Starting phenix.real_space_refine on Fri Aug 2 16:22:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/08_2024/9eog_19854.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/08_2024/9eog_19854.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/9eog_19854/08_2024/9eog_19854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/08_2024/9eog_19854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/08_2024/9eog_19854.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/08_2024/9eog_19854.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= 0.002 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2202 2.51 5 N 648 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 348": "OD1" <-> "OD2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 348": "OD1" <-> "OD2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 380": "OE1" <-> "OE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 348": "OD1" <-> "OD2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 380": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3522 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 3.31, per 1000 atoms: 0.94 Number of scatterers: 3522 At special positions: 0 Unit cell: (74.984, 153.264, 37.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 666 8.00 N 648 7.00 C 2202 6.00 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: 1.33 Conformation dependent library (CDL) restraints added in 637.2 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 59.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.494A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.775A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 319 removed outlier: 6.347A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 322 through 330 removed outlier: 8.880A pdb=" N CYS A 322 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU B 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N SER A 324 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N ASN B 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLY A 326 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N HIS B 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER E 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER F 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU E 325 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY F 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN E 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 346 removed outlier: 6.859A pdb=" N VAL B 337 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU A 338 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS A 340 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER B 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU A 342 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU E 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N VAL E 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N LYS F 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N VAL E 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLU F 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER E 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU F 344 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS E 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE F 346 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP E 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 362 removed outlier: 8.868A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N SER B 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 355 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP B 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ILE B 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER A 352 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS E 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 354 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY E 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER E 352 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS F 353 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E 354 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY F 355 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 379 removed outlier: 6.603A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE E 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS E 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU F 372 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE E 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS F 374 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR E 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU F 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS E 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE F 378 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR E 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.493A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR D 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.775A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 317 through 319 Processing sheet with id=AB2, first strand: chain 'C' and resid 322 through 330 removed outlier: 6.808A pdb=" N SER D 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 325 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY D 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN C 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 346 removed outlier: 9.035A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU D 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS C 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N PHE D 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 351 through 362 removed outlier: 6.867A pdb=" N SER C 352 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS D 353 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY D 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 369 through 379 removed outlier: 6.603A pdb=" N LYS C 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLU D 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU D 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS C 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE D 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR C 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 58 hydrogen bonds defined for protein. 174 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: 0.76 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 843 1.33 - 1.45: 816 1.45 - 1.57: 1911 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3576 Sorted by residual: bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.307 0.047 1.10e-02 8.26e+03 1.80e+01 bond pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.78e+01 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.77e+01 bond pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.77e+01 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.76e+01 ... (remaining 3571 not shown) Histogram of bond angle deviations from ideal: 102.36 - 109.10: 588 109.10 - 115.83: 1866 115.83 - 122.57: 1617 122.57 - 129.30: 699 129.30 - 136.04: 12 Bond angle restraints: 4782 Sorted by residual: angle pdb=" C ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta sigma weight residual 111.63 120.32 -8.69 1.36e+00 5.41e-01 4.08e+01 angle pdb=" C ARG C 349 " pdb=" CA ARG C 349 " pdb=" CB ARG C 349 " ideal model delta sigma weight residual 111.63 120.31 -8.68 1.36e+00 5.41e-01 4.07e+01 angle pdb=" C ARG A 349 " pdb=" CA ARG A 349 " pdb=" CB ARG A 349 " ideal model delta sigma weight residual 111.63 120.30 -8.67 1.36e+00 5.41e-01 4.07e+01 angle pdb=" C ARG E 349 " pdb=" CA ARG E 349 " pdb=" CB ARG E 349 " ideal model delta sigma weight residual 111.63 120.29 -8.66 1.36e+00 5.41e-01 4.05e+01 angle pdb=" C ARG F 349 " pdb=" CA ARG F 349 " pdb=" CB ARG F 349 " ideal model delta sigma weight residual 111.63 120.28 -8.65 1.36e+00 5.41e-01 4.05e+01 ... (remaining 4777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.95: 1664 9.95 - 19.91: 358 19.91 - 29.86: 102 29.86 - 39.81: 30 39.81 - 49.76: 24 Dihedral angle restraints: 2178 sinusoidal: 912 harmonic: 1266 Sorted by residual: dihedral pdb=" CA VAL C 318 " pdb=" C VAL C 318 " pdb=" N THR C 319 " pdb=" CA THR C 319 " ideal model delta harmonic sigma weight residual -180.00 -149.79 -30.21 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA VAL E 318 " pdb=" C VAL E 318 " pdb=" N THR E 319 " pdb=" CA THR E 319 " ideal model delta harmonic sigma weight residual 180.00 -149.80 -30.20 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA VAL D 318 " pdb=" C VAL D 318 " pdb=" N THR D 319 " pdb=" CA THR D 319 " ideal model delta harmonic sigma weight residual 180.00 -149.81 -30.19 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 2175 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.080: 251 0.080 - 0.158: 241 0.158 - 0.236: 36 0.236 - 0.314: 0 0.314 - 0.391: 6 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ARG E 349 " pdb=" N ARG E 349 " pdb=" C ARG E 349 " pdb=" CB ARG E 349 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA ARG A 349 " pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CB ARG A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 531 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 366 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLY B 366 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY B 366 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY B 367 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 366 " -0.017 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLY E 366 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY E 366 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY E 367 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 366 " 0.017 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLY C 366 " -0.063 2.00e-02 2.50e+03 pdb=" O GLY C 366 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY C 367 " 0.021 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.94: 1428 2.94 - 3.43: 3246 3.43 - 3.92: 5599 3.92 - 4.41: 5642 4.41 - 4.90: 11553 Nonbonded interactions: 27468 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.445 3.040 ... (remaining 27463 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 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 : 0.009 0.047 3576 Z= 0.594 Angle : 1.628 8.689 4782 Z= 1.047 Chirality : 0.104 0.391 534 Planarity : 0.011 0.039 612 Dihedral : 12.855 49.764 1374 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.48 % Allowed : 4.48 % Favored : 91.04 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.37 % 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: -4.10 (0.27), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS E 330 PHE 0.049 0.009 PHE C 346 TYR 0.049 0.017 TYR C 310 ARG 0.004 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 0.446 Fit side-chains REVERT: A 311 LYS cc_start: 0.8486 (tmtt) cc_final: 0.8059 (ttpt) REVERT: A 317 LYS cc_start: 0.8468 (ptpp) cc_final: 0.8197 (pttt) REVERT: A 321 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8522 (tppp) REVERT: A 331 LYS cc_start: 0.8749 (mttp) cc_final: 0.8450 (mtpm) REVERT: A 342 GLU cc_start: 0.8452 (tt0) cc_final: 0.8212 (mm-30) REVERT: A 375 LYS cc_start: 0.8509 (tttt) cc_final: 0.7763 (mptm) REVERT: B 311 LYS cc_start: 0.8545 (tmtt) cc_final: 0.7985 (mmtt) REVERT: B 316 SER cc_start: 0.9441 (p) cc_final: 0.9163 (p) REVERT: B 317 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8218 (ptpt) REVERT: B 331 LYS cc_start: 0.8732 (mttp) cc_final: 0.7249 (tmtt) REVERT: B 349 ARG cc_start: 0.7988 (ptp-170) cc_final: 0.7733 (ptm160) REVERT: B 375 LYS cc_start: 0.8417 (tttt) cc_final: 0.7672 (mptm) REVERT: C 311 LYS cc_start: 0.8620 (tmtt) cc_final: 0.8030 (mmtt) REVERT: C 317 LYS cc_start: 0.8541 (ptpp) cc_final: 0.8203 (ptmt) REVERT: C 331 LYS cc_start: 0.8796 (mttp) cc_final: 0.8470 (mtpm) REVERT: C 375 LYS cc_start: 0.8454 (tttt) cc_final: 0.7748 (mptm) REVERT: D 311 LYS cc_start: 0.8741 (tmtt) cc_final: 0.7754 (pptt) REVERT: D 317 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8384 (ptmt) REVERT: D 331 LYS cc_start: 0.8844 (mttp) cc_final: 0.8523 (mtpt) REVERT: D 375 LYS cc_start: 0.8954 (tttt) cc_final: 0.8356 (mttm) REVERT: E 311 LYS cc_start: 0.8526 (tmtt) cc_final: 0.8144 (ttmt) REVERT: E 317 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8149 (ptmt) REVERT: E 321 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8341 (mtpt) REVERT: E 331 LYS cc_start: 0.8964 (mttp) cc_final: 0.8575 (mtpt) REVERT: E 342 GLU cc_start: 0.8582 (tt0) cc_final: 0.8130 (mm-30) REVERT: E 375 LYS cc_start: 0.8655 (tttt) cc_final: 0.7951 (mttm) REVERT: F 311 LYS cc_start: 0.8705 (tmtt) cc_final: 0.7759 (pptt) REVERT: F 331 LYS cc_start: 0.8888 (mttp) cc_final: 0.8627 (mtpt) REVERT: F 375 LYS cc_start: 0.8865 (tttt) cc_final: 0.8486 (mtpm) outliers start: 18 outliers final: 1 residues processed: 140 average time/residue: 1.5324 time to fit residues: 218.9915 Evaluate side-chains 131 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 351 GLN A 374 HIS B 307 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN B 374 HIS C 307 GLN C 330 HIS C 351 GLN C 374 HIS D 307 GLN D 336 GLN D 351 GLN D 368 ASN D 374 HIS E 307 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS F 307 GLN F 368 ASN F 374 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3576 Z= 0.288 Angle : 0.664 5.513 4782 Z= 0.338 Chirality : 0.054 0.160 534 Planarity : 0.004 0.027 612 Dihedral : 6.217 30.998 484 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.74 % Allowed : 16.92 % Favored : 80.35 % 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: -3.07 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 374 PHE 0.022 0.003 PHE A 346 TYR 0.012 0.003 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.438 Fit side-chains REVERT: A 348 ASP cc_start: 0.7830 (t0) cc_final: 0.7390 (m-30) REVERT: B 311 LYS cc_start: 0.8539 (tmtt) cc_final: 0.7994 (mmtt) REVERT: B 317 LYS cc_start: 0.8654 (ptpp) cc_final: 0.8333 (ptmt) REVERT: B 331 LYS cc_start: 0.8761 (mttp) cc_final: 0.8489 (mtpt) REVERT: B 348 ASP cc_start: 0.8325 (t0) cc_final: 0.8035 (m-30) REVERT: B 358 ASP cc_start: 0.8917 (p0) cc_final: 0.8452 (p0) REVERT: C 317 LYS cc_start: 0.8499 (ptpp) cc_final: 0.8199 (ptmt) REVERT: C 331 LYS cc_start: 0.8833 (mttp) cc_final: 0.8562 (mtpm) REVERT: C 348 ASP cc_start: 0.8148 (t0) cc_final: 0.7741 (m-30) REVERT: C 358 ASP cc_start: 0.8599 (p0) cc_final: 0.8211 (p0) REVERT: D 311 LYS cc_start: 0.8705 (tmtt) cc_final: 0.7777 (pptt) REVERT: D 317 LYS cc_start: 0.8774 (ptpp) cc_final: 0.8331 (ptmt) REVERT: D 331 LYS cc_start: 0.8787 (mttp) cc_final: 0.8300 (mtpt) REVERT: D 340 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8520 (mttm) REVERT: D 347 LYS cc_start: 0.8291 (ptmt) cc_final: 0.7880 (ptmt) REVERT: D 348 ASP cc_start: 0.8361 (t0) cc_final: 0.8032 (m-30) REVERT: D 358 ASP cc_start: 0.8829 (p0) cc_final: 0.8540 (p0) REVERT: D 375 LYS cc_start: 0.8667 (tttt) cc_final: 0.8042 (mttm) REVERT: E 311 LYS cc_start: 0.8432 (tmtt) cc_final: 0.8155 (ttmt) REVERT: E 317 LYS cc_start: 0.8427 (ptpp) cc_final: 0.8107 (ptmt) REVERT: E 331 LYS cc_start: 0.8814 (mttp) cc_final: 0.8442 (mtpt) REVERT: E 340 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8377 (mttp) REVERT: E 348 ASP cc_start: 0.7946 (t0) cc_final: 0.7593 (m-30) REVERT: E 358 ASP cc_start: 0.8443 (p0) cc_final: 0.8103 (p0) REVERT: E 375 LYS cc_start: 0.8514 (tttt) cc_final: 0.7746 (mttp) REVERT: F 311 LYS cc_start: 0.8615 (tmtt) cc_final: 0.7794 (pptt) REVERT: F 317 LYS cc_start: 0.8697 (ptpt) cc_final: 0.8466 (ptmt) REVERT: F 331 LYS cc_start: 0.8795 (mttp) cc_final: 0.8517 (mtpt) REVERT: F 348 ASP cc_start: 0.8370 (t0) cc_final: 0.8054 (m-30) outliers start: 11 outliers final: 1 residues processed: 120 average time/residue: 1.1927 time to fit residues: 147.0057 Evaluate side-chains 107 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3576 Z= 0.285 Angle : 0.634 6.058 4782 Z= 0.315 Chirality : 0.053 0.147 534 Planarity : 0.004 0.026 612 Dihedral : 5.273 30.552 476 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.49 % Allowed : 20.90 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.018 0.002 PHE E 346 TYR 0.014 0.003 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.439 Fit side-chains REVERT: A 311 LYS cc_start: 0.8457 (tmtt) cc_final: 0.8125 (ttpt) REVERT: A 317 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8118 (ptmm) REVERT: A 331 LYS cc_start: 0.8738 (mttp) cc_final: 0.8450 (mtpm) REVERT: A 340 LYS cc_start: 0.8701 (ttmm) cc_final: 0.8370 (mttm) REVERT: A 348 ASP cc_start: 0.7881 (t0) cc_final: 0.7472 (m-30) REVERT: A 375 LYS cc_start: 0.8414 (tttt) cc_final: 0.7755 (mttm) REVERT: B 311 LYS cc_start: 0.8508 (tmtt) cc_final: 0.7963 (mmtm) REVERT: B 317 LYS cc_start: 0.8669 (ptpp) cc_final: 0.8372 (ptmt) REVERT: B 331 LYS cc_start: 0.8793 (mttp) cc_final: 0.8571 (mtmt) REVERT: B 348 ASP cc_start: 