttmm) outliers start: 19 outliers final: 12 residues processed: 106 average time/residue: 2.3400 time to fit residues: 258.1900 Evaluate side-chains 103 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 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 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 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: 0.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 34 optimal weight: 0.0870 overall best weight: 1.6166 ------------------------------------------------------------------------------- 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: 0.6553 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5025 Z= 0.164 Angle : 0.493 4.500 6723 Z= 0.246 Chirality : 0.050 0.150 756 Planarity : 0.003 0.031 855 Dihedral : 5.022 17.904 663 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.70 % Allowed : 15.17 % 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: -1.35 (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 0.002 0.001 HIS F 329 PHE 0.003 0.001 PHE A 346 TYR 0.011 0.002 TYR C 310 ARG 0.002 0.000 ARG G 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 113 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: D 331 LYS cc_start: 0.6237 (mttt) cc_final: 0.5361 (pptt) REVERT: D 372 GLU cc_start: 0.4798 (mm-30) cc_final: 0.4282 (mm-30) REVERT: F 325 LEU cc_start: 0.4579 (mt) cc_final: 0.4032 (mt) REVERT: C 311 LYS cc_start: 0.7886 (mtmt) cc_final: 0.7571 (mttt) REVERT: C 338 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7853 (tt0) REVERT: C 347 LYS cc_start: 0.8293 (mttt) cc_final: 0.7613 (pmtt) REVERT: C 369 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7797 (tttm) REVERT: C 375 LYS cc_start: 0.5034 (tmtt) cc_final: 0.4511 (tptp) REVERT: A 311 LYS cc_start: 0.7862 (mttt) cc_final: 0.7456 (tttm) REVERT: A 338 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7384 (tt0) REVERT: A 349 ARG cc_start: 0.7020 (mtt180) cc_final: 0.6526 (mtp85) REVERT: E 311 LYS cc_start: 0.7753 (mtmt) cc_final: 0.6925 (mmtm) REVERT: E 340 LYS cc_start: 0.7501 (mttt) cc_final: 0.7203 (mtmm) REVERT: E 347 LYS cc_start: 0.8194 (mttt) cc_final: 0.7782 (tttt) REVERT: E 369 LYS cc_start: 0.7624 (ttmt) cc_final: 0.7112 (tttm) REVERT: G 311 LYS cc_start: 0.8165 (mttt) cc_final: 0.7631 (tttm) REVERT: H 338 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7487 (tt0) REVERT: H 340 LYS cc_start: 0.7298 (mttt) cc_final: 0.7048 (mtmm) REVERT: H 347 LYS cc_start: 0.8119 (mttt) cc_final: 0.7377 (tttp) REVERT: H 369 LYS cc_start: 0.7599 (ttmt) cc_final: 0.6864 (ttmt) REVERT: I 311 LYS cc_start: 0.7787 (mttt) cc_final: 0.6973 (mmtm) REVERT: I 375 LYS cc_start: 0.7271 (tttt) cc_final: 0.6620 (ttmm) outliers start: 21 outliers final: 16 residues processed: 108 average time/residue: 2.3666 time to fit residues: 266.0433 Evaluate side-chains 100 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 368 ASN 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 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 0.0570 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN ** I 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5025 Z= 0.259 Angle : 0.533 5.766 6723 Z= 0.271 Chirality : 0.049 0.157 756 Planarity : 0.003 0.032 855 Dihedral : 5.251 19.935 663 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.06 % Allowed : 15.87 % 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: -1.38 (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 0.003 0.001 HIS E 374 PHE 0.007 0.001 PHE D 346 TYR 0.012 0.002 TYR A 310 ARG 0.005 0.001 ARG F 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 111 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 321 LYS cc_start: 0.2972 (OUTLIER) cc_final: 0.2515 (pmtt) REVERT: D 331 LYS cc_start: 0.6263 (mttt) cc_final: 0.5451 (pptt) REVERT: D 372 GLU cc_start: 0.4882 (mm-30) cc_final: 0.4539 (mm-30) REVERT: F 321 LYS cc_start: 0.6394 (OUTLIER) cc_final: 0.5690 (mtpp) REVERT: F 325 LEU cc_start: 