Starting phenix.real_space_refine on Fri Aug 7 07:03:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu6_60891/08_2026/9iu6_60891.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu6_60891/08_2026/9iu6_60891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iu6_60891/08_2026/9iu6_60891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu6_60891/08_2026/9iu6_60891.map" model { file = "/net/cci-nas-00/data/ceres_data/9iu6_60891/08_2026/9iu6_60891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu6_60891/08_2026/9iu6_60891.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.029 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 196 5.49 5 S 60 5.16 5 C 11574 2.51 5 N 3620 2.21 5 O 4018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19472 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "C" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "D" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "E1" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "E2" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F1" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F2" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "G1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G2" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H2" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2429 SG CYS A 304 111.884 153.611 47.856 1.00296.06 S ATOM 2447 SG CYS A 307 108.725 151.829 48.605 1.00296.02 S ATOM 2598 SG CYS A 326 109.726 151.732 45.537 1.00296.09 S ATOM 2670 SG CYS A 335 108.686 155.250 46.727 1.00296.31 S ATOM 6292 SG CYS B 304 72.394 31.943 110.998 1.00251.20 S ATOM 6310 SG CYS B 307 72.731 33.624 107.725 1.00251.06 S ATOM 6461 SG CYS B 326 69.794 33.615 108.992 1.00251.07 S ATOM 6533 SG CYS B 335 71.019 30.126 107.949 1.00251.46 S ATOM 10155 SG CYS C 304 40.656 152.339 52.749 1.00266.31 S ATOM 10173 SG CYS C 307 38.660 149.689 54.369 1.00266.27 S ATOM 10324 SG CYS C 326 38.967 149.399 51.181 1.00265.94 S ATOM 10396 SG CYS C 335 36.905 152.403 52.174 1.00265.83 S ATOM 14018 SG CYS D 304 61.046 25.620 40.875 1.00220.41 S ATOM 14036 SG CYS D 307 61.784 28.012 38.188 1.00220.21 S ATOM 14187 SG CYS D 326 58.829 28.225 39.384 1.00219.20 S ATOM 14259 SG CYS D 335 59.449 24.974 37.465 1.00219.46 S Time building chain proxies: 4.36, per 1000 atoms: 0.22 Number of scatterers: 19472 At special positions: 0 Unit cell: (150.977, 182.019, 149.566, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 60 16.00 P 196 15.00 O 4018 8.00 N 3620 7.00 C 11574 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 - 3.00 Amino acid : True - 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: 1.58 Conformation dependent library (CDL) restraints added in 498.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 335 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 304 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 307 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 326 " pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 335 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 304 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 307 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 326 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 335 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 307 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 304 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 326 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 335 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 307 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 304 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 326 " Number of angles added : 24 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3632 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 24 sheets defined 49.6% alpha, 13.8% beta 93 base pairs and 166 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.634A pdb=" N TRP A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 118 through 151 Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 197 through 208 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 271 through 284 removed outlier: 4.121A pdb=" N LYS A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.794A pdb=" N VAL A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 423 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'B' and resid 18 through 34 Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.616A pdb=" N TRP B 64 " --> pdb=" O ASN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 118 through 151 Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 197 through 208 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 271 through 284 removed outlier: 4.029A pdb=" N LYS B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 342 through 358 Processing helix chain 'B' and resid 371 through 390 removed outlier: 3.654A pdb=" N LEU B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 422 Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 478 through 486 Processing helix chain 'C' and resid 18 through 34 Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.634A pdb=" N TRP C 64 " --> pdb=" O ASN C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 118 through 151 Processing helix chain 'C' and resid 177 through 193 Processing helix chain 'C' and resid 197 through 208 Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 271 through 283 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 342 through 358 Processing helix chain 'C' and resid 373 through 390 removed outlier: 3.700A pdb=" N LEU C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 423 Processing helix chain 'C' and resid 439 through 446 Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 478 through 486 Processing helix chain 'D' and resid 18 through 34 Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.642A pdb=" N TRP D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 86 through 100 Processing helix chain 'D' and resid 118 through 151 Processing helix chain 'D' and resid 177 through 193 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 242 through 246 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 342 through 358 Processing helix chain 'D' and resid 373 through 390 removed outlier: 3.693A pdb=" N LEU D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 422 Processing helix chain 'D' and resid 439 through 446 Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 478 through 486 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 44 removed outlier: 7.518A pdb=" N VAL A 5 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 40 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 7 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU A 42 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU A 9 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU A 44 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 2 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 76 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU A 4 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AA4, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 368 removed outlier: 7.087A pdb=" N ARG A 362 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 44 removed outlier: 7.505A pdb=" N VAL B 5 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 40 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 7 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU B 42 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU B 9 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU B 44 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG B 2 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL B 76 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 4 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 168 Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 250 Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 304 Processing sheet with id=AB2, first strand: chain 'B' and resid 311 through 315 Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 368 removed outlier: 7.092A pdb=" N ARG B 362 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 36 through 44 removed outlier: 7.517A pdb=" N VAL C 5 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL C 40 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 7 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU C 42 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU C 9 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU C 44 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG C 2 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL C 76 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU C 4 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 249 through 250 Processing sheet with id=AB7, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AB8, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 368 removed outlier: 7.097A pdb=" N ARG C 362 " --> pdb=" O THR C 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 36 through 44 removed outlier: 7.485A pdb=" N VAL D 5 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL D 40 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE D 7 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU D 42 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU D 9 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU D 44 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG D 2 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL D 76 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU D 4 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 163 through 168 Processing sheet with id=AC3, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AC4, first strand: chain 'D' and resid 302 through 304 Processing sheet with id=AC5, first strand: chain 'D' and resid 311 through 314 Processing sheet with id=AC6, first strand: chain 'D' and resid 361 through 368 removed outlier: 7.122A pdb=" N ARG D 362 " --> pdb=" O THR D 435 " (cutoff:3.500A) 813 hydrogen bonds defined for protein. 