Starting phenix.real_space_refine on Mon Jun 24 16:30:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoh_19855/06_2024/9eoh_19855.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoh_19855/06_2024/9eoh_19855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoh_19855/06_2024/9eoh_19855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoh_19855/06_2024/9eoh_19855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoh_19855/06_2024/9eoh_19855.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoh_19855/06_2024/9eoh_19855.pdb" } resolution = 2.8 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= 0.001 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 12 5.16 5 C 2142 2.51 5 N 630 2.21 5 O 630 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 342": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 379": "NH1" <-> "NH2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 379": "NH1" <-> "NH2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 379": "NH1" <-> "NH2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 379": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3414 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 569 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 569 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 569 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 569 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "E" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 569 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 569 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Time building chain proxies: 3.44, per 1000 atoms: 1.01 Number of scatterers: 3414 At special positions: 0 Unit cell: (144.673, 80.697, 36.35, 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 12 16.00 O 630 8.00 N 630 7.00 C 2142 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: 1.04 Conformation dependent library (CDL) restraints added in 892.3 milliseconds 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 62.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.609A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.874A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.330A pdb=" N VAL A 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LYS D 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N SER A 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330 removed outlier: 6.899A pdb=" N GLY B 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN A 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLY A 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N HIS D 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 356 removed outlier: 6.416A pdb=" N GLN A 336 " --> pdb=" O MET B 337 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL B 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N SER B 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS A 340 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS B 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N GLU A 342 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N ASP B 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N LEU A 344 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N LYS B 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE A 346 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N ARG B 349 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ASP A 348 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLN B 351 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N VAL A 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N LYS B 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N SER A 352 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N GLY B 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS A 343 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU D 344 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP A 345 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE D 346 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS A 347 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL D 350 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLN A 351 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER D 352 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS A 353 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE D 354 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY A 355 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.507A pdb=" N ASN A 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N HIS D 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR A 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.522A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.610A pdb=" N GLN C 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR E 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL E 309 " --> pdb=" O TYR F 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: 