0.4663 (mt) cc_final: 0.4160 (mt) REVERT: F 336 GLN cc_start: 0.4444 (tp40) cc_final: 0.3794 (tp40) REVERT: F 375 LYS cc_start: 0.4056 (OUTLIER) cc_final: 0.3847 (mmtp) REVERT: C 338 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7869 (tt0) REVERT: C 342 GLU cc_start: 0.7847 (tt0) cc_final: 0.7355 (tp30) REVERT: C 347 LYS cc_start: 0.8326 (mttt) cc_final: 0.7699 (pmtt) REVERT: C 369 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7812 (tttm) REVERT: A 311 LYS cc_start: 0.7879 (mttt) cc_final: 0.7449 (tttm) REVERT: A 338 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7332 (tt0) REVERT: A 349 ARG cc_start: 0.7103 (mtt180) cc_final: 0.6535 (mtp85) REVERT: E 311 LYS cc_start: 0.7802 (mtmt) cc_final: 0.7060 (mmtm) REVERT: E 347 LYS cc_start: 0.8206 (mttt) cc_final: 0.7763 (tttt) REVERT: E 369 LYS cc_start: 0.7649 (ttmt) cc_final: 0.7114 (tttm) REVERT: G 311 LYS cc_start: 0.8135 (mttt) cc_final: 0.7619 (tttm) REVERT: H 340 LYS cc_start: 0.7316 (mttt) cc_final: 0.6974 (mtmm) REVERT: H 347 LYS cc_start: 0.8129 (mttt) cc_final: 0.7397 (tttp) REVERT: H 369 LYS cc_start: 0.7644 (ttmt) cc_final: 0.6910 (ttmt) REVERT: I 311 LYS cc_start: 0.7882 (mttt) cc_final: 0.7058 (mmtm) REVERT: I 375 LYS cc_start: 0.7259 (tttt) cc_final: 0.6609 (ttmm) outliers start: 23 outliers final: 15 residues processed: 106 average time/residue: 2.3778 time to fit residues: 262.3965 Evaluate side-chains 102 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 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 D residue 356 SER Chi-restraints excluded: chain D residue 368 ASN 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 375 LYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.0970 chunk 17 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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: 0.6556 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5025 Z= 0.153 Angle : 0.493 4.889 6723 Z= 0.246 Chirality : 0.051 0.152 756 Planarity : 0.003 0.030 855 Dihedral : 4.901 17.853 663 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.82 % Allowed : 16.75 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.002 0.000 HIS C 329 PHE 0.003 0.001 PHE D 346 TYR 0.009 0.001 TYR C 310 ARG 0.001 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 105 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 321 LYS cc_start: 0.3025 (OUTLIER) cc_final: 0.2730 (pmtt) REVERT: F 325 LEU cc_start: 0.4561 (mt) cc_final: 0.4032 (mp) REVERT: C 338 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7894 (tt0) REVERT: C 342 GLU cc_start: 0.7851 (tt0) cc_final: 0.7356 (tp30) REVERT: C 347 LYS cc_start: 0.8323 (mttt) cc_final: 0.7831 (pmtt) REVERT: C 369 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7810 (tttm) REVERT: C 375 LYS cc_start: 0.5107 (tmtt) cc_final: 0.4491 (tptp) REVERT: A 311 LYS cc_start: 0.7846 (mttt) cc_final: 0.7440 (tttm) REVERT: A 338 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7353 (tt0) REVERT: A 349 ARG cc_start: 0.7078 (mtt180) cc_final: 0.6502 (mtp85) REVERT: E 311 LYS cc_start: 0.7736 (mtmt) cc_final: 0.6994 (mmtm) REVERT: E 347 LYS cc_start: 0.8194 (mttt) cc_final: 0.7789 (tttt) REVERT: E 369 LYS cc_start: 0.7637 (ttmt) cc_final: 0.7137 (tttm) REVERT: G 311 LYS cc_start: 0.8132 (mttt) cc_final: 0.7634 (tttm) REVERT: H 338 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7452 (tt0) REVERT: H 340 LYS cc_start: 0.7275 (mttt) cc_final: 0.6952 (mtmm) REVERT: H 347 LYS cc_start: 0.8127 (mttt) cc_final: 0.7432 (mmtt) REVERT: H 369 LYS cc_start: 0.7598 (ttmt) cc_final: 0.6875 (ttmt) REVERT: I 311 LYS cc_start: 0.7875 (mttt) cc_final: 0.7040 (mmtm) REVERT: I 375 LYS cc_start: 0.7256 (tttt) cc_final: 0.6596 (ttmm) outliers start: 16 outliers final: 11 residues processed: 102 average time/residue: 2.4782 time to fit residues: 262.6294 Evaluate side-chains 93 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain F residue 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 