2301 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 241 hydrogen bonds 482 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 166 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 2.14 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: 4047 1.34 - 1.46: 7198 1.46 - 1.58: 8565 1.58 - 1.70: 384 1.70 - 1.83: 92 Bond restraints: 20286 Sorted by residual: bond pdb=" NE ARG A 79 " pdb=" CZ ARG A 79 " ideal model delta sigma weight residual 1.326 1.380 -0.054 1.10e-02 8.26e+03 2.38e+01 bond pdb=" CZ ARG A 79 " pdb=" NH1 ARG A 79 " ideal model delta sigma weight residual 1.323 1.386 -0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" P DCH2 1 " pdb=" O5' DCH2 1 " ideal model delta sigma weight residual 1.593 1.622 -0.029 1.00e-02 1.00e+04 8.62e+00 bond pdb=" C HIS C 321 " pdb=" N PRO C 322 " ideal model delta sigma weight residual 1.330 1.365 -0.035 1.22e-02 6.72e+03 8.36e+00 bond pdb=" C3' DGF1 31 " pdb=" O3' DGF1 31 " ideal model delta sigma weight residual 1.435 1.398 0.037 1.30e-02 5.92e+03 7.98e+00 ... (remaining 20281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 26502 3.44 - 6.88: 1720 6.88 - 10.32: 99 10.32 - 13.76: 12 13.76 - 17.20: 5 Bond angle restraints: 28338 Sorted by residual: angle pdb=" O4' DGG2 36 " pdb=" C1' DGG2 36 " pdb=" N9 DGG2 36 " ideal model delta sigma weight residual 108.00 114.71 -6.71 7.00e-01 2.04e+00 9.18e+01 angle pdb=" O3' DGF1 32 " pdb=" P DTF1 33 " pdb=" O5' DTF1 33 " ideal model delta sigma weight residual 104.00 86.80 17.20 1.90e+00 2.77e-01 8.20e+01 angle pdb=" CD ARG B 140 " pdb=" NE ARG B 140 " pdb=" CZ ARG B 140 " ideal model delta sigma weight residual 124.40 136.60 -12.20 1.40e+00 5.10e-01 7.60e+01 angle pdb=" O3' DGE2 32 " pdb=" P DTE2 33 " pdb=" O5' DTE2 33 " ideal model delta sigma weight residual 104.00 88.96 15.04 1.90e+00 2.77e-01 6.27e+01 angle pdb=" N VAL D 255 " pdb=" CA VAL D 255 " pdb=" CB VAL D 255 " ideal model delta sigma weight residual 110.53 118.83 -8.30 1.09e+00 8.42e-01 5.80e+01 ... (remaining 28333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 9512 17.90 - 35.80: 1012 35.80 - 53.70: 867 53.70 - 71.61: 203 71.61 - 89.51: 22 Dihedral angle restraints: 11616 sinusoidal: 6004 harmonic: 5612 Sorted by residual: dihedral pdb=" C ASP B 359 " pdb=" N ASP B 359 " pdb=" CA ASP B 359 " pdb=" CB ASP B 359 " ideal model delta harmonic sigma weight residual -122.60 -136.87 14.27 0 2.50e+00 1.60e-01 3.26e+01 dihedral pdb=" C HIS C 199 " pdb=" N HIS C 199 " pdb=" CA HIS C 199 " pdb=" CB HIS C 199 " ideal model delta harmonic sigma weight residual -122.60 -135.20 12.60 0 2.50e+00 1.60e-01 2.54e+01 dihedral pdb=" N ASP B 359 " pdb=" C ASP B 359 " pdb=" CA ASP B 359 " pdb=" CB ASP B 359 " ideal model delta harmonic sigma weight residual 122.80 134.83 -12.03 0 2.50e+00 1.60e-01 2.31e+01 ... (remaining 11613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2760 0.130 - 0.260: 326 0.260 - 0.390: 16 0.390 - 0.521: 2 0.521 - 0.651: 4 Chirality restraints: 3108 Sorted by residual: chirality pdb=" P DCH2 1 " pdb=" OP1 DCH2 1 " pdb=" OP2 DCH2 1 " pdb=" O5' DCH2 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DGE1 1 " pdb=" OP1 DGE1 1 " pdb=" OP2 DGE1 1 " pdb=" O5' DGE1 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DTF2 1 " pdb=" OP1 DTF2 1 " pdb=" OP2 DTF2 1 " pdb=" O5' DTF2 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 3105 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 35 " -0.044 2.00e-02 2.50e+03 2.17e-02 1.18e+01 pdb=" CG TRP D 35 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP D 35 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP D 35 " 0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP D 35 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 35 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 35 " 0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 35 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 35 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP D 35 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCE2 30 " 0.039 2.00e-02 2.50e+03 2.11e-02 1.00e+01 pdb=" N1 DCE2 30 " -0.041 2.00e-02 2.50e+03 pdb=" C2 DCE2 30 " -0.018 2.00e-02 2.50e+03 pdb=" O2 DCE2 30 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DCE2 30 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DCE2 30 " 0.010 2.00e-02 2.50e+03 pdb=" N4 DCE2 30 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DCE2 30 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DCE2 30 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 199 " -0.025 2.00e-02 2.50e+03 2.18e-02 7.10e+00 pdb=" CG HIS D 199 " 0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS D 199 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS D 199 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS D 199 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS D 199 " -0.007 2.00e-02 2.50e+03 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 5 2.26 - 2.92: 6777 2.92 - 3.58: 28261 3.58 - 4.24: 47334 4.24 - 4.90: 77050 Nonbonded interactions: 159427 Sorted by model distance: nonbonded pdb=" OG SER A 10 " pdb=" P DCF1 28 " model vdw 1.606 3.400 nonbonded pdb=" OG SER D 10 " pdb=" P DCG2 25 " model vdw 1.607 3.400 nonbonded pdb=" OG SER B 10 " pdb=" P DCE2 28 " model vdw 1.609 3.400 nonbonded pdb=" OG SER C 10 " pdb=" P DCH1 25 " model vdw 1.610 3.400 nonbonded pdb=" OH TYR B 312 " pdb=" OP2 DTE2 43 " model vdw 2.081 3.040 ... (remaining 159422 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' } 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 group one per residue 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: 0.570 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.430 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5741 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 : 0.010 0.073 20302 Z= 0.643 Angle : 1.816 20.569 28362 Z= 1.248 Chirality : 0.086 0.651 3108 Planarity : 0.006 0.070 3020 Dihedral : 21.269 89.507 7984 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.86 % Favored : 97.99 % Rotamer: Outliers : 3.87 % Allowed : 7.23 % Favored : 88.90 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 1936 helix: 0.56 (0.14), residues: 922 sheet: 0.24 (0.28), residues: 263 loop : 0.15 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.004 ARG A 142 TYR 0.027 0.004 TYR D 482 PHE 0.019 0.004 PHE D 118 TRP 0.044 0.004 TRP D 35 HIS 0.017 0.003 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00978 / 0.64 (20286) covalent geometry : angle 1.79577 / 1.25 (28338) hydrogen bonds : bond 0.16035 / 10.80 ( 1054) hydrogen bonds : angle 5.98674 / 4.32 ( 2783) metal coordination : bond 0.05815 / 3.59 ( 16) metal coordination : angle 9.49656 / 7.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 490 time to evaluate : 0.583 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.7774 (mt) cc_final: 0.7520 (mt) REVERT: A 8 ARG cc_start: 0.6161 (ttp80) cc_final: 0.5954 (ttp-170) REVERT: A 10 SER cc_start: 0.6878 (OUTLIER) cc_final: 0.6426 (t) REVERT: A 24 GLU cc_start: 0.7531 (tp30) cc_final: 0.7043 (tm-30) REVERT: A 27 GLN cc_start: 0.8293 (mt0) cc_final: 0.7930 (mt0) REVERT: A 33 ARG cc_start: 0.7807 (mmt90) cc_final: 0.6715 (mtm-85) REVERT: A 35 TRP cc_start: 0.7745 (m-10) cc_final: 0.6299 (m-10) REVERT: A 47 SER cc_start: 0.7292 (t) cc_final: 0.7079 (p) REVERT: A 79 ARG cc_start: 0.6388 (mtp180) cc_final: 0.5264 (mtm-85) REVERT: A 81 ASP cc_start: 0.7533 (p0) cc_final: 0.7200 (p0) REVERT: A 108 THR cc_start: 0.7020 (p) cc_final: 0.5850 (t) REVERT: A 109 GLU cc_start: 0.6460 (mt-10) cc_final: 0.5924 (mp0) REVERT: A 132 MET cc_start: 0.7474 (mtm) cc_final: 0.6906 (mtm) REVERT: A 135 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7020 (pp20) REVERT: A 137 ILE cc_start: 0.6687 (mt) cc_final: 0.6393 (mt) REVERT: A 148 ASN cc_start: 0.8752 (m-40) cc_final: 0.8546 (m-40) REVERT: A 150 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8060 (ttm-80) REVERT: A 174 LEU cc_start: 0.6996 (mt) cc_final: 0.6690 (mt) REVERT: A 177 ASP cc_start: 0.6635 (t0) cc_final: 0.6001 (t0) REVERT: A 182 GLU cc_start: 0.8725 (tt0) cc_final: 0.8273 (tm-30) REVERT: A 230 TRP cc_start: 0.7555 (m100) cc_final: 0.7319 (m100) REVERT: A 236 LYS cc_start: 0.8724 (tttt) cc_final: 0.8445 (tttt) REVERT: A 239 MET cc_start: 0.7975 (mmm) cc_final: 0.7519 (mmm) REVERT: A 244 MET cc_start: 0.7376 (mmt) cc_final: 0.7058 (mmt) REVERT: A 276 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7676 (pt0) REVERT: A 397 ARG cc_start: -0.1266 (OUTLIER) cc_final: -0.2034 (ttm170) REVERT: A 481 GLU cc_start: -0.3057 (OUTLIER) cc_final: -0.3289 (mp0) REVERT: B 26 CYS cc_start: 0.8592 (m) cc_final: 0.8357 (m) REVERT: B 27 GLN cc_start: 0.8267 (mt0) cc_final: 0.7776 (mt0) REVERT: B 28 GLN cc_start: 0.7619 (tp-100) cc_final: 0.7406 (tp-100) REVERT: B 36 ASP cc_start: 0.4671 (p0) cc_final: 0.4350 (p0) REVERT: B 37 VAL cc_start: 0.8183 (t) cc_final: 0.7979 (p) REVERT: B 45 ASP cc_start: 0.7748 (m-30) cc_final: 0.7361 (p0) REVERT: B 56 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7567 (tmmm) REVERT: B 