6.874A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL E 313 " --> pdb=" O ASP F 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 322 Processing sheet with id=AB2, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.899A pdb=" N GLY E 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN C 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY F 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN E 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 356 removed outlier: 6.416A pdb=" N GLN C 336 " --> pdb=" O MET E 337 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL E 339 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU C 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N SER E 341 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS C 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS E 343 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N GLU C 342 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N ASP E 345 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N LEU C 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N LYS E 347 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE C 346 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N ARG E 349 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N ASP C 348 " --> pdb=" O ARG E 349 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLN E 351 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N VAL C 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N LYS E 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N SER C 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N GLY E 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE C 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN E 336 " --> pdb=" O MET F 337 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL F 339 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU E 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N SER F 341 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS E 340 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS F 343 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N GLU E 342 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N ASP F 345 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N LEU E 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N LYS F 347 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE E 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N ARG F 349 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N ASP E 348 " --> pdb=" O ARG F 349 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLN F 351 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N VAL E 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N LYS F 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N SER E 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N GLY F 355 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE E 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 359 through 362 Processing sheet with id=AB5, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.523A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU E 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE E 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR C 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS E 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLU F 372 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE E 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N HIS F 374 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR E 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU F 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS E 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE F 378 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR E 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 55 hydrogen bonds defined for protein. 165 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: 0.99 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 833 1.34 - 1.46: 811 1.46 - 1.57: 1806 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3468 Sorted by residual: bond pdb=" CG HIS F 362 " pdb=" CD2 HIS F 362 " ideal model delta sigma weight residual 1.354 1.303 0.051 1.10e-02 8.26e+03 2.16e+01 bond pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 1.354 1.303 0.051 1.10e-02 8.26e+03 2.15e+01 bond pdb=" CG HIS E 362 " pdb=" CD2 HIS E 362 " ideal model delta sigma weight residual 1.354 1.303 0.051 1.10e-02 8.26e+03 2.14e+01 bond pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 1.354 1.303 0.051 1.10e-02 8.26e+03 2.13e+01 bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.303 0.051 1.10e-02 8.26e+03 2.11e+01 ... (remaining 3463 not shown) Histogram of bond angle deviations from ideal: 97.92 - 104.96: 72 104.96 - 111.99: 1563 111.99 - 119.02: 1350 119.02 - 126.05: 1605 126.05 - 133.09: 42 Bond angle restraints: 4632 Sorted by residual: angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.80 117.24 -6.44 1.41e+00 5.03e-01 2.09e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.80 117.24 -6.44 1.41e+00 5.03e-01 2.08e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.80 117.23 -6.43 1.41e+00 5.03e-01 2.08e+01 angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.80 117.23 -6.43 1.41e+00 5.03e-01 2.08e+01 angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.80 117.23 -6.43 1.41e+00 5.03e-01 2.08e+01 ... (remaining 4627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.55: 1902 13.55 - 27.11: 174 27.11 - 40.66: 42 40.66 - 54.21: 0 54.21 - 67.76: 6 Dihedral angle restraints: 2124 sinusoidal: 900 harmonic: 1224 Sorted by residual: dihedral pdb=" C LYS C 347 " pdb=" N LYS C 347 " pdb=" CA LYS C 347 " pdb=" CB LYS C 347 " ideal model delta harmonic sigma weight residual -122.60 -136.49 13.89 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C LYS A 347 " pdb=" N LYS A 347 " pdb=" CA LYS A 347 " pdb=" CB LYS A 347 " ideal model delta harmonic sigma weight residual -122.60 -136.47 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C LYS D 347 " pdb=" N LYS D 347 " pdb=" CA LYS D 347 " pdb=" CB LYS D 347 " ideal model delta harmonic sigma weight residual -122.60 -136.47 13.87 0 2.50e+00 1.60e-01 3.08e+01 ... (remaining 2121 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.105: 428 0.105 - 0.210: 82 0.210 - 0.315: 0 0.315 - 0.420: 0 0.420 - 0.525: 6 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LYS C 347 " pdb=" N LYS C 347 " pdb=" C LYS C 347 " pdb=" CB LYS C 347 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" CA LYS B 347 " pdb=" N LYS B 347 " pdb=" C LYS B 347 " pdb=" CB LYS B 347 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" CA LYS A 347 " pdb=" N LYS A 347 " pdb=" C LYS A 347 " pdb=" CB LYS A 347 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.85e+00 ... (remaining 513 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.026 2.00e-02 2.50e+03 1.53e-02 4.66e+00 pdb=" CG TYR F 310 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.026 2.00e-02 2.50e+03 1.52e-02 4.62e+00 pdb=" CG TYR C 310 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.026 2.00e-02 2.50e+03 1.52e-02 4.60e+00 pdb=" CG TYR A 310 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.007 2.00e-02 2.50e+03 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 1412 2.95 - 3.44: 2902 3.44 - 3.93: 5653 3.93 - 4.41: 5488 4.41 - 4.90: 10833 Nonbonded interactions: 26288 Sorted by model distance: nonbonded pdb=" O ASP E 348 " pdb=" O LYS F 347 " model vdw 2.465 3.040 nonbonded pdb=" O ASP C 348 " pdb=" O LYS E 347 " model vdw 2.466 3.040 nonbonded pdb=" O ASP A 348 " pdb=" O LYS B 347 " model vdw 2.466 3.040 nonbonded pdb=" O LYS A 347 " pdb=" O ASP D 348 " model vdw 2.466 3.040 nonbonded pdb=" OG SER E 320 " pdb=" ND2 ASN F 368 " model vdw 2.585 2.520 ... (remaining 26283 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.870 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.930 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 0.060 3468 Z= 0.609 Angle : 1.450 6.444 4632 Z= 0.954 Chirality : 0.093 0.525 516 Planarity : 0.008 0.032 588 Dihedral : 11.762 67.764 1344 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 1.54 % 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: -3.95 (0.27), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.20), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.005 HIS F 362 PHE 0.017 0.004 PHE B 346 TYR 0.034 0.010 TYR F 310 ARG 0.004 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: B 307 GLN cc_start: 0.8127 (tt0) cc_final: 0.7783 (pm20) REVERT: B 375 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8508 (pmtt) REVERT: C 307 GLN cc_start: 0.8944 (tt0) cc_final: 0.8483 (tp40) REVERT: C 313 VAL cc_start: 0.9155 (t) cc_final: 0.8892 (p) REVERT: C 331 LYS cc_start: 0.8757 (mttm) cc_final: 0.7679 (tmtt) REVERT: C 378 PHE cc_start: 0.8385 (t80) cc_final: 0.7265 (p90) REVERT: F 311 LYS cc_start: 0.8945 (tttt) cc_final: 0.8711 (pptt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 1.1314 time to fit residues: 215.8416 Evaluate side-chains 164 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN C 330 HIS ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 HIS ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3468 Z= 0.335 Angle : 0.726 6.489 4632 Z= 0.374 Chirality : 0.052 0.195 516 Planarity : 0.003 0.021 588 Dihedral : 5.777 14.768 456 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.36 % Allowed : 20.77 % Favored : 74.87 % 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: -3.43 (0.29), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.22), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.009 0.001 PHE A 378 TYR 0.009 0.002 TYR A 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 307 GLN cc_start: 0.8087 (tt0) cc_final: 0.7684 (pm20) REVERT: B 311 LYS cc_start: 0.9025 (tttt) cc_final: 0.8814 (pptt) REVERT: C 307 GLN cc_start: 0.8916 (tt0) cc_final: 0.8478 (tp40) REVERT: C 331 LYS cc_start: 0.8801 (mttm) cc_final: 0.7704 (tmtt) REVERT: C 349 ARG cc_start: 0.8255 (mtm180) cc_final: 0.6601 (mmt-90) REVERT: C 378 PHE cc_start: 0.8487 (t80) cc_final: 0.7288 (p90) REVERT: E 319 THR cc_start: 0.8577 (m) cc_final: 0.8337 (p) REVERT: E 331 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8724 (mttt) REVERT: F 311 LYS cc_start: 0.9029 (tttt) cc_final: 0.8810 (pptt) outliers start: 17 outliers final: 9 residues processed: 177 average time/residue: 1.1914 time to fit residues: 216.0769 Evaluate side-chains 175 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain F residue 309 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 330 HIS ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3468 Z= 0.252 Angle : 0.661 6.624 4632 Z= 0.332 Chirality : 0.050 0.171 516 Planarity : 0.002 0.014 588 Dihedral : 5.432 14.485 456 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.10 % Allowed : 23.85 % Favored : 72.05 % 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: -3.13 (0.29), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.22), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 330 PHE 0.007 0.001 PHE E 378 TYR 0.011 0.002 TYR A 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 307 GLN cc_start: 0.7985 (tt0) cc_final: 0.7592 (pm20) REVERT: C 307 GLN cc_start: 0.8804 (tt0) cc_final: 0.8344 (tp-100) REVERT: C 331 LYS cc_start: 0.8800 (mttm) cc_final: 0.7671 (tmtt) REVERT: C 349 ARG cc_start: 0.8218 (mtm180) cc_final: 0.6652 (mmt-90) REVERT: C 378 PHE cc_start: 0.8533 (t80) cc_final: 0.7181 (p90) REVERT: D 379 ARG cc_start: 0.8214 (mtm180) cc_final: 0.7787 (mmp-170) REVERT: F 311 LYS cc_start: 0.9038 (tttt) cc_final: 0.8831 (pptt) outliers start: 16 outliers final: 6 residues processed: 175 average time/residue: 1.1697 time to fit residues: 209.8584 Evaluate side-chains 173 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 167 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 309 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 overall best weight: 1.9262 ------------------------------------------------------------------------------- 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3468 Z= 0.216 Angle : 0.644 7.212 4632 Z= 0.317 Chirality : 0.049 0.153 516 Planarity : 0.002 0.014 588 Dihedral : 5.193 13.831 456 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.36 % Allowed : 25.38 % Favored : 70.26 % 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: -3.01 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 330 PHE 0.007 0.001 PHE E 378 TYR 0.012 0.002 TYR A 310 ARG 0.003 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 0.408 Fit side-chains REVERT: A 379 ARG cc_start: 0.8536 (mtm110) cc_final: 0.8229 (mtm-85) REVERT: B 307 GLN cc_start: 0.7960 (tt0) cc_final: 0.7440 (pm20) REVERT: B 321 LYS cc_start: 0.9011 (ttmm) cc_final: 0.8093 (pmtt) REVERT: C 307 GLN cc_start: 0.8794 (tt0) cc_final: 0.8358 (tp-100) REVERT: C 331 LYS cc_start: 0.8758 (mttm) cc_final: 0.7659 (tmtt) REVERT: C 349 ARG cc_start: 0.8215 (mtm180) cc_final: 0.6670 (mmt-90) REVERT: C 378 PHE cc_start: 0.8383 (t80) cc_final: 0.7102 (p90) REVERT: D 378 PHE cc_start: 0.8340 (t80) cc_final: 0.6789 (p90) REVERT: D 379 ARG cc_start: 0.8224 (mtm180) cc_final: 0.7727 (mmp-170) REVERT: E 331 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8815 (mttt) REVERT: E 353 LYS cc_start: 0.8773 (mtpm) cc_final: 0.8523 (mttm) REVERT: F 311 LYS cc_start: 0.9048 (tttt) cc_final: 0.8848 (pptt) REVERT: F 321 LYS cc_start: 0.9121 (ttmm) cc_final: 0.8781 (tmmt) outliers start: 17 outliers final: 10 residues processed: 169 average time/residue: 1.2180 time to fit residues: 210.8149 Evaluate side-chains 176 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3468 Z= 0.482 Angle : 0.770 8.463 4632 Z= 0.393 Chirality : 0.052 0.201 516 Planarity : 0.003 0.027 588 Dihedral : 5.767 16.253 456 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 7.44 % Allowed : 22.56 % Favored : 70.00 % 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: -2.94 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.008 0.002 PHE D 378 TYR 0.012 0.003 TYR A 310 ARG 0.006 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 0.453 Fit side-chains REVERT: A 349 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7866 (ttp80) REVERT: A 379 ARG cc_start: 0.8558 (mtm110) cc_final: 0.8149 (mtp-110) REVERT: B 307 GLN cc_start: 0.7999 (tt0) cc_final: 0.7522 (pm20) REVERT: B 311 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6462 (pptt) REVERT: B 321 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8142 (pmtt) REVERT: B 349 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7874 (ttp80) REVERT: C 307 GLN cc_start: 0.8786 (tt0) cc_final: 0.8380 (tp-100) REVERT: C 331 LYS cc_start: 0.8812 (mttm) cc_final: 0.7697 (tmtt) REVERT: C 378 PHE cc_start: 0.8655 (t80) cc_final: 0.7217 (p90) REVERT: D 311 LYS cc_start: 0.4291 (OUTLIER) cc_final: 0.3630 (mmtt) REVERT: D 379 ARG cc_start: 0.8266 (mtm180) cc_final: 0.7480 (mmp-170) REVERT: E 311 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8716 (mptm) REVERT: E 331 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8849 (mttt) REVERT: E 353 LYS cc_start: 0.8784 (mtpm) cc_final: 0.8539 (mttm) REVERT: F 379 ARG cc_start: 0.7792 (mtm180) cc_final: 0.7420 (pmt170) outliers start: 29 outliers final: 17 residues processed: 167 average time/residue: 1.2781 time to fit residues: 218.4991 Evaluate side-chains 184 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3468 Z= 0.250 Angle : 0.685 8.354 4632 Z= 0.337 Chirality : 0.050 0.158 516 Planarity : 0.003 0.037 588 Dihedral : 5.325 14.062 456 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.38 % Allowed : 25.64 % Favored : 68.97 % 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: -2.83 (0.31), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 330 PHE 0.006 0.001 PHE E 378 TYR 0.011 0.002 TYR A 310 ARG 0.002 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 0.408 Fit side-chains REVERT: A 307 GLN cc_start: 0.9113 (pp30) cc_final: 0.8822 (pp30) REVERT: A 379 ARG cc_start: 0.8573 (mtm110) cc_final: 0.8278 (mtm-85) REVERT: B 307 GLN cc_start: 0.7860 (tt0) cc_final: 0.7373 (pm20) REVERT: B 378 PHE cc_start: 0.9043 (t80) cc_final: 0.8797 (t80) REVERT: C 307 GLN cc_start: 0.8771 (tt0) cc_final: 0.8390 (tp-100) REVERT: C 331 LYS cc_start: 0.8791 (mttm) cc_final: 0.7690 (tmtt) REVERT: C 378 PHE cc_start: 0.8534 (t80) cc_final: 0.7184 (p90) REVERT: D 311 LYS cc_start: 0.4399 (OUTLIER) cc_final: 0.3706 (mmpt) REVERT: D 375 LYS cc_start: 0.8988 (tptm) cc_final: 0.8728 (tptt) REVERT: D 378 PHE cc_start: 0.8210 (t80) cc_final: 0.6767 (p90) REVERT: D 379 ARG cc_start: 0.8252 (mtm180) cc_final: 0.7513 (mmp-170) REVERT: E 331 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8844 (mttt) REVERT: E 353 LYS cc_start: 0.8736 (mtpm) cc_final: 0.8507 (mttm) REVERT: F 377 THR cc_start: 0.8964 (m) cc_final: 0.8738 (p) outliers start: 21 outliers final: 14 residues processed: 173 average time/residue: 1.2331 time to fit residues: 218.4541 Evaluate side-chains 184 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3468 Z= 0.201 Angle : 0.672 8.858 4632 Z= 0.321 Chirality : 0.049 0.141 516 Planarity : 0.003 0.038 588 Dihedral : 5.009 14.400 456 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.64 % Allowed : 26.67 % Favored : 67.69 % 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: -2.79 (0.31), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.005 0.001 PHE E 378 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 0.428 Fit side-chains REVERT: A 307 GLN cc_start: 0.9079 (pp30) cc_final: 0.8817 (pp30) REVERT: A 379 ARG cc_start: 0.8579 (mtm110) cc_final: 0.8274 (mtp-110) REVERT: B 307 GLN cc_start: 0.7851 (tt0) cc_final: 0.7347 (pm20) REVERT: B 321 LYS cc_start: 0.8982 (ttmm) cc_final: 0.8058 (pmtt) REVERT: B 377 THR cc_start: 0.8774 (m) cc_final: 0.8538 (p) REVERT: B 378 PHE cc_start: 0.8906 (t80) cc_final: 0.8532 (t80) REVERT: C 307 GLN cc_start: 0.8750 (tt0) cc_final: 0.8387 (tp-100) REVERT: C 311 LYS cc_start: 0.4432 (OUTLIER) cc_final: 0.4231 (mmmt) REVERT: C 331 LYS cc_start: 0.8780 (mttm) cc_final: 0.7690 (tmtt) REVERT: C 378 PHE cc_start: 0.8475 (t80) cc_final: 0.7129 (p90) REVERT: D 378 PHE cc_start: 0.8232 (t80) cc_final: 0.6754 (p90) REVERT: D 379 ARG cc_start: 0.8249 (mtm180) cc_final: 0.7514 (mmp-170) REVERT: E 331 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8816 (mttt) REVERT: E 353 LYS cc_start: 0.8743 (mtpm) cc_final: 0.8502 (mttm) outliers start: 22 outliers final: 13 residues processed: 171 average time/residue: 1.2299 time to fit residues: 215.3374 Evaluate side-chains 182 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN B 359 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3468 Z= 0.217 Angle : 0.691 8.999 4632 Z= 0.329 Chirality : 0.049 0.138 516 Planarity : 0.003 0.038 588 Dihedral : 5.006 15.060 456 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.36 % Allowed : 28.46 % Favored : 67.18 % 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: -2.75 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.006 0.001 PHE E 378 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 0.463 Fit side-chains REVERT: A 307 GLN cc_start: 0.9054 (pp30) cc_final: 0.8824 (pp30) REVERT: A 379 ARG cc_start: 0.8576 (mtm110) cc_final: 0.8200 (mtm-85) REVERT: B 307 GLN cc_start: 0.7857 (tt0) cc_final: 0.7320 (pm20) REVERT: B 378 PHE cc_start: 0.8922 (t80) cc_final: 0.8597 (t80) REVERT: C 307 GLN cc_start: 0.8742 (tt0) cc_final: 0.8409 (tp-100) REVERT: C 311 LYS cc_start: 0.4354 (mmpt) cc_final: 0.4133 (mmmt) REVERT: C 331 LYS