Starting phenix.real_space_refine on Fri Aug 2 15:43:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoh_19855/08_2024/9eoh_19855.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoh_19855/08_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_19855/08_2024/9eoh_19855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoh_19855/08_2024/9eoh_19855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoh_19855/08_2024/9eoh_19855.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoh_19855/08_2024/9eoh_19855.cif" } 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-5409/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: 3.02, per 1000 atoms: 0.88 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: 1.15 Conformation dependent library (CDL) restraints added in 629.9 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: 0.46 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: 0.74 Time building geometry restraints manager: 1.23 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 3.120 ... (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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.930 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.060 ------------------------------------------------------------------------------- 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 : 0.373 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: 1.2122 time to fit residues: 231.0504 Evaluate side-chains 164 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3468 Z= 0.286 Angle : 0.722 6.356 4632 Z= 0.369 Chirality : 0.052 0.187 516 Planarity : 0.003 0.019 588 Dihedral : 5.729 14.898 456 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.62 % Allowed : 19.74 % Favored : 75.64 % 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: -3.44 (0.29), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.22), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.010 0.001 PHE A 378 TYR 0.011 0.002 TYR A 310 ARG 0.001 0.000 ARG F 349 *********************** 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 188 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: B 307 GLN cc_start: 0.8079 (tt0) cc_final: 0.7686 (pm20) REVERT: B 311 LYS cc_start: 0.9008 (tttt) cc_final: 0.8785 (pptt) REVERT: C 307 GLN cc_start: 0.8915 (tt0) cc_final: 0.8469 (tp40) REVERT: C 313 VAL cc_start: 0.9233 (t) cc_final: 0.9024 (p) REVERT: C 331 LYS cc_start: 0.8800 (mttm) cc_final: 0.7691 (tmtt) REVERT: C 349 ARG cc_start: 0.8219 (mtm180) cc_final: 0.6577 (mmt-90) REVERT: C 378 PHE cc_start: 0.8422 (t80) cc_final: 0.7286 (p90) REVERT: E 319 THR cc_start: 0.8565 (m) cc_final: 0.8328 (p) REVERT: E 331 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8727 (mttt) REVERT: F 311 LYS cc_start: 0.8986 (tttt) cc_final: 0.8751 (pptt) outliers start: 18 outliers final: 9 residues processed: 173 average time/residue: 1.1972 time to fit residues: 212.4009 Evaluate side-chains 172 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL 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 306 VAL 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: 7.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 336 GLN ** 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** ** 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: 0.8563 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3468 Z= 0.307 Angle : 0.695 6.829 4632 Z= 0.352 Chirality : 0.051 0.179 516 Planarity : 0.003 0.016 588 Dihedral : 5.572 15.000 456 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.62 % Allowed : 22.82 % Favored : 72.56 % 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 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 330 PHE 0.008 0.001 PHE E 378 TYR 0.012 0.003 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 190 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 0.378 Fit side-chains REVERT: B 307 GLN cc_start: 0.8088 (tt0) cc_final: 0.7666 (pm20) REVERT: B 311 LYS cc_start: 0.9030 (tttt) cc_final: 0.8827 (pptt) REVERT: B 349 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7863 (ttp80) REVERT: C 307 GLN cc_start: 0.8815 (tt0) cc_final: 0.8350 (tp-100) REVERT: C 331 LYS cc_start: 0.8804 (mttm) cc_final: 0.7654 (tmtt) REVERT: C 378 PHE cc_start: 0.8564 (t80) cc_final: 0.7184 (p90) REVERT: D 375 LYS cc_start: 0.8876 (tptp) cc_final: 0.8639 (tptm) REVERT: D 379 ARG cc_start: 0.8257 (mtm180) cc_final: 0.7711 (mmp-170) REVERT: E 331 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8736 (mttt) REVERT: F 311 LYS cc_start: 0.8999 (tttt) cc_final: 0.8791 (pptt) outliers start: 18 outliers final: 11 residues processed: 176 average time/residue: 1.1721 time to fit residues: 211.4711 Evaluate side-chains 179 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 319 THR 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 309 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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** ** 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: 0.8555 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3468 Z= 0.284 Angle : 0.692 7.285 4632 Z= 0.343 Chirality : 0.050 0.166 516 Planarity : 0.002 0.013 588 Dihedral : 5.453 14.804 456 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.87 % Allowed : 25.13 % 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: -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 0.006 0.001 HIS C 330 PHE 0.008 0.001 PHE A 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 191 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 0.326 Fit side-chains REVERT: A 379 ARG cc_start: 0.8526 (mtm110) cc_final: 0.8166 (mtm-85) REVERT: B 307 GLN cc_start: 0.7894 (tt0) cc_final: 0.7393 (pm20) REVERT: B 378 PHE cc_start: 0.8988 (t80) cc_final: 0.8775 (t80) REVERT: C 307 GLN cc_start: 0.8833 (tt0) cc_final: 0.8396 (tp-100) REVERT: C 331 LYS cc_start: 0.8762 (mttm) cc_final: 0.7670 (tmtt) REVERT: C 378 PHE cc_start: 0.8567 (t80) cc_final: 0.7139 (p90) REVERT: D 379 ARG cc_start: 0.8294 (mtm180) cc_final: 0.7675 (mmp-170) REVERT: E 353 LYS cc_start: 0.8782 (mtpm) cc_final: 0.8539 (mttm) REVERT: F 311 LYS cc_start: 0.9014 (tttt) cc_final: 0.8810 (pptt) REVERT: F 321 LYS cc_start: 0.9141 (ttmm) cc_final: 0.8803 (tmmt) outliers start: 19 outliers final: 14 residues processed: 174 average time/residue: 1.2785 time to fit residues: 227.7347 Evaluate side-chains 182 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 168 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 C residue 353 LYS Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 320 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 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3468 Z= 0.349 Angle : 0.721 8.272 4632 Z= 0.362 Chirality : 0.050 0.172 516 Planarity : 0.002 0.015 588 Dihedral : 5.554 14.948 456 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.90 % Allowed : 25.13 % 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: -2.88 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.008 0.001 PHE E 378 TYR 0.012 0.003 TYR B 310 ARG 0.004 0.000 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 192 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7810 (ttp80) REVERT: A 379 ARG cc_start: 0.8541 (mtm110) cc_final: 0.8273 (mtm-85) REVERT: B 307 GLN cc_start: 0.7942 (tt0) cc_final: 0.7489 (pm20) REVERT: B 349 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7781 (ttp80) REVERT: B 378 PHE cc_start: 0.9001 (t80) cc_final: 0.8753 (t80) REVERT: C 307 GLN cc_start: 0.8795 (tt0) cc_final: 0.8393 (tp-100) REVERT: C 331 LYS cc_start: 0.8781 (mttm) cc_final: 0.7655 (tmtt) REVERT: C 378 PHE cc_start: 0.8560 (t80) cc_final: 0.7165 (p90) REVERT: D 311 LYS cc_start: 0.4491 (OUTLIER) cc_final: 0.3758 (mmtt) REVERT: D 379 ARG cc_start: 0.8302 (mtm180) cc_final: 0.7548 (mmp-170) REVERT: E 331 