60 ASN cc_start: 0.7382 (m-40) cc_final: 0.6949 (m110) REVERT: B 70 GLN cc_start: 0.8416 (mt0) cc_final: 0.8194 (mt0) REVERT: B 73 ASP cc_start: 0.7587 (m-30) cc_final: 0.6976 (p0) REVERT: B 102 LYS cc_start: 0.8010 (mmtp) cc_final: 0.7391 (mmmt) REVERT: B 108 THR cc_start: 0.7185 (m) cc_final: 0.6942 (m) REVERT: B 109 GLU cc_start: 0.5948 (mt-10) cc_final: 0.5299 (mp0) REVERT: B 132 MET cc_start: 0.7087 (mtm) cc_final: 0.6850 (mtm) REVERT: B 142 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.7030 (ttp80) REVERT: B 146 HIS cc_start: 0.7407 (m170) cc_final: 0.7125 (m-70) REVERT: B 153 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7466 (mtmp) REVERT: B 177 ASP cc_start: 0.6068 (t0) cc_final: 0.5601 (t0) REVERT: B 186 GLU cc_start: 0.8825 (tt0) cc_final: 0.8173 (tt0) REVERT: B 189 HIS cc_start: 0.7244 (m-70) cc_final: 0.7027 (m-70) REVERT: B 200 LEU cc_start: 0.8117 (mt) cc_final: 0.7878 (mt) REVERT: B 204 ASP cc_start: 0.7860 (t70) cc_final: 0.7615 (t0) REVERT: B 206 ASN cc_start: 0.6878 (m-40) cc_final: 0.6602 (m110) REVERT: B 215 ASP cc_start: 0.8020 (m-30) cc_final: 0.7813 (m-30) REVERT: B 216 TYR cc_start: 0.6962 (t80) cc_final: 0.6677 (t80) REVERT: B 229 GLU cc_start: 0.7436 (pt0) cc_final: 0.6852 (tt0) REVERT: B 236 LYS cc_start: 0.7597 (tttt) cc_final: 0.7359 (ttpp) REVERT: B 244 MET cc_start: 0.8162 (mmt) cc_final: 0.7933 (mmm) REVERT: B 245 LEU cc_start: 0.7933 (mt) cc_final: 0.7600 (mt) REVERT: B 269 ILE cc_start: 0.8330 (mm) cc_final: 0.7747 (mm) REVERT: B 270 LEU cc_start: 0.7703 (mt) cc_final: 0.7329 (mm) REVERT: B 276 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 278 LEU cc_start: 0.8232 (tp) cc_final: 0.7929 (tt) REVERT: B 282 LEU cc_start: 0.8227 (mt) cc_final: 0.7982 (mm) REVERT: B 284 LYS cc_start: 0.8331 (mtmt) cc_final: 0.7645 (mtmt) REVERT: B 344 GLU cc_start: 0.8766 (tt0) cc_final: 0.8391 (tt0) REVERT: B 351 GLU cc_start: 0.9118 (tt0) cc_final: 0.8831 (pt0) REVERT: B 379 GLU cc_start: 0.8929 (pt0) cc_final: 0.8433 (mt-10) REVERT: B 406 LEU cc_start: 0.8912 (tp) cc_final: 0.8572 (mt) REVERT: B 416 ARG cc_start: 0.8808 (mmm160) cc_final: 0.8439 (mmm160) REVERT: B 417 GLN cc_start: 0.9031 (tm-30) cc_final: 0.8799 (tm-30) REVERT: B 442 TRP cc_start: 0.8432 (t60) cc_final: 0.7475 (t60) REVERT: B 457 SER cc_start: 0.8069 (t) cc_final: 0.7230 (p) REVERT: B 458 MET cc_start: 0.8196 (mmt) cc_final: 0.7445 (mmt) REVERT: B 478 ASP cc_start: 0.8368 (m-30) cc_final: 0.7876 (p0) REVERT: C 54 ASP cc_start: 0.5108 (t0) cc_final: 0.4673 (t0) REVERT: C 55 ARG cc_start: 0.6325 (mmm-85) cc_final: 0.5840 (tpp80) REVERT: C 56 LYS cc_start: 0.8088 (tppp) cc_final: 0.7813 (tppp) REVERT: C 70 GLN cc_start: 0.7294 (mt0) cc_final: 0.6700 (mt0) REVERT: C 72 PHE cc_start: 0.6919 (p90) cc_final: 0.6322 (p90) REVERT: C 78 TYR cc_start: 0.6991 (t80) cc_final: 0.6592 (t80) REVERT: C 126 MET cc_start: 0.5857 (mmm) cc_final: 0.5492 (mmm) REVERT: C 140 ARG cc_start: 0.6894 (mtm-85) cc_final: 0.6341 (ttm-80) REVERT: C 149 ILE cc_start: 0.7734 (mm) cc_final: 0.7340 (mm) REVERT: C 150 ARG cc_start: 0.7799 (mtt-85) cc_final: 0.7484 (tpp80) REVERT: C 199 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.6905 (p-80) REVERT: C 228 ARG cc_start: 0.6116 (mtt-85) cc_final: 0.5588 (mtm-85) REVERT: C 235 LEU cc_start: 0.8731 (mt) cc_final: 0.8032 (pp) REVERT: C 239 MET cc_start: 0.7823 (mmm) cc_final: 0.7380 (mmm) REVERT: C 241 SER cc_start: 0.7228 (m) cc_final: 0.6863 (p) REVERT: C 342 MET cc_start: 0.4576 (OUTLIER) cc_final: 0.4307 (mmm) REVERT: D 7 ILE cc_start: 0.7808 (mt) cc_final: 0.7564 (mm) REVERT: D 25 SER cc_start: 0.7628 (m) cc_final: 0.7214 (m) REVERT: D 27 GLN cc_start: 0.7870 (mt0) cc_final: 0.7574 (mt0) REVERT: D 30 CYS cc_start: 0.8205 (m) cc_final: 0.7730 (m) REVERT: D 72 PHE cc_start: 0.7631 (p90) cc_final: 0.7395 (p90) REVERT: D 73 ASP cc_start: 0.7349 (m-30) cc_final: 0.6836 (m-30) REVERT: D 88 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7496 (mtp180) REVERT: D 102 LYS cc_start: 0.6894 (mmtt) cc_final: 0.6559 (mmtm) REVERT: D 115 THR cc_start: 0.6694 (p) cc_final: 0.5412 (p) REVERT: D 125 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7279 (tt) REVERT: D 137 ILE cc_start: 0.7156 (mt) cc_final: 0.6931 (mm) REVERT: D 149 ILE cc_start: 0.8161 (mm) cc_final: 0.7926 (tt) REVERT: D 154 TYR cc_start: 0.6012 (t80) cc_final: 0.5414 (t80) REVERT: D 164 LEU cc_start: 0.6590 (tp) cc_final: 0.6236 (mt) REVERT: D 166 THR cc_start: 0.5629 (OUTLIER) cc_final: 0.5344 (t) REVERT: D 173 ARG cc_start: 0.6933 (ttm110) cc_final: 0.6521 (mmm-85) REVERT: D 190 ARG cc_start: 0.8217 (mtp180) cc_final: 0.7085 (ttp80) REVERT: D 203 HIS cc_start: 0.8173 (t70) cc_final: 0.7965 (t-90) REVERT: D 206 ASN cc_start: 0.6743 (m-40) cc_final: 0.6171 (m110) REVERT: D 215 ASP cc_start: 0.7675 (m-30) cc_final: 0.7398 (m-30) REVERT: D 216 TYR cc_start: 0.7877 (t80) cc_final: 0.7487 (t80) REVERT: D 230 TRP cc_start: 0.8025 (m100) cc_final: 0.6820 (m100) REVERT: D 235 LEU cc_start: 0.8493 (mt) cc_final: 0.8208 (mm) REVERT: D 236 LYS cc_start: 0.8680 (tttt) cc_final: 0.8467 (ttmm) REVERT: D 242 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7948 (mt-10) REVERT: D 244 MET cc_start: 0.8297 (mmt) cc_final: 0.7932 (mmm) REVERT: D 276 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7668 (mm-30) REVERT: D 281 GLU cc_start: 0.8309 (tp30) cc_final: 0.8009 (tp30) REVERT: D 282 LEU cc_start: 0.8911 (mp) cc_final: 0.8701 (mm) REVERT: D 296 SER cc_start: 0.7677 (OUTLIER) cc_final: 0.7206 (t) REVERT: D 327 ARG cc_start: 0.8087 (ttt180) cc_final: 0.7781 (ttp80) REVERT: D 350 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7467 (tp30) REVERT: D 458 MET cc_start: 0.7290 (mmt) cc_final: 0.6541 (mmt) REVERT: D 459 ASN cc_start: 0.8235 (m110) cc_final: 0.7765 (p0) outliers start: 62 outliers final: 20 residues processed: 532 average time/residue: 0.1771 time to fit residues: 132.7387 Evaluate side-chains 462 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 432 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 296 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN B 22 GLN B 446 GLN C 100 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 HIS D 221 GLN D 251 ASN D 452 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.215248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.167743 restraints weight = 40466.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.167367 restraints weight = 24012.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.169250 restraints weight = 13802.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.169659 restraints weight = 11402.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.169900 restraints weight = 9036.010| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20302 Z= 0.201 Angle : 0.805 13.690 28362 Z= 0.441 Chirality : 0.056 0.266 3108 Planarity : 0.006 0.104 3020 Dihedral : 23.602 87.149 4344 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.55 % Allowed : 11.72 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.18), residues: 1936 helix: 2.22 (0.16), residues: 916 sheet: -0.14 (0.27), residues: 279 loop : 0.77 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 228 TYR 0.016 0.002 TYR C 482 PHE 0.037 0.002 PHE A 331 TRP 0.017 0.002 TRP C 230 HIS 0.010 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.20 (20286) covalent geometry : angle 0.79178 / 0.44 (28338) hydrogen bonds : bond 0.05676 / 3.92 ( 1054) hydrogen bonds : angle 4.08375 / 2.97 ( 2783) metal coordination : bond 0.00521 / 0.28 ( 16) metal coordination : angle 5.08656 / 3.73 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 429 time to evaluate : 0.523 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8172 (mt) cc_final: 0.7629 (mm) REVERT: A 33 ARG cc_start: 0.7641 (mmt90) cc_final: 0.7095 (tpp80) REVERT: A 45 ASP cc_start: 0.4738 (m-30) cc_final: 0.4350 (m-30) REVERT: A 57 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7634 (mtt-85) REVERT: A 70 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7650 (mm-40) REVERT: A 109 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7180 (mt-10) REVERT: A 131 GLN cc_start: 0.7620 (tt0) cc_final: 0.6803 (tt0) REVERT: A 139 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7204 (mm-30) REVERT: A 148 ASN cc_start: 0.8331 (m-40) cc_final: 0.8058 (m-40) REVERT: A 150 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7587 (ttm-80) REVERT: A 164 LEU cc_start: 0.8382 (mm) cc_final: 0.8164 (mm) REVERT: A 182 GLU cc_start: 0.8571 (tt0) cc_final: 0.8138 (tm-30) REVERT: A 183 ARG cc_start: 0.8443 (mmt-90) cc_final: 0.8212 (mmm160) REVERT: A 236 LYS cc_start: 0.8540 (tttt) cc_final: 0.8257 (tttt) REVERT: A 239 MET cc_start: 0.7311 (mmm) cc_final: 0.7107 (mmm) REVERT: A 244 MET cc_start: 0.7636 (mmt) cc_final: 0.6929 (mmt) REVERT: A 276 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7669 (pt0) REVERT: A 397 ARG cc_start: -0.1765 (OUTLIER) cc_final: -0.2500 (ttm170) REVERT: A 481 GLU cc_start: -0.2344 (OUTLIER) cc_final: -0.2828 (mp0) REVERT: B 22 GLN cc_start: 0.8237 (mt0) cc_final: 0.7495 (mt0) REVERT: B 26 CYS cc_start: 0.8277 (m) cc_final: 0.7998 (m) REVERT: B 27 GLN cc_start: 0.7871 (mt0) cc_final: 0.7533 (mt0) REVERT: B 102 LYS cc_start: 0.7952 (mmtp) cc_final: 0.7456 (mmmt) REVERT: B 113 ASP cc_start: 0.6643 (t0) cc_final: 0.6211 (t0) REVERT: B 142 ARG cc_start: 0.7706 (ttp-110) cc_final: 0.7319 (ttp80) REVERT: B 177 ASP cc_start: 0.7267 (t0) cc_final: 0.6977 (t0) REVERT: B 189 HIS cc_start: 0.7072 (m-70) cc_final: 0.6603 (m-70) REVERT: B 190 