cc_start: 0.8787 (mttm) cc_final: 0.7695 (tmtt) REVERT: C 378 PHE cc_start: 0.8408 (t80) cc_final: 0.7106 (p90) REVERT: D 375 LYS cc_start: 0.8918 (tptm) cc_final: 0.8678 (tptt) REVERT: D 378 PHE cc_start: 0.8141 (t80) cc_final: 0.6702 (p90) REVERT: D 379 ARG cc_start: 0.8210 (mtm180) cc_final: 0.7459 (mmp-170) REVERT: E 353 LYS cc_start: 0.8748 (mtpm) cc_final: 0.8492 (mttm) REVERT: F 314 ASP cc_start: 0.8449 (t0) cc_final: 0.8226 (t0) outliers start: 17 outliers final: 12 residues processed: 169 average time/residue: 1.2509 time to fit residues: 216.4673 Evaluate side-chains 179 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.0020 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 0.0770 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3468 Z= 0.211 Angle : 0.709 8.984 4632 Z= 0.330 Chirality : 0.048 0.139 516 Planarity : 0.003 0.040 588 Dihedral : 4.941 15.504 456 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.10 % Allowed : 29.74 % Favored : 66.15 % 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: -2.71 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.006 0.001 PHE C 378 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 0.422 Fit side-chains REVERT: A 311 LYS cc_start: 0.9361 (mtpt) cc_final: 0.8804 (pttm) REVERT: A 379 ARG cc_start: 0.8521 (mtm110) cc_final: 0.8167 (mtm-85) REVERT: B 307 GLN cc_start: 0.7889 (tt0) cc_final: 0.7324 (pm20) REVERT: B 378 PHE cc_start: 0.8906 (t80) cc_final: 0.8526 (t80) REVERT: C 307 GLN cc_start: 0.8741 (tt0) cc_final: 0.8396 (tp-100) REVERT: C 311 LYS cc_start: 0.4150 (OUTLIER) cc_final: 0.3944 (mmmt) REVERT: C 331 LYS cc_start: 0.8780 (mttm) cc_final: 0.7676 (tmtt) REVERT: C 378 PHE cc_start: 0.8115 (t80) cc_final: 0.7132 (p90) REVERT: D 375 LYS cc_start: 0.8910 (tptm) cc_final: 0.8639 (tptt) REVERT: D 378 PHE cc_start: 0.8139 (t80) cc_final: 0.6714 (p90) REVERT: D 379 ARG cc_start: 0.8236 (mtm180) cc_final: 0.7457 (mmp-170) REVERT: E 353 LYS cc_start: 0.8744 (mtpm) cc_final: 0.8486 (mttm) outliers start: 16 outliers final: 12 residues processed: 170 average time/residue: 1.1999 time to fit residues: 208.9322 Evaluate side-chains 178 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.3980 chunk 26 optimal weight: 0.0570 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3468 Z= 0.193 Angle : 0.748 8.838 4632 Z= 0.349 Chirality : 0.048 0.127 516 Planarity : 0.003 0.041 588 Dihedral : 4.814 15.086 456 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.31 % Allowed : 30.77 % Favored : 66.92 % 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: -2.66 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.003 0.001 PHE A 346 TYR 0.009 0.002 TYR A 310 ARG 0.001 0.000 ARG E 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 0.425 Fit side-chains REVERT: A 311 LYS cc_start: 0.9359 (mtpt) cc_final: 0.8780 (pttm) REVERT: A 379 ARG cc_start: 0.8523 (mtm110) cc_final: 0.8169 (mtm-85) REVERT: B 307 GLN cc_start: 0.7685 (tt0) cc_final: 0.7130 (pm20) REVERT: B 378 PHE cc_start: 0.8852 (t80) cc_final: 0.8549 (t80) REVERT: C 307 GLN cc_start: 0.8741 (tt0) cc_final: 0.8378 (tp-100) REVERT: C 331 LYS cc_start: 0.8782 (mttm) cc_final: 0.7713 (tmtt) REVERT: C 349 ARG cc_start: 0.8266 (mtm180) cc_final: 0.6731 (mmt-90) REVERT: D 375 LYS cc_start: 0.8853 (tptm) cc_final: 0.8587 (tptt) REVERT: D 378 PHE cc_start: 0.8131 (t80) cc_final: 0.6778 (p90) REVERT: D 379 ARG cc_start: 0.8212 (mtm180) cc_final: 0.7551 (mmp-170) REVERT: E 349 ARG cc_start: 0.7931 (mtm180) cc_final: 0.7632 (mtp180) REVERT: E 353 LYS cc_start: 0.8739 (mtpm) cc_final: 0.8489 (mttm) REVERT: E 375 LYS cc_start: 0.8833 (tppt) cc_final: 0.8329 (tptm) REVERT: F 321 LYS cc_start: 0.9082 (ttmm) cc_final: 0.8747 (tmmt) outliers start: 9 outliers final: 7 residues processed: 163 average time/residue: 1.2616 time to fit residues: 210.4869 Evaluate side-chains 164 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 320 SER 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: 10.0000 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** 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 = 0.4280 r_free = 0.4280 target = 0.144606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.123186 restraints weight = 4212.083| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.44 r_work: 0.3897 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3468 Z= 0.214 Angle : 0.772 9.647 4632 Z= 0.356 Chirality : 0.048 0.129 516 Planarity : 0.003 0.042 588 Dihedral : 4.801 15.564 456 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.79 % Allowed : 31.54 % Favored : 66.67 % 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: -2.61 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.004 0.001 PHE F 378 TYR 0.009 0.002 TYR A 310 ARG 0.001 0.000 ARG E 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3375.37 seconds wall clock time: 59 minutes 9.87 seconds (3549.87 seconds total)