Starting phenix.real_space_refine on Thu Jul 18 20:49:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/07_2024/9eog_19854.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/07_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_19854/07_2024/9eog_19854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/07_2024/9eog_19854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/07_2024/9eog_19854.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eog_19854/07_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-5388/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: 3.27, per 1000 atoms: 0.93 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: 1.25 Conformation dependent library (CDL) restraints added in 637.6 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: 0.47 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: 0.79 Time building geometry restraints manager: 1.38 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 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.445 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.445 2.440 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.445 2.440 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.445 2.440 ... (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 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: 2.640 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.000 Find NCS groups from input model: 0.140 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:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.970 ------------------------------------------------------------------------------- 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 : 0.481 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: 1.4718 time to fit residues: 210.3834 Evaluate side-chains 131 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 7.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 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 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 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8722 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3576 Z= 0.426 Angle : 0.733 6.082 4782 Z= 0.375 Chirality : 0.056 0.166 534 Planarity : 0.005 0.027 612 Dihedral : 6.490 27.618 484 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.48 % Allowed : 16.42 % Favored : 79.10 % 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: -3.15 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 374 PHE 0.025 0.003 PHE A 346 TYR 0.019 0.005 TYR F 310 ARG 0.002 0.001 ARG D 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 141 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.437 Fit side-chains REVERT: A 311 LYS cc_start: 0.8522 (tmtt) cc_final: 0.8186 (ttpt) REVERT: A 317 LYS cc_start: 0.8381 (ptpp) cc_final: 0.8043 (ptmt) REVERT: A 331 LYS cc_start: 0.8758 (mttp) cc_final: 0.8452 (mtpm) REVERT: A 348 ASP cc_start: 0.7880 (t0) cc_final: 0.7504 (m-30) REVERT: A 356 SER cc_start: 0.8899 (OUTLIER) cc_final: 0.8546 (m) REVERT: A 358 ASP cc_start: 0.8709 (p0) cc_final: 0.7963 (p0) REVERT: A 375 LYS cc_start: 0.8387 (tttt) cc_final: 0.7667 (mttm) REVERT: B 311 LYS cc_start: 0.8578 (tmtt) cc_final: 0.8075 (mmtt) REVERT: B 316 SER cc_start: 0.9397 (p) cc_final: 