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7408 (mtm-85) REVERT: B 196 GLU cc_start: 0.7391 (tt0) cc_final: 0.7139 (mt-10) REVERT: B 198 LEU cc_start: 0.8684 (pt) cc_final: 0.8298 (mt) REVERT: B 200 LEU cc_start: 0.8228 (mt) cc_final: 0.7862 (mt) REVERT: B 206 ASN cc_start: 0.8020 (m-40) cc_final: 0.7240 (m-40) REVERT: B 224 GLU cc_start: 0.6944 (pp20) cc_final: 0.6326 (pp20) REVERT: B 276 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7723 (mt-10) REVERT: B 279 ARG cc_start: 0.7759 (ptp90) cc_final: 0.7463 (ptp90) REVERT: B 281 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7091 (tp30) REVERT: B 344 GLU cc_start: 0.8401 (tt0) cc_final: 0.7695 (tm-30) REVERT: B 406 LEU cc_start: 0.8613 (tp) cc_final: 0.8281 (mt) REVERT: B 457 SER cc_start: 0.8247 (t) cc_final: 0.7402 (p) REVERT: B 458 MET cc_start: 0.8160 (mmt) cc_final: 0.7366 (mmt) REVERT: C 27 GLN cc_start: 0.8132 (pp30) cc_final: 0.7701 (pp30) REVERT: C 30 CYS cc_start: 0.7345 (m) cc_final: 0.7020 (p) REVERT: C 33 ARG cc_start: 0.7774 (tpp80) cc_final: 0.7090 (ttm110) REVERT: C 42 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6517 (mt-10) REVERT: C 56 LYS cc_start: 0.7649 (tppp) cc_final: 0.6970 (tppp) REVERT: C 70 GLN cc_start: 0.7323 (mt0) cc_final: 0.7067 (mt0) REVERT: C 78 TYR cc_start: 0.7968 (t80) cc_final: 0.7670 (t80) REVERT: C 92 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7218 (mt0) REVERT: C 140 ARG cc_start: 0.6695 (mtm-85) cc_final: 0.6036 (ttm-80) REVERT: C 142 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.7085 (ttm-80) REVERT: C 149 ILE cc_start: 0.8356 (mm) cc_final: 0.7978 (mm) REVERT: C 199 HIS cc_start: 0.7708 (OUTLIER) cc_final: 0.6929 (p-80) REVERT: C 212 SER cc_start: 0.6334 (p) cc_final: 0.4876 (m) REVERT: C 235 LEU cc_start: 0.8759 (mt) cc_final: 0.8338 (mt) REVERT: C 239 MET cc_start: 0.7107 (mmm) cc_final: 0.6903 (mmm) REVERT: C 274 GLN cc_start: 0.8248 (mt0) cc_final: 0.7678 (mt0) REVERT: C 342 MET cc_start: 0.5047 (OUTLIER) cc_final: 0.4826 (mmm) REVERT: D 17 THR cc_start: 0.7756 (p) cc_final: 0.7353 (p) REVERT: D 20 GLU cc_start: 0.8161 (mp0) cc_final: 0.7566 (pm20) REVERT: D 22 GLN cc_start: 0.8022 (mt0) cc_final: 0.7561 (mt0) REVERT: D 25 SER cc_start: 0.7413 (m) cc_final: 0.7047 (p) REVERT: D 57 ARG cc_start: 0.7304 (mtm-85) cc_final: 0.6977 (mtm-85) REVERT: D 68 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7419 (mm-30) REVERT: D 72 PHE cc_start: 0.8125 (p90) cc_final: 0.7722 (p90) REVERT: D 73 ASP cc_start: 0.7567 (m-30) cc_final: 0.6935 (t0) REVERT: D 135 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7441 (tp30) REVERT: D 137 ILE cc_start: 0.8079 (mt) cc_final: 0.7820 (mm) REVERT: D 139 GLU cc_start: 0.7348 (tp30) cc_final: 0.6967 (tp30) REVERT: D 140 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7081 (ttp80) REVERT: D 148 ASN cc_start: 0.7906 (m-40) cc_final: 0.7678 (m-40) REVERT: D 189 HIS cc_start: 0.7938 (t70) cc_final: 0.7678 (t70) REVERT: D 190 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7393 (mtp180) REVERT: D 206 ASN cc_start: 0.7038 (m-40) cc_final: 0.6554 (m110) REVERT: D 212 SER cc_start: 0.8553 (p) cc_final: 0.8179 (m) REVERT: D 221 GLN cc_start: 0.8586 (mm110) cc_final: 0.8131 (mm-40) REVERT: D 226 GLN cc_start: 0.7679 (mp10) cc_final: 0.6539 (mm110) REVERT: D 230 TRP cc_start: 0.8232 (m100) cc_final: 0.7463 (m100) REVERT: D 235 LEU cc_start: 0.8821 (mt) cc_final: 0.8454 (mm) REVERT: D 236 LYS cc_start: 0.8729 (tttt) cc_final: 0.8308 (ttmm) REVERT: D 242 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7672 (mt-10) REVERT: D 247 TYR cc_start: 0.7943 (m-10) cc_final: 0.7091 (m-10) REVERT: D 275 LEU cc_start: 0.8057 (tp) cc_final: 0.7670 (tp) REVERT: D 276 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7030 (pt0) REVERT: D 278 LEU cc_start: 0.8347 (mt) cc_final: 0.8096 (mm) REVERT: D 327 ARG cc_start: 0.8358 (ttt180) cc_final: 0.7795 (ttp80) REVERT: D 328 SER cc_start: 0.8234 (t) cc_final: 0.6875 (p) REVERT: D 331 PHE cc_start: 0.6171 (m-10) cc_final: 0.5448 (m-80) REVERT: D 458 MET cc_start: 0.7447 (mmt) cc_final: 0.6661 (mmt) REVERT: D 459 ASN cc_start: 0.8126 (m110) cc_final: 0.7731 (p0) outliers start: 57 outliers final: 33 residues processed: 464 average time/residue: 0.1739 time to fit residues: 114.6889 Evaluate side-chains 434 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 396 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 255 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 129 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 132 optimal weight: 50.0000 chunk 107 optimal weight: 0.5980 chunk 196 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 GLN B 60 ASN B 70 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 70 GLN D 111 HIS D 189 HIS ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.210020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.161112 restraints weight = 39862.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.160905 restraints weight = 17881.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.161704 restraints weight = 13202.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162305 restraints weight = 11001.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162347 restraints weight = 8915.120| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20302 Z= 0.243 Angle : 0.731 12.363 28362 Z= 0.409 Chirality : 0.049 0.265 3108 Planarity : 0.006 0.064 3020 Dihedral : 23.510 86.279 4310 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.62 % Allowed : 13.72 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.19), residues: 1936 helix: 1.86 (0.16), residues: 919 sheet: -0.28 (0.27), residues: 289 loop : 0.70 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 279 TYR 0.016 0.002 TYR D 154 PHE 0.033 0.002 PHE A 331 TRP 0.038 0.002 TRP C 230 HIS 0.014 0.002 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.24 (20286) covalent geometry : angle 0.72410 / 0.41 (28338) hydrogen bonds : bond 0.05773 / 3.93 ( 1054) hydrogen bonds : angle 4.16345 / 3.03 ( 2783) metal coordination : bond 0.00620 / 0.33 ( 16) metal coordination : angle 3.49963 / 2.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 421 time to evaluate : 0.578 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: 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: A 24 GLU cc_start: 0.6783 (tp30) cc_final: 0.6156 (tm-30) REVERT: A 78 TYR cc_start: 0.7910 (t80) cc_final: 0.7532 (t80) REVERT: A 128 THR cc_start: 0.7987 (p) cc_final: 0.7614 (m) REVERT: A 131 GLN cc_start: 0.7698 (tt0) cc_final: 0.7323 (tt0) REVERT: A 139 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7243 (mm-30) REVERT: A 150 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7533 (ttm-80) REVERT: A 164 LEU cc_start: 0.8485 (mm) cc_final: 0.8165 (mm) REVERT: A 182 GLU cc_start: 0.8538 (tt0) cc_final: 0.7985 (tm-30) REVERT: A 221 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7888 (mp10) REVERT: A 239 MET cc_start: 0.7385 (mmm) cc_final: 0.7180 (mmm) REVERT: A 244 MET cc_start: 0.7722 (mmt) cc_final: 0.7004 (mmt) REVERT: A 276 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7603 (pt0) REVERT: A 342 MET cc_start: 0.2568 (mtp) cc_final: 0.2355 (mtp) REVERT: A 397 ARG cc_start: -0.1810 (OUTLIER) cc_final: -0.2471 (ttm170) REVERT: A 481 GLU cc_start: -0.2282 (OUTLIER) cc_final: -0.2753 (mp0) REVERT: B 26 CYS cc_start: 0.8240 (m) cc_final: 0.7693 (m) REVERT: B 27 GLN cc_start: 0.7822 (mt0) cc_final: 0.7455 (mt0) REVERT: B 28 GLN cc_start: 0.7539 (tp-100) cc_final: 0.7238 (tp40) REVERT: B 37 VAL cc_start: 0.8907 (t) cc_final: 0.8586 (p) REVERT: B 101 LYS cc_start: 0.7796 (mptt) cc_final: 0.7517 (mptt) REVERT: B 102 LYS cc_start: 0.8142 (mmtp) cc_final: 0.7834 (mmmt) REVERT: B 109 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7031 (mp0) REVERT: B 113 ASP cc_start: 0.6657 (t0) cc_final: 0.6312 (t0) REVERT: B 132 MET cc_start: 0.6853 (mtm) cc_final: 0.6479 (mmm) REVERT: B 142 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.7475 (ttp80) REVERT: B 173 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7471 (mtp85) REVERT: B 174 LEU cc_start: 0.8250 (mt) cc_final: 0.7904 (mp) REVERT: B 177 ASP cc_start: 0.7503 (t0) cc_final: 0.7190 (t0) REVERT: B 186 GLU cc_start: 0.7789 (tt0) cc_final: 0.6841 (tm-30) REVERT: B 189 HIS cc_start: 0.7116 (m-70) cc_final: 0.6737 (m-70) REVERT: B 196 GLU cc_start: 0.7811 (tt0) cc_final: 0.7530 (mt-10) REVERT: B 198 LEU cc_start: 0.8824 (pt) cc_final: 0.8456 (mt) REVERT: B 200 LEU cc_start: 0.8334 (mt) cc_final: 0.7971 (mt) REVERT: B 236 LYS cc_start: 0.8313 (ttpp) cc_final: 0.8076 (ttpp) REVERT: B 272 ARG cc_start: 0.6629 (tpp80) cc_final: 0.6236 (tpp80) REVERT: B 276 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7913 (mt-10) REVERT: B 281 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7225 (tp30) REVERT: B 344 GLU cc_start: 0.8477 (tt0) cc_final: 0.7896 (tm-30) REVERT: B 406 LEU cc_start: 0.8584 (tp) cc_final: 0.8290 (mt) REVERT: B 457 SER cc_start: 0.8043 (t) cc_final: 0.7377 (p) REVERT: B 458 MET cc_start: 0.7970 (mmt) cc_final: 0.7632 (mmt) REVERT: C 9 LEU cc_start: 0.7969 (tp) cc_final: 0.7766 (tp) REVERT: C 27 GLN cc_start: 0.8123 (pp30) cc_final: 0.7820 (pp30) REVERT: C 30 CYS cc_start: 0.7510 (m) cc_final: 0.7113 (p) REVERT: C 33 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7194 (tpp80) REVERT: C 46 VAL cc_start: 0.8113 (t) cc_final: 0.7882 (m) REVERT: C 56 LYS cc_start: 0.7700 (tppp) cc_final: 0.7078 (tppp) REVERT: C 70 GLN cc_start: 0.7644 (mt0) cc_final: 0.7298 (mt0) REVERT: C 78 TYR cc_start: 