Starting phenix.real_space_refine on Wed Feb 14 15:21:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkv_14054/02_2024/7qkv_14054.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkv_14054/02_2024/7qkv_14054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkv_14054/02_2024/7qkv_14054.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkv_14054/02_2024/7qkv_14054.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkv_14054/02_2024/7qkv_14054.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkv_14054/02_2024/7qkv_14054.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 2934 2.51 5 N 864 2.21 5 O 891 1.98 5 H 4887 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 338": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 338": "OE1" <-> "OE2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 338": "OE1" <-> "OE2" Residue "H PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 338": "OE1" <-> "OE2" Residue "I PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9585 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "A" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "C" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "D" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "E" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "F" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "G" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "H" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "I" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Time building chain proxies: 5.04, per 1000 atoms: 0.53 Number of scatterers: 9585 At special positions: 0 Unit cell: (128.544, 131.84, 33.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 891 8.00 N 864 7.00 C 2934 6.00 H 4887 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.28 Conformation dependent library (CDL) restraints added in 1.3 seconds 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.960A pdb=" N VAL B 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 317 through 318 removed outlier: 6.348A pdb=" N LYS B 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 324 through 330 removed outlier: 9.642A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N ASN D 327 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 325 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY G 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN B 327 " --> pdb=" O GLY G 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.553A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLU D 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER B 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.391A pdb=" N ASP B 345 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.468A pdb=" N GLN B 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE G 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS B 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N SER G 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY B 355 " --> pdb=" O SER G 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.381A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 369 through 374 removed outlier: 6.448A pdb=" N LYS B 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLU G 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N HIS G 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR B 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.914A pdb=" N VAL A 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 317 through 318 removed outlier: 6.355A pdb=" N LYS A 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 324 through 330 removed outlier: 9.663A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N ASN E 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLY A 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS E 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 325 " --> pdb=" O SER H 324 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY H 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN A 327 " --> pdb=" O GLY H 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 337 through 342 removed outlier: 6.532A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.493A pdb=" N ASP A 345 " --> pdb=" O PHE H 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 350 through 357 removed outlier: 6.277A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLY E 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU E 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER A 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 360 through 362 removed outlier: 6.353A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 369 through 374 removed outlier: 6.321A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS A 369 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLU H 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 371 