0.9157 (p) REVERT: B 317 LYS cc_start: 0.8645 (ptpp) cc_final: 0.8363 (ptmt) REVERT: B 331 LYS cc_start: 0.8789 (mttp) cc_final: 0.8480 (mtpt) REVERT: B 348 ASP cc_start: 0.8351 (t0) cc_final: 0.8045 (m-30) REVERT: B 358 ASP cc_start: 0.9011 (p0) cc_final: 0.8498 (p0) REVERT: C 311 LYS cc_start: 0.8613 (tmtt) cc_final: 0.8085 (mmtt) REVERT: C 317 LYS cc_start: 0.8502 (ptpp) cc_final: 0.8183 (ptmt) REVERT: C 331 LYS cc_start: 0.8835 (mttp) cc_final: 0.8565 (mtpm) REVERT: C 348 ASP cc_start: 0.8162 (t0) cc_final: 0.7769 (m-30) REVERT: C 358 ASP cc_start: 0.8692 (p0) cc_final: 0.8256 (p0) REVERT: C 375 LYS cc_start: 0.8265 (tttt) cc_final: 0.7550 (mttm) REVERT: D 311 LYS cc_start: 0.8773 (tmtt) cc_final: 0.7882 (pptt) REVERT: D 317 LYS cc_start: 0.8781 (ptpp) cc_final: 0.8398 (ptmt) REVERT: D 331 LYS cc_start: 0.8915 (mttp) cc_final: 0.8417 (mtpt) REVERT: D 340 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8528 (ttmm) REVERT: D 347 LYS cc_start: 0.8334 (ptmt) cc_final: 0.7909 (ptmt) REVERT: D 348 ASP cc_start: 0.8408 (t0) cc_final: 0.7851 (m-30) REVERT: D 349 ARG cc_start: 0.7594 (ptm160) cc_final: 0.5573 (ppt170) REVERT: D 358 ASP cc_start: 0.8853 (p0) cc_final: 0.8084 (p0) REVERT: D 375 LYS cc_start: 0.8803 (tttt) cc_final: 0.8111 (mttm) REVERT: E 311 LYS cc_start: 0.8538 (tmtt) cc_final: 0.8245 (ttmt) REVERT: E 317 LYS cc_start: 0.8411 (ptpp) cc_final: 0.8095 (ptmt) REVERT: E 331 LYS cc_start: 0.8900 (mttp) cc_final: 0.8509 (mtpt) REVERT: E 340 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8425 (mttm) REVERT: E 348 ASP cc_start: 0.7961 (t0) cc_final: 0.7585 (m-30) REVERT: E 358 ASP cc_start: 0.8513 (p0) cc_final: 0.8185 (p0) REVERT: F 311 LYS cc_start: 0.8669 (tmtt) cc_final: 0.7830 (pptt) REVERT: F 331 LYS cc_start: 0.8947 (mttp) cc_final: 0.8650 (mtpt) REVERT: F 348 ASP cc_start: 0.8414 (t0) cc_final: 0.8093 (m-30) outliers start: 18 outliers final: 3 residues processed: 127 average time/residue: 1.3522 time to fit residues: 175.8475 Evaluate side-chains 117 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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: 0.8715 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3576 Z= 0.343 Angle : 0.658 5.936 4782 Z= 0.332 Chirality : 0.054 0.153 534 Planarity : 0.004 0.027 612 Dihedral : 5.519 28.785 476 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.99 % Allowed : 19.40 % 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: -2.51 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.019 0.003 PHE E 346 TYR 0.015 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 117 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.460 Fit side-chains REVERT: A 311 LYS cc_start: 0.8486 (tttt) cc_final: 0.8134 (ttpt) REVERT: A 317 LYS cc_start: 0.8473 (ptpp) cc_final: 0.8130 (ptmt) REVERT: A 331 LYS cc_start: 0.8761 (mttp) cc_final: 0.8478 (mtpm) REVERT: A 348 ASP cc_start: 0.7899 (t0) cc_final: 0.7503 (m-30) REVERT: A 375 LYS cc_start: 0.8398 (tttt) cc_final: 0.7733 (mttm) REVERT: B 311 LYS cc_start: 0.8526 (tttt) cc_final: 0.7988 (mmtt) REVERT: B 317 LYS cc_start: 0.8658 (ptpp) cc_final: 0.8363 (ptmt) REVERT: B 331 LYS cc_start: 0.8750 (mttp) cc_final: 0.8492 (mtpt) REVERT: B 348 ASP cc_start: 0.8382 (t0) cc_final: 0.8019 (m-30) REVERT: B 358 ASP cc_start: 0.8950 (p0) cc_final: 0.8615 (p0) REVERT: C 311 LYS cc_start: 0.8600 (tttt) cc_final: 0.8063 (mmtm) REVERT: C 317 LYS cc_start: 0.8520 (ptpp) cc_final: 0.8199 (ptmt) REVERT: C 331 LYS cc_start: 0.8841 (mttp) cc_final: 0.8510 (mtpt) REVERT: C 348 ASP cc_start: 0.8181 (t0) cc_final: 0.7760 (m-30) REVERT: C 358 ASP cc_start: 0.8606 (p0) cc_final: 0.8204 (p0) REVERT: C 375 LYS cc_start: 0.8319 (tttt) cc_final: 0.7580 (mttm) REVERT: D 311 LYS cc_start: 0.8733 (tmtt) cc_final: 0.7852 (pptt) REVERT: D 317 LYS cc_start: 0.8778 (ptpp) cc_final: 0.8365 (ptmm) REVERT: D 331 LYS cc_start: 0.8864 (mttp) cc_final: 0.8582 (mtpm) REVERT: D 347 LYS cc_start: 0.8343 (ptmt) cc_final: 0.7891 (ptmt) REVERT: D 348 ASP cc_start: 0.8283 (t0) cc_final: 0.7730 (m-30) REVERT: D 349 ARG cc_start: 0.7604 (ptm160) cc_final: 0.5451 (ppt170) REVERT: D 375 LYS cc_start: 0.8795 (tttt) cc_final: 0.8119 (mttp) REVERT: E 311 LYS cc_start: 0.8482 (tmtt) cc_final: 0.8189 (ttmt) REVERT: E 331 LYS cc_start: 0.8874 (mttp) cc_final: 0.8490 (mtpt) REVERT: E 348 ASP cc_start: 0.7974 (t0) cc_final: 0.7540 (m-30) REVERT: E 358 ASP cc_start: 0.8340 (p0) cc_final: 0.8090 (p0) REVERT: F 311 LYS cc_start: 0.8637 (tttt) cc_final: 0.7761 (pptt) REVERT: F 331 LYS cc_start: 0.8966 (mttp) cc_final: 0.8702 (mtpt) outliers start: 12 outliers final: 5 residues processed: 110 average time/residue: 1.3365 time to fit residues: 150.6115 Evaluate side-chains 109 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 324 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 overall best weight: 2.4146 ------------------------------------------------------------------------------- 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: 0.8703 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3576 Z= 0.284 Angle : 0.619 5.733 4782 Z= 0.307 Chirality : 0.052 0.146 534 Planarity : 0.003 0.026 612 Dihedral : 5.217 30.014 476 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.24 % Allowed : 20.15 % 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: -2.14 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.016 0.002 PHE E 346 TYR 0.012 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 107 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.440 Fit side-chains REVERT: A 311 LYS cc_start: 0.8414 (tttt) cc_final: 0.8076 (ttpt) REVERT: A 317 LYS cc_start: 0.8491 (ptpp) cc_final: 0.8150 (ptmt) REVERT: A 331 LYS cc_start: 0.8743 (mttp) cc_final: 0.8478 (mtpm) REVERT: A 348 ASP cc_start: 0.7899 (t0) cc_final: 0.7477 (m-30) REVERT: A 375 LYS cc_start: 0.8432 (tttt) cc_final: 0.7769 (mttm) REVERT: B 311 LYS cc_start: 0.8500 (tttt) cc_final: 0.7965 (mmtt) REVERT: B 317 LYS cc_start: 0.8690 (ptpp) cc_final: 0.8397 (ptmt) REVERT: B 331 LYS cc_start: 0.8782 (mttp) cc_final: 0.8508 (mtpt) REVERT: B 348 ASP cc_start: 0.8331 (t0) cc_final: 0.7985 (m-30) REVERT: B 358 ASP cc_start: 0.8907 (p0) cc_final: 0.8583 (p0) REVERT: C 311 LYS cc_start: 0.8538 (tttt) cc_final: 0.8030 (mmtt) REVERT: C 317 LYS cc_start: 0.8503 (ptpp) cc_final: 0.8183 (ptmt) REVERT: C 331 LYS cc_start: 0.8843 (mttp) cc_final: 0.8541 (mtpt) REVERT: C 348 ASP cc_start: 0.8150 (t0) cc_final: 0.7792 (m-30) REVERT: C 375 LYS cc_start: 0.8349 (tttt) cc_final: 0.7612 (mttm) REVERT: D 311 LYS cc_start: 0.8698 (tttt) cc_final: 0.7814 (pptt) REVERT: D 317 LYS cc_start: 0.8761 (ptpp) cc_final: 0.8352 (ptmm) REVERT: D 331 LYS cc_start: 0.8809 (mttp) cc_final: 0.8438 (mtpt) REVERT: D 340 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8671 (mttp) REVERT: D 347 LYS cc_start: 0.8329 (ptmt) cc_final: 0.7893 (ptmt) REVERT: D 349 ARG cc_start: 0.7614 (ptm160) cc_final: 0.5386 (ppt170) REVERT: E 311 LYS cc_start: 0.8428 (tttt) cc_final: 0.8152 (ttmt) REVERT: E 331 LYS cc_start: 0.8868 (mttp) cc_final: 0.8490 (mtpt) REVERT: E 348 ASP cc_start: 0.7983 (t0) cc_final: 0.7538 (m-30) REVERT: F 311 LYS cc_start: 0.8604 (tttt) cc_final: 0.7762 (pptt) REVERT: F 331 LYS cc_start: 0.8940 (mttp) cc_final: 0.8694 (mtpt) outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 1.4140 time to fit residues: 146.2025 Evaluate side-chains 98 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 324 SER 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: 0.4980 chunk 16 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 0 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- 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: 0.8667 moved from start: 0.3598 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= 0.185 Angle : 0.566 6.839 4782 Z= 0.277 Chirality : 0.050 0.135 534 Planarity : 0.003 0.023 612 Dihedral : 4.804 33.820 476 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: -1.86 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.012 0.001 PHE A 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG D 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 97 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.424 Fit side-chains REVERT: A 317 LYS cc_start: 0.8466 (ptpp) cc_final: 0.8146 (ptmt) REVERT: A 331 LYS cc_start: 0.8699 (mttp) cc_final: 0.8250 (mtpt) REVERT: A 348 ASP cc_start: 0.7950 (t0) cc_final: 0.7580 (m-30) REVERT: B 311 LYS cc_start: 0.8485 (tttt) cc_final: 0.7948 (mmtt) REVERT: B 317 LYS cc_start: 0.8693 (ptpp) cc_final: 0.8423 (ptmt) REVERT: B 331 LYS cc_start: 0.8775 (mttp) cc_final: 0.8518 (mtpt) REVERT: B 348 ASP cc_start: 0.8219 (t0) cc_final: 0.7856 (m-30) REVERT: B 358 ASP cc_start: 0.8836 (p0) cc_final: 0.8546 (p0) REVERT: C 317 LYS cc_start: 0.8545 (ptpp) cc_final: 0.8211 (ptmt) REVERT: C 331 LYS cc_start: 0.8810 (mttp) cc_final: 0.8520 (mtpt) REVERT: C 375 LYS cc_start: 0.8351 (tttt) cc_final: 0.7622 (mttm) REVERT: D 311 LYS cc_start: 0.8625 (tttt) cc_final: 0.7824 (pptt) REVERT: D 317 LYS cc_start: 0.8737 (ptpp) cc_final: 0.8348 (ptmt) REVERT: D 331 LYS cc_start: 0.8728 (mttp) cc_final: 0.8376 (mtpt) REVERT: D 358 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8391 (m-30) REVERT: E 311 LYS cc_start: 0.8333 (tttt) cc_final: 0.8098 (ttmt) REVERT: E 331 LYS cc_start: 0.8818 (mttp) cc_final: 0.8490 (mtpt) REVERT: E 348 ASP cc_start: 0.8000 (t0) cc_final: 0.7743 (m-30) REVERT: E 356 SER cc_start: 0.8951 (m) cc_final: 0.8651 (t) REVERT: F 311 LYS cc_start: 0.8536 (tttt) cc_final: 0.7702 (pptt) REVERT: F 331 LYS cc_start: 0.8826 (mttp) cc_final: 0.8626 (mtpt) outliers start: 7 outliers final: 3 residues processed: 92 average time/residue: 1.3132 time to fit residues: 123.9794 Evaluate side-chains 91 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E 