0.8146 (t80) cc_final: 0.7899 (t80) REVERT: C 79 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7534 (mtp-110) REVERT: C 126 MET cc_start: 0.7424 (mmm) cc_final: 0.6492 (mtp) REVERT: C 142 ARG cc_start: 0.7443 (ttp-110) cc_final: 0.7242 (ttm-80) REVERT: C 149 ILE cc_start: 0.8467 (mm) cc_final: 0.8155 (mm) REVERT: C 199 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.7011 (p-80) REVERT: C 213 PRO cc_start: 0.8159 (Cg_exo) cc_final: 0.7618 (Cg_endo) REVERT: C 228 ARG cc_start: 0.7388 (mtt90) cc_final: 0.7181 (ttp-170) REVERT: C 235 LEU cc_start: 0.8756 (mt) cc_final: 0.8321 (mt) REVERT: C 274 GLN cc_start: 0.8256 (mt0) cc_final: 0.7753 (mt0) REVERT: C 342 MET cc_start: 0.4983 (OUTLIER) cc_final: 0.4763 (mmm) REVERT: D 7 ILE cc_start: 0.8381 (mm) cc_final: 0.8170 (mm) REVERT: D 17 THR cc_start: 0.7845 (p) cc_final: 0.7580 (p) REVERT: D 20 GLU cc_start: 0.8169 (mp0) cc_final: 0.7967 (mp0) REVERT: D 22 GLN cc_start: 0.8282 (mt0) cc_final: 0.8051 (mt0) REVERT: D 68 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7334 (mm-30) REVERT: D 72 PHE cc_start: 0.8108 (p90) cc_final: 0.7687 (p90) REVERT: D 73 ASP cc_start: 0.7716 (m-30) cc_final: 0.7445 (m-30) REVERT: D 109 GLU cc_start: 0.7375 (mp0) cc_final: 0.7107 (mt-10) REVERT: D 135 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7200 (tp30) REVERT: D 140 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7077 (ttp-170) REVERT: D 189 HIS cc_start: 0.7773 (t-90) cc_final: 0.7497 (t-90) REVERT: D 190 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7564 (mtm180) REVERT: D 211 LEU cc_start: 0.7981 (mm) cc_final: 0.7604 (mm) REVERT: D 215 ASP cc_start: 0.7431 (m-30) cc_final: 0.7128 (m-30) REVERT: D 230 TRP cc_start: 0.8259 (m100) cc_final: 0.7663 (m100) REVERT: D 235 LEU cc_start: 0.8868 (mt) cc_final: 0.8517 (mm) REVERT: D 236 LYS cc_start: 0.8746 (tttt) cc_final: 0.8435 (tttp) REVERT: D 242 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7609 (mt-10) REVERT: D 247 TYR cc_start: 0.8045 (m-10) cc_final: 0.7303 (m-10) REVERT: D 273 GLU cc_start: 0.7854 (pp20) cc_final: 0.7637 (pp20) REVERT: D 278 LEU cc_start: 0.8557 (mt) cc_final: 0.7624 (mm) REVERT: D 327 ARG cc_start: 0.8456 (ttt180) cc_final: 0.7878 (ttp80) REVERT: D 328 SER cc_start: 0.8408 (t) cc_final: 0.7044 (p) REVERT: D 331 PHE cc_start: 0.6284 (m-10) cc_final: 0.5391 (m-80) REVERT: D 351 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8080 (tm-30) REVERT: D 413 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8469 (pp) REVERT: D 458 MET cc_start: 0.7553 (mmt) cc_final: 0.6786 (mmt) REVERT: D 459 ASN cc_start: 0.8225 (m110) cc_final: 0.7774 (p0) outliers start: 58 outliers final: 42 residues processed: 458 average time/residue: 0.1530 time to fit residues: 100.9476 Evaluate side-chains 462 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 413 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 251 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 413 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 97 optimal weight: 0.9980 chunk 186 optimal weight: 20.0000 chunk 197 optimal weight: 30.0000 chunk 169 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 145 optimal weight: 0.0370 chunk 202 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.213777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166847 restraints weight = 40063.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.166587 restraints weight = 17910.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.167889 restraints weight = 11816.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.168442 restraints weight = 9900.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.168406 restraints weight = 8620.565| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20302 Z= 0.155 Angle : 0.640 12.855 28362 Z= 0.356 Chirality : 0.044 0.195 3108 Planarity : 0.005 0.124 3020 Dihedral : 23.570 84.446 4305 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.74 % Allowed : 15.40 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 1936 helix: 2.18 (0.16), residues: 918 sheet: -0.32 (0.27), residues: 298 loop : 0.80 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 150 TYR 0.021 0.002 TYR B 154 PHE 0.024 0.002 PHE B 348 TRP 0.031 0.002 TRP C 230 HIS 0.010 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (20286) covalent geometry : angle 0.63285 / 0.36 (28338) hydrogen bonds : bond 0.04767 / 3.28 ( 1054) hydrogen bonds : angle 3.87909 / 2.82 ( 2783) metal coordination : bond 0.00415 / 0.23 ( 16) metal coordination : angle 3.43136 / 2.39 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 412 time to evaluate : 0.576 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8002 (tp) cc_final: 0.7202 (mt) REVERT: A 24 GLU cc_start: 0.6818 (tp30) cc_final: 0.6466 (tm-30) REVERT: A 33 ARG cc_start: 0.7669 (mmt90) cc_final: 0.6945 (mmm-85) REVERT: A 51 ASP cc_start: 0.8173 (t0) cc_final: 0.7957 (t0) REVERT: A 70 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7466 (mm-40) REVERT: A 131 GLN cc_start: 0.7693 (tt0) cc_final: 0.7365 (tt0) REVERT: A 139 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7356 (mm-30) REVERT: A 142 ARG cc_start: 0.7840 (ptm160) cc_final: 0.7622 (ttp80) REVERT: A 149 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 150 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7591 (ttm-80) REVERT: A 164 LEU cc_start: 0.8480 (mm) cc_final: 0.8214 (mm) REVERT: A 177 ASP cc_start: 0.8047 (t0) cc_final: 0.7704 (t0) REVERT: A 182 GLU cc_start: 0.8252 (tt0) cc_final: 0.8034 (tm-30) REVERT: A 221 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7887 (mp10) REVERT: A 239 MET cc_start: 0.7415 (mmm) cc_final: 0.7212 (mmm) REVERT: A 244 MET cc_start: 0.7726 (mmt) cc_final: 0.7008 (mmt) REVERT: A 276 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7597 (pt0) REVERT: A 342 MET cc_start: 0.2532 (mtp) cc_final: 0.2191 (mtp) REVERT: A 397 ARG cc_start: -0.1164 (OUTLIER) cc_final: -0.1709 (ttm170) REVERT: A 481 GLU cc_start: -0.2330 (OUTLIER) cc_final: -0.2774 (mp0) REVERT: B 26 CYS cc_start: 0.8325 (m) cc_final: 0.7674 (m) REVERT: B 27 GLN cc_start: 0.7891 (mt0) cc_final: 0.7610 (mt0) REVERT: B 28 GLN cc_start: 0.7529 (tp-100) cc_final: 0.7196 (tp40) REVERT: B 37 VAL cc_start: 0.8861 (t) cc_final: 0.8568 (p) REVERT: B 98 GLU cc_start: 0.7464 (tp30) cc_final: 0.7217 (tp30) REVERT: B 101 LYS cc_start: 0.7820 (mptt) cc_final: 0.7528 (mptt) REVERT: B 102 LYS cc_start: 0.8111 (mmtp) cc_final: 0.7778 (mmmt) REVERT: B 113 ASP cc_start: 0.6688 (t0) cc_final: 0.6332 (t0) REVERT: B 142 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7489 (ttp80) REVERT: B 173 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7403 (mtp85) REVERT: B 174 LEU cc_start: 0.8224 (mt) cc_final: 0.7889 (mp) REVERT: B 177 ASP cc_start: 0.7569 (t0) cc_final: 0.7002 (t0) REVERT: B 183 ARG cc_start: 0.8124 (mmm160) cc_final: 0.7898 (mmp80) REVERT: B 186 GLU cc_start: 0.8062 (tt0) cc_final: 0.6938 (tm-30) REVERT: B 189 HIS cc_start: 0.7113 (m-70) cc_final: 0.6723 (m-70) REVERT: B 198 LEU cc_start: 0.8791 (pt) cc_final: 0.8368 (mt) REVERT: B 200 LEU cc_start: 0.8196 (mt) cc_final: 0.7822 (mt) REVERT: B 236 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7716 (ttmm) REVERT: B 270 LEU cc_start: 0.7785 (mm) cc_final: 0.7580 (mm) REVERT: B 272 ARG cc_start: 0.6570 (tpp80) cc_final: 0.6221 (tpp80) REVERT: B 276 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 279 ARG cc_start: 0.7840 (ptp-170) cc_final: 0.7362 (ptp-170) REVERT: B 281 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7210 (tp30) REVERT: B 344 GLU cc_start: 0.8470 (tt0) cc_final: 0.7875 (tm-30) REVERT: B 426 ARG cc_start: 0.3570 (OUTLIER) cc_final: 0.3177 (tpm170) REVERT: B 458 MET cc_start: 0.7629 (mmt) cc_final: 0.7360 (mmt) REVERT: C 9 LEU cc_start: 0.8052 (tp) cc_final: 0.7839 (tp) REVERT: C 27 GLN cc_start: 0.8183 (pp30) cc_final: 0.7837 (pp30) REVERT: C 33 ARG cc_start: 0.7754 (tpp80) cc_final: 0.7064 (tpp80) REVERT: C 46 VAL cc_start: 0.8086 (t) cc_final: 0.7854 (m) REVERT: C 56 LYS cc_start: 0.7715 (tppp) cc_final: 0.7073 (tppp) REVERT: C 70 GLN cc_start: 0.7759 (mt0) cc_final: 0.7293 (mt0) REVERT: C 78 TYR cc_start: 0.8202 (t80) cc_final: 0.7122 (t80) REVERT: C 79 ARG cc_start: 0.7822 (mtp-110) cc_final: 0.7498 (mtp-110) REVERT: C 126 MET cc_start: 0.7441 (mmm) cc_final: 0.6569 (mtp) REVERT: C 128 THR cc_start: 0.8305 (p) cc_final: 0.7970 (t) REVERT: C 132 MET cc_start: 0.7924 (tpp) cc_final: 0.7291 (mpp) REVERT: C 142 ARG cc_start: 0.7506 (ttp-110) cc_final: 0.7243 (ttm-80) REVERT: C 149 ILE cc_start: 0.8529 (mm) cc_final: 0.7981 (mm) REVERT: C 181 ARG cc_start: 0.8238 (ttp80) cc_final: 0.8003 (tmm-80) REVERT: C 199 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.6962 (p-80) REVERT: C 213 PRO cc_start: 0.8202 (Cg_exo) cc_final: 0.7755 (Cg_endo) REVERT: C 228 ARG cc_start: 0.7483 (mtt90) cc_final: 0.7060 (mmm-85) REVERT: C 235 LEU cc_start: 0.8698 (mt) cc_final: 0.8319 (mt) REVERT: C 274 GLN cc_start: 0.8274 (mt0) cc_final: 0.7809 (mt0) REVERT: D 22 GLN cc_start: 0.8277 (mt0) cc_final: 0.7836 (mt0) REVERT: D 25 SER cc_start: 0.7459 (m) cc_final: 0.7168 (p) REVERT: D 72 PHE cc_start: 0.8061 (p90) cc_final: 0.7580 (p90) REVERT: D 73 ASP cc_start: 0.7858 (m-30) cc_final: 0.7383 (m-30) REVERT: D 140 ARG cc_start: 0.7695 (ttp-110) cc_final: 0.7025 (ttp-170) REVERT: D 154 TYR cc_start: 0.7313 (t80) cc_final: 0.6293 (t80) REVERT: D 190 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7297 (ttp80) REVERT: D 206 ASN cc_start: 0.6831 (m-40) cc_final: 0.6585 (m110) REVERT: D 211 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7636 (mm) REVERT: D 221 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8457 (mm-40) REVERT: D 226 GLN cc_start: 0.8483 (mm110) cc_final: 0.8275 (mm110) REVERT: D 230 TRP cc_start: 0.8302 (m100) cc_final: 0.7704 (m100) REVERT: D 236 LYS cc_start: 0.8740 (tttt) cc_final: 0.8339 (tttp) REVERT: D 242 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8082 (mt-10) REVERT: D 247 TYR cc_start: 0.8050 (m-10) cc_final: 0.7679 (m-80) REVERT: D 269 ILE cc_start: 0.8095 (mm) cc_final: 0.7703 (mm) REVERT: D 278 LEU cc_start: 0.8393 (mt) cc_final: 0.8168 (mm) REVERT: D 327 ARG cc_start: 0.8429 (ttt180) cc_final: 0.7855 (ttp80) REVERT: D 328 SER cc_start: 0.8435 (t) cc_final: 0.7033 (p) REVERT: D 331 PHE cc_start: 0.6278 (m-10) cc_final: 0.5322 (m-80) REVERT: D 351 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: D 458 MET cc_start: 0.7690 (mmt) cc_final: 0.6712 (mmt) REVERT: D 459 ASN cc_start: 0.8186 (m110) cc_final: 0.7719 (p0) outliers start: 60 outliers final: 40 residues processed: 447 average time/residue: 0.1759 time to fit residues: 111.8082 Evaluate side-chains 458 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 411 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 251 ASN Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 159 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 54 optimal weight: 0.0980 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 142 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN B 32 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.214599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.167819 restraints weight = 40150.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.167685 restraints weight = 17822.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169069 restraints weight = 11708.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.169625 restraints weight = 9999.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169555 restraints weight = 8613.075| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20302 Z= 0.136 Angle : 0.618 12.553 28362 Z= 0.342 Chirality : 0.042 0.213 3108 Planarity : 0.005 0.108 3020 Dihedral : 23.567 84.279 4299 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.68 % Allowed : 16.58 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.19), residues: 1936 helix: 2.31 (0.17), residues: 919 sheet: -0.27 (0.28), residues: 296 loop : 0.87 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG D 173 TYR 0.026 0.002 TYR D 216 PHE 0.069 0.002 PHE C 303 TRP 0.049 0.001 TRP C 230 HIS 0.009 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (20286) covalent geometry : angle 0.61044 / 0.34 (28338) hydrogen bonds : bond 0.04373 / 3.01 ( 1054) hydrogen bonds : angle 3.76627 / 2.74 ( 2783) metal coordination : bond 0.00410 / 0.27 ( 16) metal coordination : angle 3.43356 / 2.33 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 415 time to evaluate : 0.502 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.7961 (tp) cc_final: 0.7221 (mt) REVERT: A 20 GLU cc_start: 0.7137 (mp0) cc_final: 0.6906 (pm20) REVERT: A 33 ARG cc_start: 0.7676 (mmt90) cc_final: 0.6901 (mmm-85) REVERT: A 51 ASP cc_start: 0.8162 (t0) cc_final: 0.7920 (t0) REVERT: A 65 LEU cc_start: 0.7878 (mt) cc_final: 0.7668 (mp) REVERT: A 128 THR cc_start: 0.8142 (m) cc_final: 0.7524 (m) REVERT: A 131 GLN cc_start: 0.7666 (tt0) cc_final: 0.7283 (tt0) REVERT: A 132 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7526 (mpp) REVERT: A 150 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7696 (ttm-80) REVERT: A 164 LEU cc_start: 0.8414 (mm) cc_final: 0.8102 (mm) REVERT: A 221 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7887 (mp10) REVERT: A 239 MET cc_start: 0.7502 (mmm) cc_final: 0.7234 (mmm) REVERT: A 244 MET cc_start: 0.7769 (mmt) cc_final: 0.7136 (mmt) REVERT: A 276 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7617 (pt0) REVERT: A 342 MET cc_start: 0.2362 (mtp) cc_final: 0.2066 (mtp) REVERT: A 397 ARG cc_start: -0.1175 (OUTLIER) cc_final: -0.1679 (ttm170) REVERT: A 481 GLU cc_start: -0.2336 (OUTLIER) cc_final: -0.2755 (mp0) REVERT: B 26 CYS cc_start: 0.8382 (m) cc_final: 0.7746 (m) REVERT: B 27 GLN cc_start: 0.8000 (mt0) cc_final: 0.7693 (mt0) REVERT: B 28 GLN cc_start: 0.7514 (tp-100) cc_final: 0.7238 (tp40) REVERT: B 37 VAL cc_start: 0.8844 (t) cc_final: 0.8614 (p) REVERT: B 98 GLU cc_start: 0.7509 (tp30) cc_final: 0.7227 (tp30) REVERT: B 101 LYS cc_start: 0.7824 (mptt) cc_final: 0.7378 (mptt) REVERT: B 102 LYS cc_start: 0.8103 (mmtp) cc_final: 0.7813 (mmmt) REVERT: B 113 ASP cc_start: 0.6803 (t0) cc_final: 0.6503 (t0) REVERT: B 142 ARG cc_start: 0.7817 (ttp-110) cc_final: 0.7500 (ttp80) REVERT: B 173 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7368 (mtp85) REVERT: B 174 LEU cc_start: 0.8184 (mt) cc_final: 0.7774 (mp) REVERT: B 177 ASP cc_start: 0.7616 (t0) cc_final: 0.6961 (t0) REVERT: B 186 GLU cc_start: 0.7992 (tt0) cc_final: 0.7357 (tm-30) REVERT: B 189 HIS cc_start: 0.7156 (m-70) cc_final: 0.6795 (m-70) REVERT: B 190 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7560 (mtm180) REVERT: B 196 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7289 (mt-10) REVERT: B 198 LEU cc_start: 0.8778 (pt) cc_final: 0.8391 (mt) REVERT: B 200 LEU cc_start: 0.8146 (mt) cc_final: 0.7772 (mt) REVERT: B 224 GLU cc_start: 0.7035 (pp20) cc_final: 0.6607 (pp20) REVERT: B 236 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7848 (tppp) REVERT: B 270 LEU cc_start: 0.7826 (mm) cc_final: 0.7516 (mm) REVERT: B 272 ARG cc_start: 0.6635 (tpp80) cc_final: 0.6269 (tpp80) REVERT: B 276 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7759 (mt-10) REVERT: B 279 ARG cc_start: 0.7954 (ptp-170) cc_final: 0.7710 (ptp-170) REVERT: B 281 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7272 (tp30) REVERT: B 344 GLU cc_start: 0.8455 (tt0) cc_final: 0.7881 (tm-30) REVERT: B 352 GLN cc_start: 0.8274 (mm-40) cc_final: 0.8060 (mm-40) REVERT: B 426 ARG cc_start: 0.3424 (OUTLIER) cc_final: 0.3046 (tpm170) REVERT: B 458 MET cc_start: 0.7610 (mmt) cc_final: 0.7304 (mmt) REVERT: C 33 ARG cc_start: 0.7672 (tpp80) cc_final: 0.6986 (tpp80) REVERT: C 46 VAL cc_start: 0.8224 (t) cc_final: 0.7983 (m) REVERT: C 56 LYS cc_start: 0.7748 (tppp) cc_final: 0.7065 (tppp) REVERT: C 69 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7134 (mm-30) REVERT: C 70 GLN cc_start: 0.7769 (mt0) cc_final: 0.7337 (mt0) REVERT: C 78 TYR cc_start: 0.8197 (t80) cc_final: 0.7874 (t80) REVERT: C 79 ARG cc_start: 0.7741 (mtp-110) cc_final: 0.7263 (mtp-110) REVERT: C 101 LYS cc_start: 0.8328 (ttmm) cc_final: 0.8097 (ttmm) REVERT: C 126 MET cc_start: 0.7526 (mmm) cc_final: 0.6529 (mtp) REVERT: C 128 THR cc_start: 0.8318 (p) cc_final: 0.7605 (t) REVERT: C 132 MET cc_start: 0.7902 (tpp) cc_final: 0.6931 (mpp) REVERT: C 142 ARG cc_start: 0.7569 (ttp-110) cc_final: 0.7295 (ttm-80) REVERT: C 181 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7992 (ttp80) REVERT: C 199 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.6933 (p-80) REVERT: C 228 ARG cc_start: 0.7537 (mtt90) cc_final: 0.7069 (mmm-85) REVERT: C 235 LEU cc_start: 0.8653 (mt) cc_final: 0.8448 (mm) REVERT: C 274 GLN cc_start: 0.8326 (mt0) cc_final: 0.7828 (mt0) REVERT: C 342 MET cc_start: 0.4871 (mmm) cc_final: 0.4580 (mmm) REVERT: D 22 GLN cc_start: 0.8224 (mt0) cc_final: 0.7631 (mt0) REVERT: D 25 SER cc_start: 0.7496 (m) cc_final: 0.7207 (p) REVERT: D 72 PHE cc_start: 0.8027 (p90) cc_final: 0.7483 (p90) REVERT: D 73 ASP cc_start: 0.7646 (m-30) cc_final: 0.7220 (m-30) REVERT: D 125 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7776 (tp) REVERT: D 168 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7723 (m) REVERT: D 177 ASP cc_start: 0.6262 (t0) cc_final: 0.5782 (t0) REVERT: D 190 ARG cc_start: 0.8113 (mtp85) cc_final: 0.7315 (ttp80) REVERT: D 206 ASN cc_start: 0.6780 (m-40) cc_final: 0.6378 (m110) REVERT: D 226 GLN cc_start: 0.8494 (mm110) cc_final: 0.8226 (mm110) REVERT: D 230 TRP cc_start: 0.8248 (m100) cc_final: 0.7657 (m100) REVERT: D 235 LEU cc_start: 0.8919 (mt) cc_final: 0.8672 (mt) REVERT: D 236 LYS cc_start: 0.8729 (tttt) cc_final: 0.8374 (tttp) REVERT: D 242 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7784 (mt-10) REVERT: D 247 TYR cc_start: 0.8060 (m-10) cc_final: 0.7396 (m-10) REVERT: D 269 ILE cc_start: 0.8145 (mm) cc_final: 0.7757 (mm) REVERT: D 278 LEU cc_start: 0.8402 (mt) cc_final: 0.8159 (mm) REVERT: D 327 ARG cc_start: 0.8401 (ttt180) cc_final: 0.8026 (ttp80) REVERT: D 351 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: D 409 ARG cc_start: 0.8138 (ttt180) cc_final: 0.7925 (tpt-90) REVERT: D 458 MET cc_start: 0.7670 (mmt) cc_final: 0.6684 (mmt) REVERT: D 459 ASN cc_start: 0.8200 (m110) cc_final: 0.7734 (p0) outliers start: 59 outliers final: 41 residues processed: 448 average time/residue: 0.1587 time to fit residues: 101.9589 Evaluate side-chains 456 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 407 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 99 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 44 optimal weight: 50.0000 chunk 163 optimal weight: 6.9990 chunk 38 optimal weight: 30.0000 chunk 161 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 60 ASN A 91 GLN A 194 ASN A 219 GLN B 32 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS D 146 HIS ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.210033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.161606 restraints weight = 39908.