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N HIS H 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR A 373 " --> pdb=" O HIS H 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 313 through 314 removed outlier: 6.953A pdb=" N VAL C 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 317 through 318 removed outlier: 6.425A pdb=" N LYS C 317 " --> pdb=" O VAL I 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 324 through 330 removed outlier: 9.636A pdb=" N SER C 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N ASN F 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY C 326 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N HIS F 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C 325 " --> pdb=" O SER I 324 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY I 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 327 " --> pdb=" O GLY I 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 337 through 342 removed outlier: 6.574A pdb=" N VAL C 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N LYS F 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLU F 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER C 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 345 through 346 removed outlier: 6.557A pdb=" N ASP C 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 350 through 357 removed outlier: 6.275A pdb=" N VAL C 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYS F 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER C 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLY F 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE C 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU F 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER C 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 360 through 362 removed outlier: 6.395A pdb=" N THR C 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 369 through 374 removed outlier: 6.483A pdb=" N LYS C 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLU I 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N HIS I 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR C 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) 70 hydrogen bonds defined for protein. 210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 7.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 4878 1.11 - 1.28: 792 1.28 - 1.45: 1147 1.45 - 1.63: 2831 1.63 - 1.80: 9 Bond restraints: 9657 Sorted by residual: bond pdb=" N GLN A 336 " pdb=" H GLN A 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ASN D 359 " pdb=" H ASN D 359 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY H 367 " pdb=" H GLY H 367 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 GLN B 336 " pdb="HE21 GLN B 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS D 331 " pdb=" H LYS D 331 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 9652 not shown) Histogram of bond angle deviations from ideal: 96.66 - 103.44: 58 103.44 - 110.21: 9328 110.21 - 116.99: 3715 116.99 - 123.77: 3845 123.77 - 130.55: 685 Bond angle restraints: 17631 Sorted by residual: angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.42 118.54 -8.12 1.49e+00 4.50e-01 2.97e+01 angle pdb=" C LYS A 375 " pdb=" N LEU A 376 " pdb=" CA LEU A 376 " ideal model delta sigma weight residual 122.36 130.55 -8.19 1.60e+00 3.91e-01 2.62e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 121.31 128.60 -7.29 1.49e+00 4.50e-01 2.39e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.55 118.57 -8.02 1.64e+00 3.72e-01 2.39e+01 angle pdb=" C ASP F 348 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " ideal model delta sigma weight residual 121.31 128.52 -7.21 1.49e+00 4.50e-01 2.34e+01 ... (remaining 17626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.16: 3682 13.16 - 26.31: 423 26.31 - 39.47: 145 39.47 - 52.62: 62 52.62 - 65.78: 134 Dihedral angle restraints: 4446 sinusoidal: 2556 harmonic: 1890 Sorted by residual: dihedral pdb=" CA VAL C 318 " pdb=" C VAL C 318 " pdb=" N THR C 319 " pdb=" CA THR C 319 " ideal model delta harmonic sigma weight residual -180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA LYS H 375 " pdb=" C LYS H 375 " pdb=" N LEU H 376 " pdb=" CA LEU H 376 " ideal model delta harmonic sigma weight residual 180.00 152.92 27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA VAL G 350 " pdb=" C VAL G 350 " pdb=" N GLN G 351 " pdb=" CA GLN G 351 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 4443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 364 0.065 - 0.130: 244 0.130 - 0.194: 90 0.194 - 0.259: 16 0.259 - 0.323: 6 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA LYS F 311 " pdb=" N LYS F 311 " pdb=" C LYS F 311 " pdb=" CB LYS F 311 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA LYS E 311 " pdb=" N LYS E 311 " pdb=" C LYS E 311 " pdb=" CB LYS E 311 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA ASN F 327 " pdb=" N ASN F 327 " pdb=" C ASN F 327 " pdb=" CB ASN F 327 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 717 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.336 2.00e-02 2.50e+03 1.44e-01 6.26e+02 pdb=" CG TYR E 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.103 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.101 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.091 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.063 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.289 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " 0.058 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " 0.113 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " 0.056 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 310 " -0.224 2.00e-02 2.50e+03 1.01e-01 3.05e+02 pdb=" CG TYR H 310 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR H 310 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR H 310 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 TYR H 310 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 TYR H 310 " 0.053 2.00e-02 2.50e+03 pdb=" CZ TYR H 310 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR H 310 " -0.215 2.00e-02 2.50e+03 pdb=" HD1 TYR H 310 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR H 310 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 TYR H 310 " 0.045 2.00e-02 2.50e+03 pdb=" HE2 TYR H 310 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.226 2.00e-02 2.50e+03 9.95e-02 2.97e+02 pdb=" CG TYR F 310 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.073 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.055 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.204 2.00e-02 2.50e+03 pdb=" HD1 TYR F 310 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR F 310 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR F 310 " -0.027 2.00e-02 2.50e+03 pdb=" HE2 TYR F 310 " -0.007 2.00e-02 2.50e+03 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 702 2.17 - 2.77: 16377 2.77 - 3.38: 25469 3.38 - 3.99: 33649 3.99 - 4.60: 47837 Nonbonded interactions: 124034 Sorted by model distance: nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.556 1.850 nonbonded pdb=" OD1 ASP H 314 " pdb=" HG SER H 316 " model vdw 1.559 1.850 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.563 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.610 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.618 1.850 ... (remaining 124029 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 3.110 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: 0.140 Extract box with map and model: 11.620 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 34.100 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.033 4770 Z= 0.745 Angle : 1.916 8.186 6381 Z= 1.248 Chirality : 0.094 0.323 720 Planarity : 0.015 0.166 810 Dihedral : 12.281 56.991 1836 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % 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: -2.11 (0.28), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.22), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.006 HIS G 330 PHE 0.032 0.013 PHE I 346 TYR 0.290 0.091 TYR E 310 ARG 0.004 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8125 (m-80) cc_final: 0.7866 (m-80) REVERT: B 347 LYS cc_start: 0.7885 (mttt) cc_final: 0.7276 (tmtt) REVERT: B 358 ASP cc_start: 0.8448 (m-30) cc_final: 0.8055 (t0) REVERT: A 327 ASN cc_start: 0.7512 (m-40) cc_final: 0.7309 (m-40) REVERT: A 343 LYS cc_start: 0.8500 (mttt) cc_final: 0.7686 (mttm) REVERT: A 347 LYS cc_start: 0.7999 (mttt) cc_final: 0.7434 (tptp) REVERT: A 358 ASP cc_start: 0.8546 (m-30) cc_final: 0.8066 (t0) REVERT: C 346 PHE cc_start: 0.8364 (m-80) cc_final: 0.8059 (m-80) REVERT: C 358 ASP cc_start: 0.8441 (m-30) cc_final: 0.8057 (t0) REVERT: D 311 LYS cc_start: 0.7191 (mtmt) cc_final: 0.6616 (mmtm) REVERT: D 347 LYS cc_start: 0.7807 (mttt) cc_final: 0.7558 (tmtt) REVERT: E 311 LYS cc_start: 0.7213 (mtmt) cc_final: 0.6420 (mmtm) REVERT: E 347 LYS cc_start: 0.7878 (mttt) cc_final: 0.7520 (tmtt) REVERT: F 343 LYS cc_start: 0.8191 (mttt) cc_final: 0.7456 (mmpt) REVERT: F 347 LYS cc_start: 0.7980 (mttt) cc_final: 0.7577 (tmtt) REVERT: F 351 GLN cc_start: 0.7827 (mp10) cc_final: 0.7423 (tt0) REVERT: G 345 ASP cc_start: 0.6807 (m-30) cc_final: 0.6475 (m-30) REVERT: G 347 LYS cc_start: 0.8104 (mttt) cc_final: 0.7523 (pttp) REVERT: G 358 ASP cc_start: 0.8475 (m-30) cc_final: 0.8105 (t0) REVERT: H 343 LYS cc_start: 0.8536 (mttt) cc_final: 0.8127 (mttm) REVERT: H 347 LYS cc_start: 0.7854 (mttt) cc_final: 0.7345 (pttp) REVERT: H 358 ASP cc_start: 0.8445 (m-30) cc_final: 0.8003 (t0) REVERT: I 343 LYS cc_start: 0.8423 (mttt) cc_final: 0.7840 (mttm) REVERT: I 347 LYS cc_start: 0.7730 (mttt) cc_final: 0.7290 (pttp) REVERT: I 358 ASP cc_start: 0.8454 (m-30) cc_final: 0.8043 (t0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.4186 time to fit residues: 90.9668 Evaluate side-chains 109 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS A 362 HIS C 362 HIS D 362 HIS E 362 HIS F 362 HIS G 362 HIS H 362 HIS I 362 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4770 Z= 0.400 Angle : 0.713 6.519 6381 Z= 0.376 Chirality : 0.051 0.139 720 Planarity : 0.003 0.020 810 Dihedral : 7.805 28.909 630 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.67 % Allowed : 16.67 % Favored : 81.67 % 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: -2.40 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 330 PHE 0.009 0.002 PHE E 346 TYR 0.032 0.007 TYR D 310 ARG 0.001 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: B 345 ASP cc_start: 0.7178 (m-30) cc_final: 0.6978 (m-30) REVERT: B 346 PHE cc_start: 0.8028 (m-80) cc_final: 0.7788 (m-80) REVERT: B 347 LYS cc_start: 0.8000 (mttt) cc_final: 0.7552 (tmtt) REVERT: B 358 ASP cc_start: 0.8418 (m-30) cc_final: 0.8152 (t0) REVERT: B 376 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7216 (mt) REVERT: A 347 LYS cc_start: 0.8100 (mttt) cc_final: 0.7481 (tmtt) REVERT: A 358 ASP cc_start: 0.8484 (m-30) cc_final: 0.8163 (t0) REVERT: A 376 LEU cc_start: 0.7688 (mt) cc_final: 0.7429 (mp) REVERT: C 347 LYS cc_start: 0.8154 (mttt) cc_final: 0.7545 (tmtt) REVERT: C 358 ASP cc_start: 0.8331 (m-30) cc_final: 0.8037 (t0) REVERT: C 376 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7120 (mt) REVERT: D 311 LYS cc_start: 0.7176 (mtmt) cc_final: 0.6742 (mmtm) REVERT: D 343 LYS cc_start: 0.8283 (mttt) cc_final: 0.7519 (mmpt) REVERT: D 347 LYS cc_start: 0.8028 (mttt) cc_final: 0.7767 (tmtt) REVERT: E 311 LYS cc_start: 0.7269 (mtmt) cc_final: 0.6679 (mmtm) REVERT: E 343 LYS cc_start: 0.8425 (mttt) cc_final: 0.7766 (mmpt) REVERT: F 311 LYS cc_start: 0.7128 (ttmt) cc_final: 0.6695 (mmtm) REVERT: F 347 LYS cc_start: 0.8098 (mttt) cc_final: 0.7759 (tmtt) REVERT: F 363 VAL cc_start: 0.8749 (t) cc_final: 0.8546 (m) REVERT: G 347 LYS cc_start: 0.8221 (mttt) cc_final: 0.7675 (pttp) REVERT: G 358 ASP cc_start: 0.8438 (m-30) cc_final: 0.8069 (t0) REVERT: G 376 LEU cc_start: 0.7479 (mt) cc_final: 0.6994 (mp) REVERT: H 343 LYS cc_start: 0.8653 (mttt) cc_final: 0.8252 (mttm) REVERT: H 347 LYS cc_start: 0.8106 (mttt) cc_final: 0.7564 (pttp) REVERT: H 358 ASP cc_start: 0.8506 (m-30) cc_final: 0.8099 (t0) REVERT: I 347 LYS cc_start: 0.7968 (mttt) cc_final: 0.7476 (pttp) REVERT: I 358 ASP cc_start: 0.8452 (m-30) cc_final: 0.7965 (t0) outliers start: 9 outliers final: 7 residues processed: 114 average time/residue: 0.4541 time to fit residues: 63.1340 Evaluate side-chains 106 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain I residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4770 Z= 0.238 Angle : 0.592 4.267 6381 Z= 0.314 Chirality : 0.050 0.142 720 Planarity : 0.003 0.022 810 Dihedral : 6.507 21.917 630 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.59 % Allowed : 17.59 % Favored : 79.81 % 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 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.007 0.001 PHE D 346 TYR 0.017 0.004 TYR D 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 1.128 Fit side-chains REVERT: B 311 LYS cc_start: 0.7410 (ttmt) cc_final: 0.7105 (ttpt) REVERT: B 345 ASP cc_start: 0.6988 (m-30) cc_final: 0.6573 (m-30) REVERT: B 346 PHE cc_start: 0.8086 (m-80) cc_final: 0.7873 (m-80) REVERT: B 347 LYS cc_start: 0.7984 (mttt) cc_final: 0.7445 (tmtt) REVERT: B 358 ASP cc_start: 0.8429 (m-30) cc_final: 0.8099 (t0) REVERT: B 376 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7263 (mt) REVERT: A 347 LYS cc_start: 0.7978 (mttt) cc_final: 0.7465 (tmtt) REVERT: A 358 ASP cc_start: 0.8487 (m-30) cc_final: 0.8118 (t0) REVERT: A 376 LEU cc_start: 0.7722 (mt) cc_final: 0.7177 (mp) REVERT: C 327 ASN cc_start: 0.7207 (OUTLIER) cc_final: 0.6921 (t0) REVERT: C 347 LYS cc_start: 0.8154 (mttt) cc_final: 0.7534 (tmtt) REVERT: C 358 ASP cc_start: 0.8351 (m-30) cc_final: 0.8003 (t0) REVERT: C 376 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.6881 (mt) REVERT: D 311 LYS cc_start: 0.7348 (mtmt) cc_final: 0.7042 (pttt) REVERT: D 343 LYS cc_start: 0.8345 (mttt) cc_final: 0.7562 (mmpt) REVERT: E 311 LYS cc_start: 0.7152 (mtmt) cc_final: 0.6544 (mmtm) REVERT: E 343 LYS cc_start: 0.8413 (mttt) cc_final: 0.7708 (mmpt) REVERT: F 311 LYS cc_start: 0.7284 (ttmt) cc_final: 0.6866 (mmtm) REVERT: F 347 LYS cc_start: 0.8128 (mttt) cc_final: 0.7751 (tmtt) REVERT: G 347 LYS cc_start: 0.8214 (mttt) cc_final: 0.7601 (pttp) REVERT: G 358 ASP cc_start: 0.8431 (m-30) cc_final: 0.7982 (t0) REVERT: G 376 LEU cc_start: 0.7611 (mt) cc_final: 0.7009 (mp) REVERT: H 343 LYS