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: 0.0980 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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: 0.8697 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3576 Z= 0.283 Angle : 0.619 7.265 4782 Z= 0.301 Chirality : 0.052 0.148 534 Planarity : 0.003 0.026 612 Dihedral : 4.950 30.773 476 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.49 % Allowed : 21.89 % 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: -1.80 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.016 0.002 PHE E 346 TYR 0.013 0.003 TYR F 310 ARG 0.001 0.000 ARG C 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 104 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.431 Fit side-chains REVERT: A 311 LYS cc_start: 0.8392 (tttt) cc_final: 0.8070 (ttpt) REVERT: A 317 LYS cc_start: 0.8491 (ptpp) cc_final: 0.8158 (ptmt) REVERT: A 331 LYS cc_start: 0.8744 (mttp) cc_final: 0.8473 (mtpm) REVERT: A 348 ASP cc_start: 0.7927 (t0) cc_final: 0.7624 (m-30) REVERT: A 375 LYS cc_start: 0.8437 (tttt) cc_final: 0.7795 (mttm) REVERT: B 311 LYS cc_start: 0.8476 (tttt) cc_final: 0.7970 (mmtt) REVERT: B 317 LYS cc_start: 0.8676 (ptpp) cc_final: 0.8401 (ptmt) REVERT: B 331 LYS cc_start: 0.8789 (mttp) cc_final: 0.8524 (mtpt) REVERT: B 348 ASP cc_start: 0.8265 (t0) cc_final: 0.7882 (m-30) REVERT: B 358 ASP cc_start: 0.8912 (p0) cc_final: 0.8611 (p0) REVERT: C 311 LYS cc_start: 0.8526 (tttt) cc_final: 0.8010 (mmtt) REVERT: C 317 LYS cc_start: 0.8557 (ptpp) cc_final: 0.8223 (ptmt) REVERT: C 331 LYS cc_start: 0.8853 (mttp) cc_final: 0.8554 (mtpt) REVERT: C 375 LYS cc_start: 0.8340 (tttt) cc_final: 0.7595 (mttm) REVERT: D 311 LYS cc_start: 0.8654 (tttt) cc_final: 0.7822 (pptt) REVERT: D 317 LYS cc_start: 0.8745 (ptpp) cc_final: 0.8373 (ptmt) REVERT: D 331 LYS cc_start: 0.8800 (mttp) cc_final: 0.8442 (mtpt) REVERT: D 349 ARG cc_start: 0.7610 (ptm160) cc_final: 0.5444 (ppt170) REVERT: D 358 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8435 (m-30) REVERT: E 311 LYS cc_start: 0.8395 (tttt) cc_final: 0.8140 (ttmt) REVERT: E 331 LYS cc_start: 0.8860 (mttp) cc_final: 0.8508 (mtpt) REVERT: F 311 LYS cc_start: 0.8599 (tttt) cc_final: 0.7684 (pptt) REVERT: F 331 LYS cc_start: 0.8934 (mttp) cc_final: 0.8714 (mtpt) outliers start: 10 outliers final: 4 residues processed: 99 average time/residue: 1.3312 time to fit residues: 135.1096 Evaluate side-chains 99 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 358 ASP 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: 2.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 0.0000 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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: 0.8637 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3576 Z= 0.145 Angle : 0.564 8.151 4782 Z= 0.268 Chirality : 0.049 0.130 534 Planarity : 0.003 0.029 612 Dihedral : 4.306 12.010 474 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.74 % Allowed : 22.14 % Favored : 76.12 % 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: -1.68 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 329 PHE 0.009 0.001 PHE A 346 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** 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 