0.8309 (t0) cc_final: 0.7978 (m-30) REVERT: B 358 ASP cc_start: 0.8905 (p0) cc_final: 0.8607 (p0) REVERT: C 317 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8189 (ptmt) REVERT: C 331 LYS cc_start: 0.8829 (mttp) cc_final: 0.8518 (mtpt) REVERT: C 348 ASP cc_start: 0.8155 (t0) cc_final: 0.7818 (m-30) REVERT: C 358 ASP cc_start: 0.8535 (p0) cc_final: 0.8045 (p0) REVERT: D 311 LYS cc_start: 0.8676 (tmtt) cc_final: 0.7776 (pptt) REVERT: D 317 LYS cc_start: 0.8744 (ptpp) cc_final: 0.8326 (ptmm) REVERT: D 331 LYS cc_start: 0.8794 (mttp) cc_final: 0.8431 (mtpt) REVERT: D 340 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8612 (mttp) REVERT: D 347 LYS cc_start: 0.8273 (ptmt) cc_final: 0.7848 (ptmt) REVERT: D 349 ARG cc_start: 0.7639 (ptm160) cc_final: 0.5648 (ppt170) REVERT: D 375 LYS cc_start: 0.8748 (tttt) cc_final: 0.8075 (mttm) REVERT: E 311 LYS cc_start: 0.8431 (tmtt) cc_final: 0.8161 (ttmt) REVERT: E 331 LYS cc_start: 0.8858 (mttp) cc_final: 0.8496 (mtpt) REVERT: E 348 ASP cc_start: 0.7972 (t0) cc_final: 0.7562 (m-30) REVERT: F 311 LYS cc_start: 0.8610 (tmtt) cc_final: 0.7759 (pptt) REVERT: F 317 LYS cc_start: 0.8688 (ptpt) cc_final: 0.8423 (ptmt) REVERT: F 331 LYS cc_start: 0.8909 (mttp) cc_final: 0.8678 (mtpt) outliers start: 6 outliers final: 3 residues processed: 105 average time/residue: 1.3424 time to fit residues: 144.5107 Evaluate side-chains 101 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3576 Z= 0.234 Angle : 0.608 7.039 4782 Z= 0.297 Chirality : 0.051 0.135 534 Planarity : 0.003 0.025 612 Dihedral : 4.984 32.157 476 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.74 % Allowed : 20.65 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.014 0.002 PHE A 346 TYR 0.011 0.003 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.423 Fit side-chains REVERT: A 317 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8124 (ptmm) REVERT: A 331 LYS cc_start: 0.8720 (mttp) cc_final: 0.8466 (mtpm) REVERT: A 348 ASP cc_start: 0.7901 (t0) cc_final: 0.7487 (m-30) REVERT: B 311 LYS cc_start: 0.8492 (tttt) cc_final: 0.7950 (mmtt) REVERT: B 317 LYS cc_start: 0.8660 (ptpp) cc_final: 0.8398 (ptmt) REVERT: B 348 ASP cc_start: 0.8281 (t0) cc_final: 0.7956 (m-30) REVERT: B 358 ASP cc_start: 0.8848 (p0) cc_final: 0.8565 (p0) REVERT: C 317 LYS cc_start: 0.8555 (ptpp) cc_final: 0.8240 (ptmt) REVERT: C 331 LYS cc_start: 0.8837 (mttp) cc_final: 0.8557 (mtpt) REVERT: C 348 ASP cc_start: 0.8155 (t0) cc_final: 0.7838 (m-30) REVERT: D 311 LYS cc_start: 0.8641 (tttt) cc_final: 0.7745 (pptt) REVERT: D 317 LYS cc_start: 0.8700 (ptpp) cc_final: 0.8314 (ptmt) REVERT: D 331 LYS cc_start: 0.8758 (mttp) cc_final: 0.8499 (mtpt) REVERT: D 340 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8583 (mttp) REVERT: D 349 ARG cc_start: 0.7636 (ptm160) cc_final: 0.5542 (ppt170) REVERT: D 375 LYS cc_start: 0.8743 (tttt) cc_final: 0.8084 (mttp) REVERT: E 311 LYS cc_start: 0.8358 (tttt) cc_final: 0.8120 (ttmt) REVERT: E 331 LYS cc_start: 0.8848 (mttp) cc_final: 0.8516 (mtpt) REVERT: E 336 GLN cc_start: 0.8860 (tp40) cc_final: 0.8614 (tp40) REVERT: E 348 ASP cc_start: 0.7998 (t0) cc_final: 0.7608 (m-30) REVERT: F 311 LYS cc_start: 0.8555 (tttt) cc_final: 0.7657 (pptt) REVERT: F 331 LYS cc_start: 0.8875 (mttp) cc_final: 0.8661 (mtpt) REVERT: F 358 ASP cc_start: 0.8376 (p0) cc_final: 0.7991 (m-30) outliers start: 7 outliers final: 4 residues processed: 95 average time/residue: 1.3139 time to fit residues: 128.0456 Evaluate side-chains 91 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3576 Z= 0.235 Angle : 0.608 7.844 4782 Z= 0.294 Chirality : 0.051 0.138 534 Planarity : 0.003 0.025 612 Dihedral : 4.854 32.990 476 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.99 % Allowed : 21.64 % Favored : 76.37 % 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: -1.85 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.014 0.002 PHE E 346 TYR 0.011 0.003 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.423 Fit side-chains REVERT: A 331 LYS cc_start: 0.8729 (mttp) cc_final: 0.8497 (mtpm) REVERT: A 348 ASP cc_start: 0.7940 (t0) cc_final: 0.7456 (m-30) REVERT: B 311 LYS cc_start: 0.8508 (tttt) cc_final: 0.7961 (mmtm) REVERT: B 317 LYS cc_start: 