cc_start: 0.8629 (mttt) cc_final: 0.8277 (mttm) REVERT: H 347 LYS cc_start: 0.8052 (mttt) cc_final: 0.7598 (pttp) REVERT: H 358 ASP cc_start: 0.8498 (m-30) cc_final: 0.7997 (t0) REVERT: H 376 LEU cc_start: 0.7644 (mt) cc_final: 0.7134 (mp) REVERT: I 347 LYS cc_start: 0.7922 (mttt) cc_final: 0.7488 (pttp) REVERT: I 358 ASP cc_start: 0.8496 (m-30) cc_final: 0.7959 (t0) REVERT: I 376 LEU cc_start: 0.7652 (mt) cc_final: 0.7093 (mp) outliers start: 14 outliers final: 8 residues processed: 111 average time/residue: 0.4326 time to fit residues: 58.7974 Evaluate side-chains 104 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 46 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4770 Z= 0.150 Angle : 0.512 5.432 6381 Z= 0.270 Chirality : 0.049 0.140 720 Planarity : 0.003 0.036 810 Dihedral : 5.637 16.188 630 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.11 % Allowed : 17.41 % Favored : 81.48 % 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: -2.56 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 329 PHE 0.006 0.001 PHE E 346 TYR 0.007 0.001 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7448 (ttmt) cc_final: 0.7171 (ttpt) REVERT: B 347 LYS cc_start: 0.7879 (mttt) cc_final: 0.7449 (tmtt) REVERT: B 358 ASP cc_start: 0.8439 (m-30) cc_final: 0.8099 (t0) REVERT: B 376 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7125 (mt) REVERT: A 327 ASN cc_start: 0.7921 (t0) cc_final: 0.7716 (t0) REVERT: A 343 LYS cc_start: 0.8621 (mttt) cc_final: 0.7888 (mttm) REVERT: A 347 LYS cc_start: 0.7947 (mttt) cc_final: 0.7418 (tmtt) REVERT: A 358 ASP cc_start: 0.8514 (m-30) cc_final: 0.8029 (t0) REVERT: A 376 LEU cc_start: 0.7643 (mt) cc_final: 0.7057 (mp) REVERT: C 327 ASN cc_start: 0.7203 (m-40) cc_final: 0.6984 (t0) REVERT: C 347 LYS cc_start: 0.8109 (mttt) cc_final: 0.7519 (tmtt) REVERT: C 358 ASP cc_start: 0.8390 (m-30) cc_final: 0.7921 (t0) REVERT: C 376 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6687 (mt) REVERT: D 311 LYS cc_start: 0.7260 (mtmt) cc_final: 0.6947 (pttt) REVERT: D 343 LYS cc_start: 0.8375 (mttt) cc_final: 0.7560 (mmpt) REVERT: E 343 LYS cc_start: 0.8362 (mttt) cc_final: 0.7611 (mmpt) REVERT: F 311 LYS cc_start: 0.7254 (ttmt) cc_final: 0.6805 (mmtm) REVERT: F 342 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7585 (mt-10) REVERT: F 347 LYS cc_start: 0.8109 (mttt) cc_final: 0.7770 (tmtt) REVERT: G 347 LYS cc_start: 0.8193 (mttt) cc_final: 0.7684 (pttp) REVERT: G 358 ASP cc_start: 0.8369 (m-30) cc_final: 0.7994 (t0) REVERT: G 376 LEU cc_start: 0.7522 (mt) cc_final: 0.6858 (mp) REVERT: H 311 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7194 (ttpt) REVERT: H 343 LYS cc_start: 0.8682 (mttt) cc_final: 0.8275 (mttm) REVERT: H 347 LYS cc_start: 0.8091 (mttt) cc_final: 0.7623 (pttp) REVERT: H 358 ASP cc_start: 0.8452 (m-30) cc_final: 0.7904 (t0) REVERT: I 347 LYS cc_start: 0.7961 (mttt) cc_final: 0.7520 (pttp) REVERT: I 358 ASP cc_start: 0.8487 (m-30) cc_final: 0.7864 (t0) REVERT: I 376 LEU cc_start: 0.7550 (mt) cc_final: 0.6964 (mp) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 0.4576 time to fit residues: 58.9651 Evaluate side-chains 100 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4770 Z= 0.255 Angle : 0.550 4.638 6381 Z= 0.292 Chirality : 0.049 0.142 720 Planarity : 0.004 0.040 810 Dihedral : 5.722 17.718 630 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.41 % Allowed : 16.85 % Favored : 80.74 % 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: -2.65 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.007 0.001 PHE B 346 TYR 0.016 0.004 TYR F 310 ARG 0.001 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.864 Fit side-chains REVERT: B 311 LYS cc_start: 0.7408 (ttmt) cc_final: 0.7103 (ttpt) REVERT: B 347 LYS cc_start: 0.7801 (mttt) cc_final: 0.7379 (tmtt) REVERT: B 358 ASP cc_start: 0.8473 (m-30) cc_final: 0.8042 (t0) REVERT: B 376 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7250 (mt) REVERT: A 347 LYS cc_start: 0.7913 (mttt) cc_final: 0.7375 (tmtt) REVERT: A 358 ASP cc_start: 0.8621 (m-30) cc_final: 0.8100 (t0) REVERT: A 376 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7047 (mp) REVERT: C 347 LYS cc_start: 0.8115 (mttt) cc_final: 0.7478 (tmtt) REVERT: C 358 ASP cc_start: 0.8478 (m-30) cc_final: 0.7994 (t0) REVERT: C 376 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.6794 (mt) REVERT: D 311 LYS cc_start: 0.7210 (mtmt) cc_final: 0.6894 (pttt) REVERT: D 343 LYS cc_start: 0.8442 (mttt) cc_final: 0.7626 (mmpt) REVERT: F 311 LYS cc_start: 0.7086 (ttmt) cc_final: 0.6686 (mmtm) REVERT: F 342 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7529 (mt-10) REVERT: F 347 LYS cc_start: 0.8076 (mttt) cc_final: 0.7662 (tmtt) REVERT: G 347 LYS cc_start: 0.8277 (mttt) cc_final: 0.7701 (pttm) REVERT: G 358 ASP cc_start: 0.8488 (m-30) cc_final: 