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.161575 restraints weight = 22222.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.161940 restraints weight = 14062.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162721 restraints weight = 13268.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163431 restraints weight = 10045.783| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 20302 Z= 0.243 Angle : 0.691 15.116 28362 Z= 0.378 Chirality : 0.046 0.260 3108 Planarity : 0.005 0.059 3020 Dihedral : 23.635 85.633 4295 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.24 % Allowed : 17.21 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.19), residues: 1936 helix: 2.08 (0.16), residues: 919 sheet: -0.44 (0.28), residues: 284 loop : 0.66 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 327 TYR 0.025 0.002 TYR B 188 PHE 0.037 0.002 PHE C 303 TRP 0.029 0.002 TRP A 230 HIS 0.010 0.002 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.24 (20286) covalent geometry : angle 0.68197 / 0.38 (28338) hydrogen bonds : bond 0.05229 / 3.56 ( 1054) hydrogen bonds : angle 3.94610 / 2.88 ( 2783) metal coordination : bond 0.00767 / 0.50 ( 16) metal coordination : angle 3.83380 / 2.26 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 421 time to evaluate : 0.523 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: 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: symmetry clash REVERT: A 7 ILE cc_start: 0.7969 (mt) cc_final: 0.7682 (mm) REVERT: A 9 LEU cc_start: 0.8288 (tp) cc_final: 0.7616 (mt) REVERT: A 33 ARG cc_start: 0.7759 (mmt90) cc_final: 0.7151 (tpp80) REVERT: A 111 HIS cc_start: 0.8007 (p-80) cc_final: 0.7724 (p-80) REVERT: A 131 GLN cc_start: 0.8007 (tt0) cc_final: 0.7645 (tt0) REVERT: A 221 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7915 (mp10) REVERT: A 244 MET cc_start: 0.7841 (mmt) cc_final: 0.7237 (mmt) REVERT: A 276 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7637 (pt0) REVERT: A 342 MET cc_start: 0.2372 (mtp) cc_final: 0.2086 (mtp) REVERT: A 377 LEU cc_start: 0.5327 (OUTLIER) cc_final: 0.4325 (mp) REVERT: A 481 GLU cc_start: -0.1903 (OUTLIER) cc_final: -0.2386 (mp0) REVERT: B 21 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7993 (mmm160) REVERT: B 26 CYS cc_start: 0.8464 (m) cc_final: 0.7864 (m) REVERT: B 27 GLN cc_start: 0.8035 (mt0) cc_final: 0.7715 (mt0) REVERT: B 28 GLN cc_start: 0.7549 (tp-100) cc_final: 0.7282 (tp40) REVERT: B 37 VAL cc_start: 0.8985 (t) cc_final: 0.8736 (p) REVERT: B 42 GLU cc_start: 0.7289 (tt0) cc_final: 0.6930 (mm-30) REVERT: B 98 GLU cc_start: 0.7469 (tp30) cc_final: 0.7194 (tp30) REVERT: B 101 LYS cc_start: 0.8025 (mptt) cc_final: 0.7756 (mptt) REVERT: B 102 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7808 (mmmt) REVERT: B 142 ARG cc_start: 0.7931 (ttp-110) cc_final: 0.7574 (ttp80) REVERT: B 147 PHE cc_start: 0.8082 (t80) cc_final: 0.7877 (t80) REVERT: B 149 ILE cc_start: 0.7830 (mt) cc_final: 0.7385 (tp) REVERT: B 177 ASP cc_start: 0.7800 (t0) cc_final: 0.7130 (t70) REVERT: B 189 HIS cc_start: 0.7273 (m-70) cc_final: 0.6820 (m-70) REVERT: B 190 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7574 (mtm-85) REVERT: B 196 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7274 (mt-10) REVERT: B 198 LEU cc_start: 0.8796 (pt) cc_final: 0.8520 (mt) REVERT: B 200 LEU cc_start: 0.8289 (mt) cc_final: 0.7847 (mt) REVERT: B 210 VAL cc_start: 0.7878 (t) cc_final: 0.7632 (p) REVERT: B 229 GLU cc_start: 0.6950 (mp0) cc_final: 0.6692 (mp0) REVERT: B 245 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8476 (tt) REVERT: B 276 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 281 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7343 (tp30) REVERT: B 344 GLU cc_start: 0.8578 (tt0) cc_final: 0.7933 (tm-30) REVERT: B 426 ARG cc_start: 0.3193 (OUTLIER) cc_final: 0.2841 (tpm170) REVERT: B 458 MET cc_start: 0.7681 (mmt) cc_final: 0.7349 (mmt) REVERT: C 27 GLN cc_start: 0.7958 (pp30) cc_final: 0.7713 (pp30) REVERT: C 29 LEU cc_start: 0.7340 (tp) cc_final: 0.7076 (tt) REVERT: C 33 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7102 (tpp80) REVERT: C 56 LYS cc_start: 0.7801 (tppp) cc_final: 0.7175 (tppp) REVERT: C 69 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7084 (mm-30) REVERT: C 70 GLN cc_start: 0.7800 (mt0) cc_final: 0.7409 (mt0) REVERT: C 78 TYR cc_start: 0.8190 (t80) cc_final: 0.7304 (t80) REVERT: C 79 ARG cc_start: 0.7754 (mtp-110) cc_final: 0.7152 (mtp-110) REVERT: C 101 LYS cc_start: 0.8297 (ttmm) cc_final: 0.8049 (ttmm) REVERT: C 126 MET cc_start: 0.7636 (mmm) cc_final: 0.6768 (mtp) REVERT: C 128 THR cc_start: 0.8173 (p) cc_final: 0.7838 (t) REVERT: C 132 MET cc_start: 0.7997 (tpp) cc_final: 0.7422 (mpp) REVERT: C 142 ARG cc_start: 0.7757 (ttp-110) cc_final: 0.7503 (ttm-80) REVERT: C 147 PHE cc_start: 0.7397 (t80) cc_final: 0.7135 (t80) REVERT: C 174 LEU cc_start: 0.7357 (mt) cc_final: 0.7129 (mt) REVERT: C 181 ARG cc_start: 0.8285 (ttp80) cc_final: 0.8045 (tmm-80) REVERT: C 199 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.6961 (p-80) REVERT: C 228 ARG cc_start: 0.7559 (mtt90) cc_final: 0.7041 (mmm-85) REVERT: C 235 LEU cc_start: 0.8635 (mt) cc_final: 0.8426 (mt) REVERT: C 274 GLN cc_start: 0.8350 (mt0) cc_final: 0.7862 (mt0) REVERT: C 342 MET cc_start: 0.5106 (mmm) cc_final: 0.4705 (mmm) REVERT: D 17 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7660 (p) REVERT: D 20 GLU cc_start: 0.8265 (mp0) cc_final: 0.7974 (mp0) REVERT: D 22 GLN cc_start: 0.8316 (mt0) cc_final: 0.7767 (mt0) REVERT: D 25 SER cc_start: 0.7561 (m) cc_final: 0.7302 (p) REVERT: D 42 GLU cc_start: 0.7583 (tp30) cc_final: 0.7179 (tp30) REVERT: D 43 ASP cc_start: 0.7861 (t0) cc_final: 0.7576 (t0) REVERT: D 68 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7312 (mm-30) REVERT: D 72 PHE cc_start: 0.8085 (p90) cc_final: 0.7569 (p90) REVERT: D 73 ASP cc_start: 0.7802 (m-30) cc_final: 0.7370 (m-30) REVERT: D 101 LYS cc_start: 0.8226 (mmtt) cc_final: 0.8006 (mmtt) REVERT: D 109 GLU cc_start: 0.7615 (mp0) cc_final: 0.7283 (mt-10) REVERT: D 125 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7726 (tp) REVERT: D 135 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7184 (tp30) REVERT: D 140 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.7148 (ttp-170) REVERT: D 158 LEU cc_start: 0.8930 (tp) cc_final: 0.8676 (tt) REVERT: D 168 VAL cc_start: 0.7944 (OUTLIER) cc_final: 0.7642 (p) REVERT: D 183 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8054 (tpp80) REVERT: D 190 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7389 (ttp80) REVERT: D 206 ASN cc_start: 0.6690 (m-40) cc_final: 0.6423 (m110) REVERT: D 211 LEU cc_start: 0.7993 (mm) cc_final: 0.7583 (mm) REVERT: D 226 GLN cc_start: 0.8503 (mm110) cc_final: 0.8075 (mm110) REVERT: D 230 TRP cc_start: 0.8310 (m100) cc_final: 0.7282 (m100) REVERT: D 235 LEU cc_start: 0.8943 (mt) cc_final: 0.8651 (mm) REVERT: D 242 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7893 (mt-10) REVERT: D 247 TYR cc_start: 0.8027 (m-10) cc_final: 0.7488 (m-10) REVERT: D 269 ILE cc_start: 0.8104 (mm) cc_final: 0.7803 (mm) REVERT: D 278 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8183 (mm) REVERT: D 309 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6066 (mp0) REVERT: D 327 ARG cc_start: 0.8383 (ttt180) cc_final: 0.8183 (ttp80) REVERT: D 350 GLU cc_start: 0.8341 (pt0) cc_final: 0.7680 (mt-10) REVERT: D 351 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: D 409 ARG cc_start: 0.8232 (ttt180) cc_final: 0.7994 (tpt-90) REVERT: D 458 MET cc_start: 0.7807 (mmt) cc_final: 0.7515 (mmt) outliers start: 68 outliers final: 49 residues processed: 458 average time/residue: 0.1536 time to fit residues: 100.5378 Evaluate side-chains 472 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 412 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 251 ASN Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 146 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 126 optimal weight: 30.0000 chunk 158 optimal weight: 0.9980 chunk 200 optimal weight: 50.0000 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 30 optimal weight: 40.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.211412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.163874 restraints weight = 39771.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163102 restraints weight = 17674.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.164482 restraints weight = 11926.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.164913 restraints weight = 10298.