0.8661 (ptpp) cc_final: 0.8399 (ptmt) REVERT: B 348 ASP cc_start: 0.8256 (t0) cc_final: 0.7911 (m-30) REVERT: B 358 ASP cc_start: 0.8859 (p0) cc_final: 0.8554 (p0) REVERT: C 317 LYS cc_start: 0.8576 (ptpp) cc_final: 0.8257 (ptmt) REVERT: C 331 LYS cc_start: 0.8835 (mttp) cc_final: 0.8575 (mtpt) REVERT: C 348 ASP cc_start: 0.8201 (t0) cc_final: 0.7878 (m-30) REVERT: D 311 LYS cc_start: 0.8637 (tttt) cc_final: 0.7758 (pptt) REVERT: D 317 LYS cc_start: 0.8703 (ptpp) cc_final: 0.8234 (ptmt) REVERT: D 331 LYS cc_start: 0.8768 (mttp) cc_final: 0.8501 (mtpt) REVERT: D 349 ARG cc_start: 0.7650 (ptm160) cc_final: 0.5490 (ppt170) REVERT: D 375 LYS cc_start: 0.8708 (tttt) cc_final: 0.8078 (mttp) REVERT: E 311 LYS cc_start: 0.8354 (tttt) cc_final: 0.8117 (ttmt) REVERT: E 331 LYS cc_start: 0.8859 (mttp) cc_final: 0.8538 (mtpt) REVERT: E 348 ASP cc_start: 0.8028 (t0) cc_final: 0.7753 (m-30) REVERT: F 311 LYS cc_start: 0.8570 (tttt) cc_final: 0.7714 (pptt) REVERT: F 331 LYS cc_start: 0.8875 (mttp) cc_final: 0.8674 (mtpt) REVERT: F 358 ASP cc_start: 0.8398 (p0) cc_final: 0.8089 (m-30) outliers start: 8 outliers final: 5 residues processed: 91 average time/residue: 1.3066 time to fit residues: 122.0541 Evaluate side-chains 91 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.0770 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3576 Z= 0.382 Angle : 0.673 8.681 4782 Z= 0.329 Chirality : 0.053 0.153 534 Planarity : 0.004 0.033 612 Dihedral : 5.089 29.981 476 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.74 % Allowed : 21.89 % Favored : 76.37 % 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: -1.88 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.022 0.003 PHE E 346 TYR 0.017 0.004 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.426 Fit side-chains REVERT: A 311 LYS cc_start: 0.8425 (tttt) cc_final: 0.8091 (ttpt) REVERT: A 331 LYS cc_start: 0.8816 (mttp) cc_final: 0.8375 (mtpt) REVERT: A 348 ASP cc_start: 0.7936 (t0) cc_final: 0.7477 (m-30) REVERT: A 375 LYS cc_start: 0.8448 (tttt) cc_final: 0.7795 (mttm) REVERT: B 311 LYS cc_start: 0.8507 (tttt) cc_final: 0.8009 (mmtt) REVERT: B 317 LYS cc_start: 0.8648 (ptpp) cc_final: 0.8364 (ptmt) REVERT: B 348 ASP cc_start: 0.8297 (t0) cc_final: 0.7944 (m-30) REVERT: B 358 ASP cc_start: 0.8956 (p0) cc_final: 0.8627 (p0) REVERT: C 311 LYS cc_start: 0.8545 (tttt) cc_final: 0.8045 (mmtt) REVERT: C 317 LYS cc_start: 0.8575 (ptpp) cc_final: 0.8267 (ptmt) REVERT: C 331 LYS cc_start: 0.8855 (mttp) cc_final: 0.8556 (mtpt) REVERT: C 348 ASP cc_start: 0.8293 (t0) cc_final: 0.7956 (m-30) REVERT: C 375 LYS cc_start: 0.8373 (tttt) cc_final: 0.7629 (mttm) REVERT: D 311 LYS cc_start: 0.8693 (tttt) cc_final: 0.7815 (pptt) REVERT: D 317 LYS cc_start: 0.8735 (ptpp) cc_final: 0.8294 (ptmt) REVERT: D 331 LYS cc_start: 0.8903 (mttp) cc_final: 0.8547 (mtpt) REVERT: D 349 ARG cc_start: 0.7653 (ptm160) cc_final: 0.5420 (ppt170) REVERT: D 358 ASP cc_start: 0.8736 (p0) cc_final: 0.8296 (m-30) REVERT: D 375 LYS cc_start: 0.8703 (tttt) cc_final: 0.8068 (mttp) REVERT: E 311 LYS cc_start: 0.8452 (tttt) cc_final: 0.8180 (ttmt) REVERT: E 331 LYS cc_start: 0.8931 (mttp) cc_final: 0.8553 (mtpt) REVERT: E 348 ASP cc_start: 0.8054 (t0) cc_final: 0.7597 (m-30) REVERT: F 311 LYS cc_start: 0.8652 (tttt) cc_final: 0.7772 (pptt) REVERT: F 331 LYS cc_start: 0.8984 (mttp) cc_final: 0.8735 (mtpt) outliers start: 7 outliers final: 5 residues processed: 99 average time/residue: 1.4149 time to fit residues: 143.4262 Evaluate side-chains 95 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3576 Z= 0.221 Angle : 0.623 9.026 4782 Z= 0.295 Chirality : 0.051 0.139 534 Planarity : 0.003 0.035 612 Dihedral : 4.800 33.618 476 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.99 % Allowed : 22.14 % Favored : 75.87 % 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: -1.73 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.012 0.002 PHE E 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.388 Fit side-chains REVERT: A 331 LYS cc_start: 0.8737 (mttp) cc_final: 0.8509 (mtpm) REVERT: A 348 ASP cc_start: 0.7935 (t0) cc_final: 0.7490 (m-30) REVERT: B 311 LYS cc_start: 0.8511 (tttt) cc_final: 0.7969 (mmtt) REVERT: B 317 LYS cc_start: 