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8822 (mttt) REVERT: E 353 LYS cc_start: 0.8782 (mtpm) cc_final: 0.8525 (mttm) outliers start: 23 outliers final: 14 residues processed: 172 average time/residue: 1.1993 time to fit residues: 211.3390 Evaluate side-chains 186 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 349 ARG Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 319 THR 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: 7.9990 chunk 40 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 0.0060 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3468 Z= 0.282 Angle : 0.709 8.732 4632 Z= 0.350 Chirality : 0.050 0.154 516 Planarity : 0.003 0.029 588 Dihedral : 5.392 14.418 456 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.13 % Allowed : 26.41 % Favored : 68.46 % 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 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.008 0.001 PHE E 378 TYR 0.011 0.002 TYR A 310 ARG 0.001 0.000 ARG A 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 192 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 0.415 Fit side-chains REVERT: A 307 GLN cc_start: 0.9086 (pp30) cc_final: 0.8777 (pp30) REVERT: A 349 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7713 (ttp80) REVERT: A 379 ARG cc_start: 0.8529 (mtm110) cc_final: 0.8198 (mtp-110) REVERT: B 307 GLN cc_start: 0.7859 (tt0) cc_final: 0.7378 (pm20) REVERT: B 378 PHE cc_start: 0.8965 (t80) cc_final: 0.8652 (t80) REVERT: C 307 GLN cc_start: 0.8755 (tt0) cc_final: 0.8385 (tp-100) REVERT: C 331 LYS cc_start: 0.8767 (mttm) cc_final: 0.7659 (tmtt) REVERT: C 378 PHE cc_start: 0.8528 (t80) cc_final: 0.7135 (p90) REVERT: D 311 LYS cc_start: 0.4264 (OUTLIER) cc_final: 0.3572 (mmtt) REVERT: D 375 LYS cc_start: 0.8852 (tptm) cc_final: 0.8605 (tptt) REVERT: D 378 PHE cc_start: 0.8267 (t80) cc_final: 0.6719 (p90) REVERT: D 379 ARG cc_start: 0.8286 (mtm180) cc_final: 0.7552 (mmp-170) REVERT: E 331 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8824 (mttt) REVERT: E 353 LYS cc_start: 0.8767 (mtpm) cc_final: 0.8539 (mttm) REVERT: F 377 THR cc_start: 0.8958 (m) cc_final: 0.8700 (p) outliers start: 20 outliers final: 15 residues processed: 174 average time/residue: 1.1681 time to fit residues: 208.2815 Evaluate side-chains 186 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 319 THR 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 E residue 331 LYS 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: 9.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 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: 0.8533 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3468 Z= 0.271 Angle : 0.719 9.195 4632 Z= 0.347 Chirality : 0.050 0.145 516 Planarity : 0.003 0.035 588 Dihedral : 5.285 14.665 456 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.15 % Allowed : 26.15 % 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: -2.73 (0.31), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.009 0.001 PHE E 378 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 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 196 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 0.412 Fit side-chains REVERT: A 307 GLN cc_start: 0.9111 (pp30) cc_final: 0.8815 (pp30) REVERT: A 311 LYS cc_start: 0.9335 (mmmt) cc_final: 0.8842 (pttm) REVERT: A 379 ARG cc_start: 0.8552 (mtm110) cc_final: 0.8254 (mtp-110) REVERT: B 307 GLN cc_start: 0.7879 (tt0) cc_final: 0.7388 (pm20) REVERT: B 311 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6594 (pptt) REVERT: B 349 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7715 (ttp80) REVERT: B 377 THR cc_start: 0.8780 (m) cc_final: 0.8534 (p) REVERT: B 378 PHE cc_start: 0.8916 (t80) cc_final: 0.8566 (t80) REVERT: C 307 GLN cc_start: 0.8752 (tt0) cc_final: 0.8397 (tp-100) REVERT: C 331 LYS cc_start: 0.8766 (mttm) cc_final: 0.7665 (tmtt) REVERT: C 378 PHE