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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: 0.6566 moved from start: 0.5776 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= 0.175 Angle : 0.486 4.170 6723 Z= 0.242 Chirality : 0.050 0.150 756 Planarity : 0.003 0.030 855 Dihedral : 4.799 17.652 663 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.17 % Allowed : 17.28 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.003 0.001 HIS B 374 PHE 0.004 0.001 PHE D 346 TYR 0.009 0.001 TYR C 310 ARG 0.001 0.000 ARG A 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 95 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 314 ASP cc_start: 0.4749 (t70) cc_final: 0.4255 (t70) REVERT: D 321 LYS cc_start: 0.3093 (OUTLIER) cc_final: 0.2790 (pmtt) REVERT: D 372 GLU cc_start: 0.4695 (mm-30) cc_final: 0.3662 (mm-30) REVERT: C 338 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7938 (tt0) REVERT: C 342 GLU cc_start: 0.7852 (tt0) cc_final: 0.7335 (tp30) REVERT: C 347 LYS cc_start: 0.8327 (mttt) cc_final: 0.7842 (pmtt) REVERT: C 369 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7822 (tttm) REVERT: C 375 LYS cc_start: 0.5040 (tmtt) cc_final: 0.4526 (tptp) REVERT: A 311 LYS cc_start: 0.7872 (mttt) cc_final: 0.7473 (tttm) REVERT: A 338 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7362 (tt0) REVERT: E 311 LYS cc_start: 0.7745 (mtmt) cc_final: 0.7007 (mmtm) REVERT: E 347 LYS cc_start: 0.8194 (mttt) cc_final: 0.7783 (tttt) REVERT: E 369 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7150 (tttm) REVERT: G 311 LYS cc_start: 0.8142 (mttt) cc_final: 0.7656 (tttm) REVERT: H 338 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7487 (tt0) REVERT: H 340 LYS cc_start: 0.7275 (mttt) cc_final: 0.7036 (mtmp) REVERT: H 347 LYS cc_start: 0.8138 (mttt) cc_final: 0.7715 (mmtp) REVERT: H 369 LYS cc_start: 0.7616 (ttmt) cc_final: 0.6898 (ttmt) REVERT: I 311 LYS cc_start: 0.7880 (mttt) cc_final: 0.7050 (mmtm) REVERT: I 375 LYS cc_start: 0.7254 (tttt) cc_final: 0.6600 (ttmm) outliers start: 18 outliers final: 11 residues processed: 91 average time/residue: 2.4645 time to fit residues: 233.2098 Evaluate side-chains 87 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER 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 D residue 356 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5025 Z= 0.178 Angle : 0.485 4.105 6723 Z= 0.243 Chirality : 0.050 0.150 756 Planarity : 0.003 0.028 855 Dihedral : 4.759 17.611 663 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.35 % Allowed : 16.75 % 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: -1.35 (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 0.002 0.001 HIS D 374 PHE 0.005 0.001 PHE D 346 TYR 0.009 0.001 TYR C 310 ARG 0.004 0.001 ARG B 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 fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 339 VAL cc_start: 0.6732 (t) cc_final: 0.6247 (p) REVERT: D 314 ASP cc_start: 0.4857 (t70) cc_final: 0.4410 (t70) REVERT: D 321 LYS cc_start: 0.3055 (OUTLIER) cc_final: 0.2734 (pmtt) REVERT: D 372 GLU cc_start: 0.4692 (mm-30) cc_final: 0.3564 (mm-30) REVERT: C 338 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7944 (tt0) REVERT: C 342 GLU cc_start: 0.7862 (tt0) cc_final: 0.7326 (tp30) REVERT: C 347 LYS cc_start: 0.8297 (mttt) cc_final: 0.7856 (pmtt) REVERT: C 369 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7826 (tttm) REVERT: A 311 LYS cc_start: 0.7856 (mttt) cc_final: 0.7465 (tttm) REVERT: A 338 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7375 (tt0) REVERT: E 311 LYS cc_start: 0.7759 (mtmt) cc_final: 0.7010 (mmtm) REVERT: E 347 LYS cc_start: 0.8176 (mttt) cc_final: 0.7779 (tttt) REVERT: E 369 LYS cc_start: 0.7663 (ttmt) cc_final: 0.7058 (tttm) REVERT: G 311 LYS cc_start: 0.8137 (mttt) cc_final: 0.7676 (tttm) REVERT: H 338 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7492 (tt0) REVERT: H 340 LYS cc_start: 0.7317 (mttt) cc_final: 