0.8000 (t0) REVERT: H 311 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7185 (ttpt) REVERT: H 343 LYS cc_start: 0.8713 (mttt) cc_final: 0.8298 (mttm) REVERT: H 347 LYS cc_start: 0.8101 (mttt) cc_final: 0.7621 (pttp) REVERT: H 358 ASP cc_start: 0.8543 (m-30) cc_final: 0.7964 (t0) REVERT: H 376 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7106 (mt) REVERT: I 347 LYS cc_start: 0.7947 (mttt) cc_final: 0.7491 (pttp) REVERT: I 358 ASP cc_start: 0.8558 (m-30) cc_final: 0.7964 (t0) outliers start: 13 outliers final: 7 residues processed: 93 average time/residue: 0.4575 time to fit residues: 51.4016 Evaluate side-chains 93 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain H residue 376 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4770 Z= 0.132 Angle : 0.485 3.829 6381 Z= 0.255 Chirality : 0.049 0.131 720 Planarity : 0.004 0.048 810 Dihedral : 5.046 15.077 630 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.85 % Allowed : 17.41 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 330 PHE 0.008 0.001 PHE B 346 TYR 0.003 0.001 TYR D 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7383 (ttmt) cc_final: 0.7162 (ttpt) REVERT: B 347 LYS cc_start: 0.7796 (mttt) cc_final: 0.7337 (tmtt) REVERT: B 358 ASP cc_start: 0.8485 (m-30) cc_final: 0.8059 (t0) REVERT: B 376 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7205 (mt) REVERT: A 347 LYS cc_start: 0.7978 (mttt) cc_final: 0.7426 (tmtt) REVERT: A 358 ASP cc_start: 0.8546 (m-30) cc_final: 0.8017 (t0) REVERT: A 376 LEU cc_start: 0.7616 (mt) cc_final: 0.6965 (mp) REVERT: C 347 LYS cc_start: 0.8054 (mttt) cc_final: 0.7468 (tmtt) REVERT: C 358 ASP cc_start: 0.8397 (m-30) cc_final: 0.7976 (t0) REVERT: C 376 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6719 (mt) REVERT: D 311 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6968 (pttt) REVERT: D 343 LYS cc_start: 0.8365 (mttt) cc_final: 0.7555 (mmpt) REVERT: D 351 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7288 (mt0) REVERT: F 311 LYS cc_start: 0.7260 (ttmt) cc_final: 0.6825 (mmtm) REVERT: F 327 ASN cc_start: 0.7892 (t0) cc_final: 0.7682 (t0) REVERT: F 342 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7445 (mt-10) REVERT: F 347 LYS cc_start: 0.8074 (mttt) cc_final: 0.7757 (tmtt) REVERT: G 347 LYS cc_start: 0.8193 (mttt) cc_final: 0.7646 (pttm) REVERT: G 358 ASP cc_start: 0.8411 (m-30) cc_final: 0.8007 (t0) REVERT: G 376 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7002 (mt) REVERT: H 311 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7154 (ttpt) REVERT: H 343 LYS cc_start: 0.8690 (mttt) cc_final: 0.8287 (mttm) REVERT: H 347 LYS cc_start: 0.8031 (mttt) cc_final: 0.7588 (pttm) REVERT: H 358 ASP cc_start: 0.8463 (m-30) cc_final: 0.7870 (t0) REVERT: I 347 LYS cc_start: 0.7970 (mttt) cc_final: 0.7484 (pttp) REVERT: I 358 ASP cc_start: 0.8439 (m-30) cc_final: 0.7899 (t0) outliers start: 10 outliers final: 4 residues processed: 97 average time/residue: 0.4583 time to fit residues: 53.9090 Evaluate side-chains 98 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4770 Z= 0.363 Angle : 0.589 4.944 6381 Z= 0.315 Chirality : 0.050 0.148 720 Planarity : 0.004 0.043 810 Dihedral : 5.834 18.798 630 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.44 % Allowed : 15.37 % Favored : 80.19 % 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: -2.74 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 362 PHE 0.005 0.001 PHE B 346 TYR 0.022 0.005 TYR D 310 ARG 0.001 0.000 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7515 (ttmt) cc_final: 0.6730 (ttpt) REVERT: B 347 LYS cc_start: 0.7825 (mttt) cc_final: 0.7334 (tmtt) REVERT: B 358 ASP cc_start: 0.8607 (m-30) cc_final: 0.8102 (t0) REVERT: B 376 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7358 (mt) REVERT: A 347 LYS cc_start: 0.7985 (mttt) cc_final: 0.7385 (tmtt) REVERT: A 358 ASP cc_start: 0.8621 (m-30) cc_final: 0.8088 (t0) REVERT: A 376 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7067 (mp) REVERT: C 347 LYS cc_start: 0.8019 (mttt) cc_final: 0.7397 (tmtt) REVERT: C 358 ASP cc_start: 0.8568 (m-30) cc_final: 0.8065 (t0) REVERT: C 376 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6772 (mt) REVERT: D 311 LYS cc_start: 0.7048 (mtmt) cc_final: 0.6745 (mmtm) REVERT: D 343 LYS cc_start: 0.8504 (mttt) cc_final: 0.7674 (mmpt) REVERT: D 351 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: E 311 LYS cc_start: 0.7256 (ttmt) cc_final: 0.6834 (mmtm) REVERT: F 311 LYS cc_start: 0.7071 (ttmt) cc_final: 0.6697 (mmtm) REVERT: F 342 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7473 (mt-10) REVERT: F 347 LYS cc_start: 0.8071 (mttt) cc_final: 0.7628 (tmtt) REVERT: G 347 LYS cc_start: 0.8241 (mttt) cc_final: 0.7651 (pttm) REVERT: G 358 ASP cc_start: 0.8552 (m-30) cc_final: 0.8045 (t0) REVERT: G 376 