0.8633 (ptpp) cc_final: 0.8360 (ptmt) REVERT: B 348 ASP cc_start: 0.8243 (t0) cc_final: 0.7889 (m-30) REVERT: B 358 ASP cc_start: 0.8863 (p0) cc_final: 0.8562 (p0) REVERT: C 317 LYS cc_start: 0.8588 (ptpp) cc_final: 0.8278 (ptmt) REVERT: C 331 LYS cc_start: 0.8860 (mttp) cc_final: 0.8592 (mtpt) REVERT: C 348 ASP cc_start: 0.8233 (t0) cc_final: 0.7891 (m-30) REVERT: D 311 LYS cc_start: 0.8638 (tttt) cc_final: 0.7750 (pptt) REVERT: D 317 LYS cc_start: 0.8719 (ptpp) cc_final: 0.8270 (ptmt) REVERT: D 331 LYS cc_start: 0.8826 (mttp) cc_final: 0.8466 (mtpt) REVERT: D 349 ARG cc_start: 0.7688 (ptm160) cc_final: 0.5505 (ppt170) REVERT: D 358 ASP cc_start: 0.8567 (p0) cc_final: 0.8187 (m-30) REVERT: D 375 LYS cc_start: 0.8682 (tttt) cc_final: 0.8083 (mttp) REVERT: E 311 LYS cc_start: 0.8377 (tttt) cc_final: 0.8138 (ttmt) REVERT: E 317 LYS cc_start: 0.8501 (ptpp) cc_final: 0.8155 (ptmt) REVERT: E 331 LYS cc_start: 0.8877 (mttp) cc_final: 0.8531 (mtpt) REVERT: F 311 LYS cc_start: 0.8614 (tttt) cc_final: 0.7762 (pptt) REVERT: F 331 LYS cc_start: 0.8885 (mttp) cc_final: 0.8646 (mtpt) REVERT: F 358 ASP cc_start: 0.8421 (p0) cc_final: 0.8021 (m-30) outliers start: 8 outliers final: 6 residues processed: 91 average time/residue: 1.3086 time to fit residues: 122.2241 Evaluate side-chains 90 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3576 Z= 0.419 Angle : 0.710 9.668 4782 Z= 0.341 Chirality : 0.054 0.160 534 Planarity : 0.004 0.038 612 Dihedral : 5.112 30.285 476 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.99 % Allowed : 22.39 % Favored : 75.62 % 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: -1.90 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.024 0.003 PHE E 346 TYR 0.018 0.005 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.425 Fit side-chains REVERT: A 311 LYS cc_start: 0.8438 (tttt) cc_final: 0.8100 (ttpt) REVERT: A 331 LYS cc_start: 0.8820 (mttp) cc_final: 0.8390 (mtpt) REVERT: A 348 ASP cc_start: 0.7951 (t0) cc_final: 0.7465 (m-30) REVERT: A 375 LYS cc_start: 0.8475 (tttt) cc_final: 0.7819 (mttm) REVERT: B 311 LYS cc_start: 0.8540 (tttt) cc_final: 0.8034 (mmtt) REVERT: B 317 LYS cc_start: 0.8678 (ptpp) cc_final: 0.8375 (ptmt) REVERT: B 348 ASP cc_start: 0.8276 (t0) cc_final: 0.7916 (m-30) REVERT: B 356 SER cc_start: 0.9234 (p) cc_final: 0.8887 (m) REVERT: B 358 ASP cc_start: 0.8958 (p0) cc_final: 0.8464 (p0) REVERT: C 311 LYS cc_start: 0.8540 (tttt) cc_final: 0.8028 (mmtt) REVERT: C 317 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8266 (ptmt) REVERT: C 331 LYS cc_start: 0.8872 (mttp) cc_final: 0.8567 (mtpt) REVERT: C 348 ASP cc_start: 0.8295 (t0) cc_final: 0.7907 (m-30) REVERT: C 375 LYS cc_start: 0.8338 (tttt) cc_final: 0.7617 (mttm) REVERT: D 311 LYS cc_start: 0.8697 (tttt) cc_final: 0.7815 (pptt) REVERT: D 317 LYS cc_start: 0.8740 (ptpp) cc_final: 0.8348 (ptmt) REVERT: D 331 LYS cc_start: 0.8918 (mttp) cc_final: 0.8534 (mtpt) REVERT: D 349 ARG cc_start: 0.7689 (ptm160) cc_final: 0.5397 (ppt170) REVERT: D 375 LYS cc_start: 0.8699 (tttt) cc_final: 0.8073 (mttp) REVERT: D 379 ARG cc_start: 0.8787 (mpt-90) cc_final: 0.6611 (pmt170) REVERT: E 311 LYS cc_start: 0.8459 (tttt) cc_final: 0.8184 (ttmt) REVERT: E 317 LYS cc_start: 0.8526 (ptpp) cc_final: 0.8177 (ptmt) REVERT: E 331 LYS cc_start: 0.8951 (mttp) cc_final: 0.8570 (mtpt) REVERT: E 348 ASP cc_start: 0.8079 (t0) cc_final: 0.7602 (m-30) REVERT: F 311 LYS cc_start: 0.8711 (tttt) cc_final: 0.7820 (pptt) REVERT: F 331 LYS cc_start: 0.8978 (mttp) cc_final: 0.8733 (mtpt) REVERT: F 358 ASP cc_start: 0.8544 (p0) cc_final: 0.8049 (m-30) outliers start: 8 outliers final: 6 residues processed: 101 average time/residue: 1.4643 time to fit residues: 151.3249 Evaluate side-chains 103 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0670 chunk 37 optimal weight: 0.4980 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3576 Z= 0.179 Angle : 0.635 9.962 4782 Z= 0.293 Chirality : 0.050 0.135 534 Planarity : 0.003 0.036 612 Dihedral : 4.697 35.603 476 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.74 % Allowed : 23.63 % Favored : 74.63 % 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: -1.69 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.010 0.001 