0.7050 (mtmp) REVERT: H 342 GLU cc_start: 0.7388 (tt0) cc_final: 0.6704 (tp30) REVERT: H 347 LYS cc_start: 0.8136 (mttt) cc_final: 0.7706 (mmtp) REVERT: H 369 LYS cc_start: 0.7607 (ttmt) cc_final: 0.6910 (ttmt) REVERT: I 311 LYS cc_start: 0.7900 (mttt) cc_final: 0.7075 (mmtm) REVERT: I 375 LYS cc_start: 0.7259 (tttt) cc_final: 0.6602 (ttmm) outliers start: 19 outliers final: 12 residues processed: 93 average time/residue: 2.5035 time to fit residues: 242.2008 Evaluate side-chains 88 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER 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 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 370 LYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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: 0.6576 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5025 Z= 0.181 Angle : 0.498 5.817 6723 Z= 0.247 Chirality : 0.050 0.149 756 Planarity : 0.003 0.027 855 Dihedral : 4.711 17.504 663 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.12 % Allowed : 18.34 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.29), 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 0.002 0.001 HIS B 374 PHE 0.006 0.001 PHE D 346 TYR 0.008 0.001 TYR C 310 ARG 0.001 0.000 ARG B 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 fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 339 VAL cc_start: 0.6719 (t) cc_final: 0.6246 (p) REVERT: D 314 ASP cc_start: 0.4844 (t70) cc_final: 0.4352 (t70) REVERT: D 321 LYS cc_start: 0.3047 (OUTLIER) cc_final: 0.2739 (pmtt) REVERT: D 372 GLU cc_start: 0.4769 (mm-30) cc_final: 0.3692 (mm-30) REVERT: C 338 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7944 (tt0) REVERT: C 342 GLU cc_start: 0.7869 (tt0) cc_final: 0.7327 (tp30) REVERT: C 347 LYS cc_start: 0.8316 (mttt) cc_final: 0.7864 (pmtt) REVERT: C 369 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7828 (tttm) REVERT: A 311 LYS cc_start: 0.7874 (mttt) cc_final: 0.7472 (tttm) REVERT: A 338 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7353 (tt0) REVERT: E 311 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7010 (mmtm) REVERT: E 347 LYS cc_start: 0.8198 (mttt) cc_final: 0.7789 (tttt) REVERT: E 369 LYS cc_start: 0.7661 (ttmt) cc_final: 0.7060 (tttm) REVERT: E 372 GLU cc_start: 0.7851 (tt0) cc_final: 0.7476 (tt0) REVERT: G 311 LYS cc_start: 0.8134 (mttt) cc_final: 0.7686 (tttm) REVERT: H 338 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7498 (tt0) REVERT: H 340 LYS cc_start: 0.7315 (mttt) cc_final: 0.7043 (mtmp) REVERT: H 342 GLU cc_start: 0.7413 (tt0) cc_final: 0.6717 (tp30) REVERT: H 347 LYS cc_start: 0.8140 (mttt) cc_final: 0.7740 (mmtp) REVERT: H 369 LYS cc_start: 0.7606 (ttmt) cc_final: 0.6902 (ttmt) REVERT: I 311 LYS cc_start: 0.7908 (mttt) cc_final: 0.7175 (mmtm) REVERT: I 375 LYS cc_start: 0.7262 (tttt) cc_final: 0.6608 (ttmm) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 2.5675 time to fit residues: 234.8685 Evaluate side-chains 85 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 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: 10.0000 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 = 0.4622 r_free = 0.4622 target = 0.196713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.145639 restraints weight = 17399.310| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.36 r_work: 0.3940 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5025 Z= 0.348 Angle : 0.584 5.695 6723 Z= 0.300 Chirality : 0.050 0.156 756 Planarity : 0.004 0.029 855 Dihedral : 5.442 22.123 663 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.65 % Allowed : 17.99 % Favored : 79.37 % 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: -1.53 (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 0.005 0.001 HIS F 329 PHE 0.014 0.002 PHE D 346 TYR 0.015 0.002 TYR A 310 ARG 0.002 0.001 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5462.70 seconds wall clock time: 95 minutes 17.53 seconds (5717.53 seconds total)