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7280 (mt) REVERT: H 311 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7302 (ttpt) REVERT: H 347 LYS cc_start: 0.8004 (mttt) cc_final: 0.7493 (pttm) REVERT: H 358 ASP cc_start: 0.8587 (m-30) cc_final: 0.8002 (t0) REVERT: H 376 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7334 (mt) REVERT: I 347 LYS cc_start: 0.7946 (mttt) cc_final: 0.7449 (pttp) REVERT: I 349 ARG cc_start: 0.7830 (mtm180) cc_final: 0.6749 (pmt-80) REVERT: I 358 ASP cc_start: 0.8546 (m-30) cc_final: 0.8012 (t0) REVERT: I 376 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7332 (mt) outliers start: 24 outliers final: 10 residues processed: 102 average time/residue: 0.4672 time to fit residues: 57.4165 Evaluate side-chains 102 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 49 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN E 327 ASN F 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4770 Z= 0.202 Angle : 0.522 4.355 6381 Z= 0.274 Chirality : 0.049 0.139 720 Planarity : 0.004 0.046 810 Dihedral : 5.425 16.988 630 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.52 % Allowed : 17.04 % Favored : 79.44 % 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: -2.77 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.005 0.001 PHE B 346 TYR 0.012 0.002 TYR D 310 ARG 0.001 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.847 Fit side-chains REVERT: B 311 LYS cc_start: 0.7417 (ttmt) cc_final: 0.7103 (ttpt) REVERT: B 347 LYS cc_start: 0.7814 (mttt) cc_final: 0.7335 (tmtt) REVERT: B 351 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7397 (mt0) REVERT: B 358 ASP cc_start: 0.8542 (m-30) cc_final: 0.8117 (t0) REVERT: B 376 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7271 (mt) REVERT: A 347 LYS cc_start: 0.7988 (mttt) cc_final: 0.7541 (tmtt) REVERT: A 358 ASP cc_start: 0.8535 (m-30) cc_final: 0.8086 (t0) REVERT: A 376 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7118 (mp) REVERT: C 347 LYS cc_start: 0.8023 (mttt) cc_final: 0.7414 (tmtt) REVERT: C 358 ASP cc_start: 0.8481 (m-30) cc_final: 0.8005 (t0) REVERT: C 376 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6792 (mt) REVERT: D 311 LYS cc_start: 0.7232 (mtmt) cc_final: 0.6897 (pttt) REVERT: D 343 LYS cc_start: 0.8451 (mttt) cc_final: 0.7637 (mmpt) REVERT: D 351 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7316 (mt0) REVERT: F 311 LYS cc_start: 0.7103 (ttmt) cc_final: 0.6716 (mmtm) REVERT: F 342 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7440 (mt-10) REVERT: F 347 LYS cc_start: 0.7968 (mttt) cc_final: 0.7609 (tmtt) REVERT: G 347 LYS cc_start: 0.8194 (mttt) cc_final: 0.7647 (pttm) REVERT: G 358 ASP cc_start: 0.8479 (m-30) cc_final: 0.8084 (t0) REVERT: G 376 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7192 (mt) REVERT: H 311 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7215 (ttpt) REVERT: H 347 LYS cc_start: 0.8020 (mttt) cc_final: 0.7560 (pttm) REVERT: H 358 ASP cc_start: 0.8528 (m-30) cc_final: 0.7938 (t0) REVERT: H 376 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7265 (mt) REVERT: I 311 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7154 (ttpt) REVERT: I 327 ASN cc_start: 0.7429 (t0) cc_final: 0.7229 (t0) REVERT: I 347 LYS cc_start: 0.7931 (mttt) cc_final: 0.7454 (pttp) REVERT: I 358 ASP cc_start: 0.8489 (m-30) cc_final: 0.7928 (t0) REVERT: I 376 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7333 (mt) outliers start: 19 outliers final: 7 residues processed: 95 average time/residue: 0.4863 time to fit residues: 56.6395 Evaluate side-chains 98 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4770 Z= 0.164 Angle : 0.499 4.010 6381 Z= 0.262 Chirality : 0.049 0.141 720 Planarity : 0.004 0.052 810 Dihedral : 5.118 15.955 630 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.15 % Allowed : 17.22 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.005 0.001 PHE B 346 TYR 0.008 0.002 TYR D 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.835 Fit side-chains REVERT: B 311 LYS cc_start: 0.7392 (ttmt) cc_final: 0.7083 (ttpt) REVERT: B 347 LYS cc_start: 0.7804 (mttt) cc_final: 0.7303 (tmtt) REVERT: B 351 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7356 (mt0) REVERT: B 358 ASP cc_start: 0.8505 (m-30) cc_final: 0.8112 (t0) REVERT: B 376 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7253 (mt) REVERT: A 347 LYS cc_start: 0.8007 (mttt) cc_final: 0.7551 (tmtt) REVERT: A 358 ASP cc_start: 0.8613 (m-30) cc_final: 0.8057 (t0) REVERT: A 376 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7096 (mp) REVERT: C 347 LYS cc_start: 0.8024 (mttt) cc_final: 0.7411 (tmtt) REVERT: C 376 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.6766 (mt) REVERT: D 311 LYS cc_start: 0.7232 (mtmt) cc_final: 0.6891 (pttt) REVERT: D 331 LYS cc_start: 0.6517 (OUTLIER) cc_final: 0.6186 (mmmt) REVERT: D 343 LYS cc_start: 0.8428 (mttt) cc_final: 0.7622 (mmpt) REVERT: D 351 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7322 (mt0) REVERT: F 311 LYS cc_start: 0.7122 (ttmt) cc_final: 0.6743 (mmtm) REVERT: F 342 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7498 (mt-10) REVERT: F 347 LYS cc_start: 0.7958 (mttt) cc_final: 0.7616 (tmtt) REVERT: G 347 LYS cc_start: 0.8209 (mttt) cc_final: 0.7680 (pttm) REVERT: G 358 ASP cc_start: 0.8481 (m-30) cc_final: 0.8048 (t0) REVERT: G 376 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7051 (mt) REVERT: H 311 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7183 (ttpt) REVERT: H 347 LYS cc_start: 0.8026 (mttt) cc_final: 0.7598 (pttm) REVERT: H 358 ASP cc_start: 0.8489 (m-30) cc_final: 0.7877 (t0) REVERT: H 376 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7216 (mt) REVERT: I 327 ASN cc_start: 0.7320 (t0) cc_final: 0.7052 (t0) REVERT: I 347 LYS cc_start: 0.7934 (mttt) cc_final: 0.7476 (pttp) REVERT: I 358 ASP cc_start: 0.8544 (m-30) cc_final: 0.8073 (t0) REVERT: I 376 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7287 (mt) outliers start: 17 outliers final: 5 residues processed: 97 average time/residue: 0.4482 time to fit residues: 52.8342 Evaluate side-chains 100 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 45 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4770 Z= 0.126 Angle : 0.478 4.309 6381 Z= 0.249 Chirality : 0.049 0.138 720 Planarity : 0.004 0.059 810 Dihedral : 4.509 13.988 630 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.48 % Allowed : 18.33 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.28), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.005 0.001 PHE D 346 TYR 0.003 0.001 TYR E 310 ARG 0.001 0.000 ARG G 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7419 (ttmt) cc_final: 0.7175 (ttpt) REVERT: B 327 ASN cc_start: 0.8089 (t0) cc_final: 0.7883 (t0) REVERT: B 347 LYS cc_start: 0.7823 (mttt) cc_final: 0.7469 (tmtt) REVERT: B 358 ASP cc_start: 0.8446 (m-30) cc_final: 0.7996 (t0) REVERT: B 376 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7238 (mt) REVERT: A 347 LYS cc_start: 0.8009 (mttt) cc_final: 0.7550 (tmtt) REVERT: A 358 ASP cc_start: 0.8621 (m-30) cc_final: 0.8139 (t0) REVERT: A 376 LEU cc_start: 0.7610 (mt) cc_final: 0.6990 (mp) REVERT: C 346 PHE cc_start: 0.8227 (m-80) cc_final: 0.7955 (m-80) REVERT: C 347 LYS cc_start: 0.7987 (mttt) cc_final: 0.7426 (tmtt) REVERT: C 376 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6684 (mt) REVERT: D 311 LYS cc_start: 0.7394 (mtmt) cc_final: 0.7048 (pttt) REVERT: D 343 LYS cc_start: 0.8278 (mttt) cc_final: 0.7583 (mmmt) REVERT: F 342 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7405 (mt-10) REVERT: F 347 LYS cc_start: 0.8025 (mttt) cc_final: 0.7675 (tmtt) REVERT: G 311 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7716 (ttpt) REVERT: G 316 SER cc_start: 0.8036 (m) cc_final: 0.7795 (p) REVERT: G 347 LYS cc_start: 0.8187 (mttt) cc_final: 0.7646 (pttm) REVERT: G 358 ASP cc_start: 0.8418 (m-30) cc_final: 0.7970 (t0) REVERT: G 376 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.6920 (mt) REVERT: H 311 LYS cc_start: 0.7896 (ttmt) cc_final: 0.7146 (ttpt) REVERT: H 343 LYS cc_start: 0.8661 (mttt) cc_final: 0.8292 (mttm) REVERT: H 347 LYS cc_start: 0.8021 (mttt) cc_final: 0.7626 (pttm) REVERT: H 358 ASP cc_start: 0.8384 (m-30) cc_final: 0.7834 (t0) REVERT: I 327 ASN cc_start: 0.6605 (t0) cc_final: 0.6262 (t0) REVERT: I 347 LYS cc_start: 0.7962 (mttt) cc_final: 0.7504 (pttp) REVERT: I 358 ASP cc_start: 0.8427 (m-30) cc_final: 0.7908 (t0) REVERT: I 376 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7080 (mt) outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 0.4419 time to fit residues: 61.1900 Evaluate side-chains 110 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0370 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 0.0870 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.206132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.184444 restraints weight = 17011.974| |-----------------------------------------------------------------------------| r_work (start): 0.4619 rms_B_bonded: 2.62 r_work: 0.4551 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4468 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4770 Z= 0.186 Angle : 0.501 5.188 6381 Z= 0.263 Chirality : 0.049 0.138 720 Planarity : 0.004 0.055 810 Dihedral : 4.742 14.421 630 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.04 % Allowed : 19.07 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.28), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.003 0.001 PHE B 346 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3318.57 seconds wall clock time: 59 minutes 26.35 seconds (3566.35 seconds total)