92 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.428 Fit side-chains REVERT: A 317 LYS cc_start: 0.8459 (ptpp) cc_final: 0.8148 (ptmt) REVERT: A 331 LYS cc_start: 0.8669 (mttp) cc_final: 0.8444 (mtpm) REVERT: A 348 ASP cc_start: 0.7919 (t0) cc_final: 0.7656 (m-30) REVERT: B 311 LYS cc_start: 0.8486 (tttt) cc_final: 0.7979 (mmtt) REVERT: B 317 LYS cc_start: 0.8690 (ptpp) cc_final: 0.8423 (ptmt) REVERT: B 331 LYS cc_start: 0.8755 (mttp) cc_final: 0.8511 (mtpt) REVERT: B 343 LYS cc_start: 0.8400 (ttmm) cc_final: 0.7561 (tptp) REVERT: B 348 ASP cc_start: 0.8121 (t0) cc_final: 0.7833 (m-30) REVERT: B 358 ASP cc_start: 0.8782 (p0) cc_final: 0.8509 (p0) REVERT: C 317 LYS cc_start: 0.8562 (ptpp) cc_final: 0.8228 (ptmt) REVERT: C 331 LYS cc_start: 0.8815 (mttp) cc_final: 0.8532 (mtpt) REVERT: D 311 LYS cc_start: 0.8564 (tttt) cc_final: 0.7797 (pptt) REVERT: D 317 LYS cc_start: 0.8666 (ptpp) cc_final: 0.8279 (ptmt) REVERT: D 331 LYS cc_start: 0.8684 (mttp) cc_final: 0.8444 (mtpt) REVERT: D 358 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8498 (m-30) REVERT: E 311 LYS cc_start: 0.8299 (tttt) cc_final: 0.8075 (ttmt) REVERT: E 317 LYS cc_start: 0.8472 (ptpp) cc_final: 0.8108 (ptmt) REVERT: E 331 LYS cc_start: 0.8777 (mttp) cc_final: 0.8473 (mtpt) REVERT: E 356 SER cc_start: 0.8948 (m) cc_final: 0.8688 (t) REVERT: F 311 LYS cc_start: 0.8518 (tttt) cc_final: 0.7680 (pptt) outliers start: 7 outliers final: 2 residues processed: 89 average time/residue: 1.3606 time to fit residues: 124.5328 Evaluate side-chains 84 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 358 ASP 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: 6.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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: 0.8731 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3576 Z= 0.502 Angle : 0.723 8.365 4782 Z= 0.354 Chirality : 0.055 0.168 534 Planarity : 0.004 0.037 612 Dihedral : 5.116 14.686 474 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.49 % Allowed : 21.89 % 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: -1.84 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.026 0.003 PHE E 346 TYR 0.021 0.005 TYR F 310 ARG 0.001 0.000 ARG C 349 *********************** 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 108 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.444 Fit side-chains REVERT: A 311 LYS cc_start: 0.8474 (tttt) cc_final: 0.8125 (ttpt) REVERT: A 317 LYS cc_start: 0.8508 (ptpp) cc_final: 0.8178 (ptmt) REVERT: A 331 LYS cc_start: 0.8873 (mttp) cc_final: 0.8621 (mtpm) REVERT: A 348 ASP cc_start: 0.7964 (t0) cc_final: 0.7450 (m-30) REVERT: A 375 LYS cc_start: 0.8478 (tttt) cc_final: 0.7816 (mttm) REVERT: B 311 LYS cc_start: 0.8530 (tttt) cc_final: 0.7996 (mmtt) REVERT: B 317 LYS cc_start: 0.8685 (ptpp) cc_final: 0.8382 (ptmt) REVERT: B 331 LYS cc_start: 0.8833 (mttp) cc_final: 0.8516 (mtpt) REVERT: B 343 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8256 (mtpp) REVERT: B 348 ASP cc_start: 0.8232 (t0) cc_final: 0.7864 (m-30) REVERT: B 356 SER cc_start: 0.9244 (p) cc_final: 0.8898 (m) REVERT: B 358 ASP cc_start: 0.8992 (p0) cc_final: 0.8462 (p0) REVERT: C 311 LYS cc_start: 0.8549 (tttt) cc_final: 0.8056 (mmtt) REVERT: C 