cc_start: 0.8411 (t80) cc_final: 0.7109 (p90) REVERT: D 311 LYS cc_start: 0.4191 (OUTLIER) cc_final: 0.3791 (mmpt) REVERT: D 375 LYS cc_start: 0.8786 (tptm) cc_final: 0.8479 (tptt) REVERT: D 377 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8314 (m) REVERT: D 379 ARG cc_start: 0.8304 (mtm180) cc_final: 0.7472 (mmp-170) REVERT: E 331 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8818 (mttt) REVERT: E 353 LYS cc_start: 0.8763 (mtpm) cc_final: 0.8505 (mttm) outliers start: 24 outliers final: 15 residues processed: 173 average time/residue: 1.2276 time to fit residues: 217.5635 Evaluate side-chains 189 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain A residue 324 SER 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 320 SER Chi-restraints excluded: chain C residue 353 LYS 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 D residue 377 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 ** 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: 0.8514 moved from start: 0.4762 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= 0.233 Angle : 0.696 9.013 4632 Z= 0.334 Chirality : 0.049 0.131 516 Planarity : 0.003 0.040 588 Dihedral : 5.125 15.578 456 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.90 % Allowed : 26.15 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.008 0.001 PHE E 378 TYR 0.009 0.002 TYR A 310 ARG 0.001 0.000 ARG E 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 193 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 0.408 Fit side-chains REVERT: A 307 GLN cc_start: 0.9086 (pp30) cc_final: 0.8825 (pp30) REVERT: A 311 LYS cc_start: 0.9349 (mmmt) cc_final: 0.8913 (pttm) REVERT: A 379 ARG cc_start: 0.8560 (mtm110) cc_final: 0.8233 (mtp-110) REVERT: B 307 GLN cc_start: 0.7881 (tt0) cc_final: 0.7370 (pm20) REVERT: B 311 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6545 (pptt) REVERT: B 321 LYS cc_start: 0.8998 (ttmm) cc_final: 0.8130 (pmtt) REVERT: B 378 PHE cc_start: 0.8872 (t80) cc_final: 0.8528 (t80) REVERT: C 307 GLN cc_start: 0.8748 (tt0) cc_final: 0.8395 (tp-100) REVERT: C 331 LYS cc_start: 0.8768 (mttm) cc_final: 0.7660 (tmtt) REVERT: C 378 PHE cc_start: 0.8363 (t80) cc_final: 0.6983 (p90) REVERT: D 311 LYS cc_start: 0.4134 (OUTLIER) cc_final: 0.3667 (mmpt) REVERT: D 375 LYS cc_start: 0.8759 (tptm) cc_final: 0.8502 (tptm) REVERT: D 377 THR cc_start: 0.8763 (m) cc_final: 0.8326 (m) REVERT: D 379 ARG cc_start: 0.8312 (mtm180) cc_final: 0.7486 (mmp-170) REVERT: E 331 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8818 (mttt) REVERT: E 353 LYS cc_start: 0.8780 (mtpm) cc_final: 0.8513 (mttm) outliers start: 23 outliers final: 15 residues processed: 171 average time/residue: 1.1992 time to fit residues: 210.1361 Evaluate side-chains 187 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 B residue 311 LYS 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 311 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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: 0.8498 moved from start: 0.4922 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= 0.209 Angle : 0.708 8.979 4632 Z= 0.335 Chirality : 0.048 0.127 516 Planarity : 0.003 0.044 588 Dihedral : 4.982 15.641 456 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.59 % Allowed : 29.49 % 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: -2.63 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 330 PHE 0.005 0.001 PHE E 378 TYR 0.009 0.002 TYR A 310 ARG 0.004 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 183 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.9046 (pp30) cc_final: 0.8830 (pp30) REVERT: A 311 LYS cc_start: 0.9340 (mmmt) cc_final: 0.8919 (pttm) REVERT: A 379 ARG cc_start: 0.8558 (mtm110) cc_final: 0.8260 (mtp-110) REVERT: B 307 GLN cc_start: 0.7871 (tt0) cc_final: 0.7331 (pm20) REVERT: B 349 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7673 (ttp80) REVERT: B 378 PHE cc_start: 0.8866 (t80) cc_final: 0.8525 (t80) REVERT: C 307 GLN cc_start: 0.8738 (tt0) cc_final: 0.8392 (tp-100) REVERT: C 331 LYS cc_start: 0.8776 (mttm) cc_final: 0.7692 (tmtt) REVERT: C 378 PHE cc_start: 0.8159 (t80) cc_final: 0.6894 (p90) REVERT: D 311 LYS cc_start: 0.4278 (OUTLIER) cc_final: 0.3743 (mmpt) REVERT: D 340 LYS cc_start: 0.8248 (mtpm) cc_final: 0.8025 (mttp) REVERT: D 375 LYS cc_start: 0.8715 (tptm) cc_final: 0.8457 (tptm) REVERT: D 377 THR cc_start: 0.8808 (m) cc_final: 0.8344 (m) REVERT: D 379 ARG cc_start: 0.8308 (mtm180) cc_final: 0.7425 (mmp-170) REVERT: E 331 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8819 (mttt) REVERT: E 353 LYS cc_start: 0.8775 (mtpm) cc_final: 0.8512 (mttm) outliers start: 14 outliers final: 9 residues processed: 170 average time/residue: 1.2650 time to fit residues: 220.0424 Evaluate side-chains 178 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 B residue 349 ARG Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 0.0030 chunk 35 optimal weight: 0.0970 chunk 10 optimal weight: 0.0670 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.2128 ------------------------------------------------------------------------------- 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** ** 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: 0.8479 moved from start: 0.5064 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= 0.201 Angle : 0.718 9.204 4632 Z= 0.334 Chirality : 0.048 0.128 516 Planarity : 0.003 0.044 588 Dihedral : 4.844 15.748 456 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.82 % Allowed : 30.00 % 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: -2.61 (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 0.006 0.001 HIS A 330 PHE 0.005 0.001 PHE E 378 TYR 0.008 0.002 TYR A 310 ARG 0.006 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 174 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.9029 (pp30) cc_final: 0.8827 (pp30) REVERT: A 311 LYS cc_start: 0.9341 (mmmt) cc_final: 0.8923 (pttm) REVERT: A 379 ARG cc_start: 0.8566 (mtm110) cc_final: 0.8267 (mtp-110) REVERT: B 307 GLN cc_start: 0.7826 (tt0) cc_final: 0.7317 (pm20) REVERT: B 378 PHE cc_start: 0.8849 (t80) cc_final: 0.8513 (t80) REVERT: C 307 GLN cc_start: 0.8716 (tt0) cc_final: 0.8343 (tp-100) REVERT: C 331 LYS cc_start: 0.8757 (mttm) cc_final: 0.7678 (tmtt) REVERT: C 378 PHE cc_start: 0.8076 (t80) cc_final: 0.6905 (p90) REVERT: D 375 LYS cc_start: 0.8689 (tptm) cc_final: 0.8429 (tptm) REVERT: D 377 THR cc_start: 0.8837 (m) cc_final: 0.8366 (m) REVERT: D 379 ARG cc_start: 0.8295 (mtm180) cc_final: 0.7418 (mmp-170) REVERT: E 331 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8797 (mttt) REVERT: E 353 LYS cc_start: 0.8771 (mtpm) cc_final: 0.8513 (mttm) outliers start: 11 outliers final: 9 residues processed: 164 average time/residue: 1.3110 time to fit residues: 220.0375 Evaluate side-chains 172 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain D 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 ** 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 = 0.4211 r_free = 0.4211 target = 0.138229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.117717 restraints weight = 4259.768| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.39 r_work: 0.3816 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3468 Z= 0.309 Angle : 0.782 10.273 4632 Z= 0.370 Chirality : 0.049 0.136 516 Planarity : 0.004 0.053 588 Dihedral : 5.235 17.722 456 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.08 % Allowed : 30.00 % 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: -2.62 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 330 PHE 0.005 0.001 PHE E 378 TYR 0.009 0.002 TYR A 310 ARG 0.013 0.001 ARG E 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3257.88 seconds wall clock time: 57 minutes 12.30 seconds (3432.30 seconds total)