PHE E 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.435 Fit side-chains REVERT: A 331 LYS cc_start: 0.8711 (mttp) cc_final: 0.8500 (mtpm) REVERT: A 348 ASP cc_start: 0.7949 (t0) cc_final: 0.7629 (m-30) REVERT: B 311 LYS cc_start: 0.8505 (tttt) cc_final: 0.7966 (mmtt) REVERT: B 317 LYS cc_start: 0.8658 (ptpp) cc_final: 0.8384 (ptmt) REVERT: B 348 ASP cc_start: 0.8206 (t0) cc_final: 0.7824 (m-30) REVERT: B 358 ASP cc_start: 0.8829 (p0) cc_final: 0.8528 (p0) REVERT: C 317 LYS cc_start: 0.8596 (ptpp) cc_final: 0.8279 (ptmt) REVERT: C 331 LYS cc_start: 0.8848 (mttp) cc_final: 0.8554 (mtpt) REVERT: D 311 LYS cc_start: 0.8597 (tttt) cc_final: 0.7738 (pptt) REVERT: D 317 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8308 (ptmt) REVERT: D 331 LYS cc_start: 0.8775 (mttp) cc_final: 0.8436 (mtpt) REVERT: D 349 ARG cc_start: 0.7702 (ptm160) cc_final: 0.5511 (ppt170) REVERT: D 358 ASP cc_start: 0.8624 (p0) cc_final: 0.8270 (m-30) REVERT: D 375 LYS cc_start: 0.8689 (tttt) cc_final: 0.8074 (mttp) REVERT: E 311 LYS cc_start: 0.8315 (tttt) cc_final: 0.8081 (ttmt) REVERT: E 317 LYS cc_start: 0.8491 (ptpp) cc_final: 0.8135 (ptmt) REVERT: E 331 LYS cc_start: 0.8861 (mttp) cc_final: 0.8529 (mtpt) REVERT: F 311 LYS cc_start: 0.8617 (tttt) cc_final: 0.7769 (pptt) REVERT: F 331 LYS cc_start: 0.8812 (mttp) cc_final: 0.8573 (mtpt) REVERT: F 358 ASP cc_start: 0.8402 (p0) cc_final: 0.8092 (m-30) outliers start: 7 outliers final: 4 residues processed: 91 average time/residue: 1.4144 time to fit residues: 131.8963 Evaluate side-chains 87 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0070 chunk 26 optimal weight: 0.0270 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3576 Z= 0.149 Angle : 0.634 9.869 4782 Z= 0.285 Chirality : 0.050 0.126 534 Planarity : 0.003 0.040 612 Dihedral : 4.547 37.900 476 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.00 % Allowed : 25.12 % Favored : 73.88 % 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: -1.62 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 329 PHE 0.007 0.001 PHE A 346 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG F 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8698 (mttp) cc_final: 0.8351 (mtpt) REVERT: A 348 ASP cc_start: 0.7933 (t0) cc_final: 0.7676 (m-30) REVERT: A 375 LYS cc_start: 0.8461 (tttt) cc_final: 0.7842 (mttm) REVERT: B 317 LYS cc_start: 0.8651 (ptpp) cc_final: 0.8392 (ptmt) REVERT: B 343 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7541 (tptp) REVERT: B 348 ASP cc_start: 0.8159 (t0) cc_final: 0.7835 (m-30) REVERT: B 358 ASP cc_start: 0.8748 (p0) cc_final: 0.8502 (p0) REVERT: C 317 LYS cc_start: 0.8595 (ptpp) cc_final: 0.8271 (ptmt) REVERT: C 331 LYS cc_start: 0.8840 (mttp) cc_final: 0.8565 (mtpt) REVERT: C 375 LYS cc_start: 0.8433 (tttt) cc_final: 0.7766 (mttm) REVERT: D 311 LYS cc_start: 0.8568 (tttt) cc_final: 0.7701 (pptt) REVERT: D 317 LYS cc_start: 0.8617 (ptpp) cc_final: 0.8176 (ptmt) REVERT: D 331 LYS cc_start: 0.8726 (mttp) cc_final: 0.8378 (mtpt) REVERT: D 375 LYS cc_start: 0.8727 (tttt) cc_final: 0.8118 (mttp) REVERT: E 311 LYS cc_start: 0.8307 (tttt) cc_final: 0.8107 (ttmt) REVERT: E 317 LYS cc_start: 0.8460 (ptpp) cc_final: 0.8143 (ptmt) REVERT: E 356 SER cc_start: 0.8972 (m) cc_final: 0.8662 (t) REVERT: F 311 LYS cc_start: 0.8578 (tttt) cc_final: 0.7779 (pptt) REVERT: F 356 SER cc_start: 0.8986 (m) cc_final: 0.8752 (t) outliers start: 4 outliers final: 1 residues processed: 95 average time/residue: 1.3536 time to fit residues: 131.9190 Evaluate side-chains 85 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.152690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.133054 restraints weight = 4002.000| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.43 r_work: 0.3955 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3576 Z= 0.181 Angle : 0.661 9.781 4782 Z= 0.297 Chirality : 0.050 0.130 534 Planarity : 0.003 0.033 612 Dihedral : 4.602 39.341 476 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.75 % Allowed : 28.36 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.007 0.001 PHE E 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2569.56 seconds wall clock time: 45 minutes 23.72 seconds (2723.72 seconds total)