317 LYS cc_start: 0.8548 (ptpp) cc_final: 0.8202 (ptmt) REVERT: C 331 LYS cc_start: 0.8896 (mttp) cc_final: 0.8554 (mtpt) REVERT: C 375 LYS cc_start: 0.8311 (tttt) cc_final: 0.7586 (mttm) REVERT: D 311 LYS cc_start: 0.8713 (tttt) cc_final: 0.7903 (pptt) REVERT: D 317 LYS cc_start: 0.8800 (ptpp) cc_final: 0.8417 (ptmt) REVERT: D 331 LYS cc_start: 0.8943 (mttp) cc_final: 0.8554 (mtpt) REVERT: D 349 ARG cc_start: 0.7618 (ptm160) cc_final: 0.5320 (ppt170) REVERT: D 379 ARG cc_start: 0.8796 (mpt-90) cc_final: 0.6591 (pmt170) REVERT: E 311 LYS cc_start: 0.8479 (tttt) cc_final: 0.8185 (ttmt) REVERT: E 331 LYS cc_start: 0.8931 (mttp) cc_final: 0.8567 (mtpt) REVERT: E 348 ASP cc_start: 0.8085 (t0) cc_final: 0.7591 (m-30) REVERT: F 311 LYS cc_start: 0.8654 (tttt) cc_final: 0.7788 (pptt) REVERT: F 325 LEU cc_start: 0.8884 (tt) cc_final: 0.8498 (tt) outliers start: 10 outliers final: 9 residues processed: 101 average time/residue: 1.4963 time to fit residues: 154.6053 Evaluate side-chains 107 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 373 THR 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: 0.0870 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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 ** 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: 0.8639 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3576 Z= 0.154 Angle : 0.608 8.956 4782 Z= 0.285 Chirality : 0.050 0.132 534 Planarity : 0.003 0.036 612 Dihedral : 4.335 12.301 474 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.74 % Allowed : 23.38 % Favored : 74.88 % 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: -1.65 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.008 0.001 PHE A 346 TYR 0.005 0.001 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 88 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.416 Fit side-chains REVERT: A 317 LYS cc_start: 0.8464 (ptpp) cc_final: 0.8120 (ptmt) REVERT: A 331 LYS cc_start: 0.8685 (mttp) cc_final: 0.8273 (mtpt) REVERT: A 348 ASP cc_start: 0.7940 (t0) cc_final: 0.7608 (m-30) REVERT: B 311 LYS cc_start: 0.8450 (tttt) cc_final: 0.7931 (mmtt) REVERT: B 317 LYS cc_start: 0.8710 (ptpp) cc_final: 0.8413 (ptmt) REVERT: B 331 LYS cc_start: 0.8729 (mttp) cc_final: 0.8494 (mtpt) REVERT: B 343 LYS cc_start: 0.8458 (ttmm) cc_final: 0.7580 (tptp) REVERT: B 348 ASP cc_start: 0.8126 (t0) cc_final: 0.7807 (m-30) REVERT: B 358 ASP cc_start: 0.8782 (p0) cc_final: 0.8504 (p0) REVERT: C 317 LYS cc_start: 0.8583 (ptpp) cc_final: 0.8235 (ptmt) REVERT: C 331 LYS cc_start: 0.8800 (mttp) cc_final: 0.8468 (mtmt) REVERT: D 311 LYS cc_start: 0.8595 (tttt) cc_final: 0.7777 (pptt) REVERT: D 317 LYS cc_start: 0.8679 (ptpp) cc_final: 0.8285 (ptmt) REVERT: D 331 LYS cc_start: 0.8734 (mttp) cc_final: 0.8397 (mtpt) REVERT: D 349 ARG cc_start: 0.7579 (ptm160) cc_final: 0.5431 (ppt170) REVERT: D 358 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8402 (m-30) REVERT: E 311 LYS cc_start: 0.8264 (tttt) cc_final: 0.8023 (ttmt) REVERT: E 331 LYS cc_start: 0.8784 (mttp) cc_final: 0.8490 (mtpt) REVERT: E 348 ASP cc_start: 0.7957 (t0) cc_final: 0.7713 (m-30) REVERT: E 356 SER cc_start: 0.8919 (m) cc_final: 0.8657 (t) REVERT: F 311 LYS cc_start: 0.8523 (tttt) cc_final: 0.7611 (pptt) outliers start: 7 outliers final: 3 residues processed: 84 average time/residue: 1.2797 time to fit residues: 110.3811 Evaluate side-chains 82 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0370 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 ** 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: 0.8629 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3576 Z= 0.157 Angle : 0.595 8.684 4782 Z= 0.277 Chirality : 0.049 0.129 534 Planarity : 0.003 0.041 612 Dihedral : 4.148 11.568 474 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.24 % Allowed : 24.38 % Favored : 74.38 % 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: -1.63 (0.35), 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 0.008 0.001 PHE A 346 TYR 0.007 0.001 TYR A 310 ARG 0.001 0.000 ARG B 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: 5 poor density : 92 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8458 (ptpp) cc_final: 0.8133 (ptmt) REVERT: A 331 LYS cc_start: 0.8677 (mttp) cc_final: 0.8452 (mtpm) REVERT: A 348 ASP cc_start: 0.7938 (t0) cc_final: 0.7662 (m-30) REVERT: B 311 LYS cc_start: 0.8520 (tttt) cc_final: 0.7986 (mmtt) REVERT: B 331 LYS cc_start: 0.8791 (mttp) cc_final: 0.8555 (mtpt) REVERT: B 343 LYS cc_start: 0.8454 (ttmm) cc_final: 0.7568 (tptp) REVERT: B 348 ASP cc_start: 0.8054 (t0) cc_final: 0.7770 (m-30) REVERT: B 358 ASP cc_start: 0.8786 (p0) cc_final: 0.8537 (p0) REVERT: C 311 LYS cc_start: 0.8552 (tttt) cc_final: 0.8083 (mmtt) REVERT: C 317 LYS cc_start: 0.8570 (ptpp) cc_final: 0.8235 (ptmt) REVERT: C 331 LYS cc_start: 0.8827 (mttp) cc_final: 0.8514 (mtmt) REVERT: C 375 LYS cc_start: 0.8361 (tttt) cc_final: 0.7694 (mttm) REVERT: D 311 LYS cc_start: 0.8585 (tttt) cc_final: 0.7807 (pptt) REVERT: D 317 LYS cc_start: 0.8672 (ptpp) cc_final: 0.8286 (ptmt) REVERT: D 331 LYS cc_start: 0.8760 (mttp) cc_final: 0.8407 (mtpt) REVERT: E 311 LYS cc_start: 0.8314 (tttt) cc_final: 0.8100 (ttmt) REVERT: E 317 LYS cc_start: 0.8486 (ptpp) cc_final: 0.8104 (ptmt) REVERT: E 331 LYS cc_start: 0.8812 (mttp) cc_final: 0.8542 (mtpt) REVERT: E 356 SER cc_start: 0.8945 (m) cc_final: 0.8679 (t) REVERT: F 311 LYS cc_start: 0.8537 (tttt) cc_final: 0.7656 (pptt) outliers start: 5 outliers final: 2 residues processed: 94 average time/residue: 1.3514 time to fit residues: 130.1297 Evaluate side-chains 90 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain F 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: 9.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.144076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.124235 restraints weight = 4107.785| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.45 r_work: 0.3835 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3576 Z= 0.271 Angle : 0.659 8.424 4782 Z= 0.314 Chirality : 0.051 0.146 534 Planarity : 0.003 0.036 612 Dihedral : 4.523 12.685 474 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.74 % Allowed : 25.62 % Favored : 72.64 % 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: -1.63 (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 0.001 HIS D 362 PHE 0.014 0.002 PHE E 346 TYR 0.012 0.003 TYR A 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.88 seconds wall clock time: 46 minutes 49.94 seconds (2809.94 seconds total)