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.164856 restraints weight = 9283.226| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20302 Z= 0.193 Angle : 0.674 20.781 28362 Z= 0.363 Chirality : 0.043 0.215 3108 Planarity : 0.006 0.099 3020 Dihedral : 23.661 85.111 4291 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.24 % Allowed : 18.14 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.19), residues: 1936 helix: 2.14 (0.17), residues: 920 sheet: -0.48 (0.28), residues: 282 loop : 0.60 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 150 TYR 0.024 0.002 TYR D 216 PHE 0.034 0.002 PHE C 303 TRP 0.060 0.002 TRP C 230 HIS 0.011 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.19 (20286) covalent geometry : angle 0.66708 / 0.36 (28338) hydrogen bonds : bond 0.04764 / 3.25 ( 1054) hydrogen bonds : angle 3.87215 / 2.82 ( 2783) metal coordination : bond 0.00553 / 0.34 ( 16) metal coordination : angle 3.46323 / 2.13 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 414 time to evaluate : 0.465 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: 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: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8341 (mt) cc_final: 0.8028 (mm) REVERT: A 9 LEU cc_start: 0.8285 (tp) cc_final: 0.7651 (mt) REVERT: A 23 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8203 (mm) REVERT: A 33 ARG cc_start: 0.7726 (mmt90) cc_final: 0.7129 (tpp80) REVERT: A 98 GLU cc_start: 0.6549 (tm-30) cc_final: 0.6082 (tm-30) REVERT: A 111 HIS cc_start: 0.8019 (p-80) cc_final: 0.7142 (p-80) REVERT: A 128 THR cc_start: 0.8272 (m) cc_final: 0.8045 (t) REVERT: A 131 GLN cc_start: 0.8015 (tt0) cc_final: 0.7680 (tp40) REVERT: A 132 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7607 (mpp) REVERT: A 139 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7422 (mm-30) REVERT: A 164 LEU cc_start: 0.8531 (mm) cc_final: 0.8301 (mm) REVERT: A 177 ASP cc_start: 0.8024 (t70) cc_final: 0.6991 (p0) REVERT: A 221 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7879 (mp10) REVERT: A 239 MET cc_start: 0.7677 (mmm) cc_final: 0.7473 (mmt) REVERT: A 244 MET cc_start: 0.7801 (mmt) cc_final: 0.7222 (mmt) REVERT: A 276 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7649 (pt0) REVERT: A 342 MET cc_start: 0.2436 (mtp) cc_final: 0.2161 (mtp) REVERT: A 377 LEU cc_start: 0.5126 (OUTLIER) cc_final: 0.4095 (mp) REVERT: A 481 GLU cc_start: -0.1932 (OUTLIER) cc_final: -0.2389 (mp0) REVERT: B 11 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7580 (mmm-85) REVERT: B 21 ARG cc_start: 0.8167 (mmm-85) cc_final: 0.7955 (mmm160) REVERT: B 26 CYS cc_start: 0.8452 (m) cc_final: 0.7819 (m) REVERT: B 27 GLN cc_start: 0.7959 (mt0) cc_final: 0.7639 (mt0) REVERT: B 28 GLN cc_start: 0.7557 (tp-100) cc_final: 0.7273 (tp40) REVERT: B 37 VAL cc_start: 0.8973 (t) cc_final: 0.8735 (p) REVERT: B 101 LYS cc_start: 0.8051 (mptt) cc_final: 0.7682 (mptt) REVERT: B 102 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7803 (mmmt) REVERT: B 109 GLU cc_start: 0.7869 (mp0) cc_final: 0.7660 (mp0) REVERT: B 142 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7574 (ttp80) REVERT: B 149 ILE cc_start: 0.7786 (mt) cc_final: 0.7296 (tp) REVERT: B 173 ARG cc_start: 0.7989 (ttm110) cc_final: 0.7249 (mtp85) REVERT: B 174 LEU cc_start: 0.8073 (mp) cc_final: 0.7864 (mp) REVERT: B 177 ASP cc_start: 0.7819 (t0) cc_final: 0.7107 (t70) REVERT: B 186 GLU cc_start: 0.7993 (tt0) cc_final: 0.7414 (tm-30) REVERT: B 189 HIS cc_start: 0.7213 (m-70) cc_final: 0.6767 (m-70) REVERT: B 196 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7504 (mp0) REVERT: B 198 LEU cc_start: 0.8751 (pt) cc_final: 0.8507 (mt) REVERT: B 200 LEU cc_start: 0.8249 (mt) cc_final: 0.7901 (mt) REVERT: B 229 GLU cc_start: 0.6961 (mp0) cc_final: 0.6626 (mp0) REVERT: B 245 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8472 (tt) REVERT: B 276 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7734 (mt-10) REVERT: B 279 ARG cc_start: 0.7831 (ptp-170) cc_final: 0.7375 (ptp-170) REVERT: B 281 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7304 (tp30) REVERT: B 283 VAL cc_start: 0.6818 (OUTLIER) cc_final: 0.6553 (p) REVERT: B 344 GLU cc_start: 0.8569 (tt0) cc_final: 0.7893 (tm-30) REVERT: B 416 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7874 (mmm160) REVERT: B 426 ARG cc_start: 0.3215 (OUTLIER) cc_final: 0.2855 (tpm170) REVERT: B 458 MET cc_start: 0.7615 (mmt) cc_final: 0.7324 (mmt) REVERT: B 461 ARG cc_start: 0.7255 (mmt180) cc_final: 0.6970 (mmp80) REVERT: C 20 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7696 (mp0) REVERT: C 27 GLN cc_start: 0.7956 (pp30) cc_final: 0.7643 (pp30) REVERT: C 33 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7056 (tpp80) REVERT: C 56 LYS cc_start: 0.7790 (tppp) cc_final: 0.7148 (tppp) REVERT: C 70 GLN cc_start: 0.7783 (mt0) cc_final: 0.7443 (mt0) REVERT: C 79 ARG cc_start: 0.7631 (mtp-110) cc_final: 0.7153 (mtp-110) REVERT: C 126 MET cc_start: 0.7602 (mmm) cc_final: 0.6818 (mtp) REVERT: C 128 THR cc_start: 0.8150 (p) cc_final: 0.7840 (t) REVERT: C 132 MET cc_start: 0.7991 (tpp) cc_final: 0.7497 (mpp) REVERT: C 142 ARG cc_start: 0.7722 (ttp-110) cc_final: 0.7448 (ttm-80) REVERT: C 147 PHE cc_start: 0.7344 (t80) cc_final: 0.7075 (t80) REVERT: C 174 LEU cc_start: 0.7392 (mt) cc_final: 0.7107 (mt) REVERT: C 181 ARG cc_start: 0.8296 (ttp80) cc_final: 0.8021 (tmm-80) REVERT: C 199 HIS cc_start: 0.7543 (OUTLIER) cc_final: 0.6798 (p-80) REVERT: C 228 ARG cc_start: 0.7522 (mtt90) cc_final: 0.7045 (mmm-85) REVERT: C 274 GLN cc_start: 0.8359 (mt0) cc_final: 0.7859 (mt0) REVERT: C 342 MET cc_start: 0.5195 (mmm) cc_final: 0.4794 (mmm) REVERT: D 17 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7569 (p) REVERT: D 22 GLN cc_start: 0.8304 (mt0) cc_final: 0.7753 (mt0) REVERT: D 25 SER cc_start: 0.7563 (m) cc_final: 0.7290 (p) REVERT: D 42 GLU cc_start: 0.7575 (tp30) cc_final: 0.6850 (tp30) REVERT: D 68 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7301 (mm-30) REVERT: D 72 PHE cc_start: 0.8076 (p90) cc_final: 0.7573 (p90) REVERT: D 73 ASP cc_start: 0.7793 (m-30) cc_final: 0.7388 (m-30) REVERT: D 98 GLU cc_start: 0.6920 (tp30) cc_final: 0.6479 (tp30) REVERT: D 101 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7986 (mmtt) REVERT: D 109 GLU cc_start: 0.7575 (mp0) cc_final: 0.7292 (mt-10) REVERT: D 125 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7688 (tp) REVERT: D 135 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7218 (tp30) REVERT: D 139 GLU cc_start: 0.7676 (tp30) cc_final: 0.7127 (tp30) REVERT: D 140 ARG cc_start: 0.7781 (ttp-110) cc_final: 0.7215 (ttp-170) REVERT: D 158 LEU cc_start: 0.8870 (tp) cc_final: 0.8566 (tt) REVERT: D 183 ARG cc_start: 0.8476 (tpp80) cc_final: 0.8242 (tpp80) REVERT: D 190 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7441 (ttp-170) REVERT: D 206 ASN cc_start: 0.6680 (m-40) cc_final: 0.6415 (m110) REVERT: D 226 GLN cc_start: 0.8345 (mm110) cc_final: 0.8059 (mm110) REVERT: D 235 LEU cc_start: 0.8906 (mt) cc_final: 0.8616 (mm) REVERT: D 236 LYS cc_start: 0.8577 (tttp) cc_final: 0.8280 (tttp) REVERT: D 242 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7884 (mt-10) REVERT: D 247 TYR cc_start: 0.7999 (m-10) cc_final: 0.7417 (m-10) REVERT: D 269 ILE cc_start: 0.8141 (mm) cc_final: 0.7797 (mm) REVERT: D 278 LEU cc_start: 0.8413 (mt) cc_final: 0.8159 (mm) REVERT: D 309 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6058 (mp0) REVERT: D 327 ARG cc_start: 0.8369 (ttt180) cc_final: 0.8148 (ttp80) REVERT: D 351 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: D 367 TRP cc_start: 0.6805 (t-100) cc_final: 0.6252 (t-100) REVERT: D 458 MET cc_start: 0.7694 (mmt) cc_final: 0.7444 (mmt) outliers start: 68 outliers final: 44 residues processed: 450 average time/residue: 0.1589 time to fit residues: 102.1280 Evaluate side-chains 470 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 414 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 251 ASN Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 25 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 ASN B 32 GLN B 206 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.206021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155787 restraints weight = 39307.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.155924 restraints weight = 17642.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.156584 restraints weight = 12512.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157057 restraints weight = 10205.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.157167 restraints weight = 8816.484| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 20302 Z= 0.322 Angle : 0.768 15.669 28362 Z= 0.416 Chirality : 0.048 0.299 3108 Planarity : 0.006 0.077 3020 Dihedral : 23.740 86.158 4283 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.36 % Allowed : 18.70 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 1936 helix: 1.67 (0.16), residues: 913 sheet: -0.81 (0.27), residues: 295 loop : 0.24 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 11 TYR 0.021 0.002 TYR B 188 PHE 0.033 0.003 PHE B 348 TRP 0.058 0.003 TRP C 230 HIS 0.012 0.002 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.32 (20286) covalent geometry : angle 0.76284 / 0.42 (28338) hydrogen bonds : bond 0.05930 / 4.02 ( 1054) hydrogen bonds : angle 4.22731 / 3.08 ( 2783) metal coordination : bond 0.00787 / 0.46 ( 16) metal coordination : angle 3.22798 / 2.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 426 time to evaluate : 0.372 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8163 (mt) cc_final: 0.7809 (mm) REVERT: A 9 LEU cc_start: 0.8343 (tp) cc_final: 0.7656 (mt) REVERT: A 139 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7053 (tm-30) REVERT: A 164 LEU cc_start: 0.8600 (mm) cc_final: 0.8381 (mm) REVERT: A 177 ASP cc_start: 0.8082 (t70) cc_final: 0.7874 (t0) REVERT: A 183 ARG cc_start: 0.8453 (mmt-90) cc_final: 0.8149 (mmm160) REVERT: A 186 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 244 MET cc_start: 0.7900 (mmt) cc_final: 0.7338 (mmt) REVERT: A 276 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7691 (pt0) REVERT: A 342 MET cc_start: 0.2416 (mtp) cc_final: 0.2151 (mtp) REVERT: A 377 LEU cc_start: 0.5109 (OUTLIER) cc_final: 0.4094 (mp) REVERT: A 481 GLU cc_start: -0.1902 (OUTLIER) cc_final: -0.2355 (mp0) REVERT: B 26 CYS cc_start: 0.8396 (m) cc_final: 0.7627 (m) REVERT: B 27 GLN cc_start: 0.7915 (mt0) cc_final: 0.7486 (mt0) REVERT: B 30 CYS cc_start: 0.6906 (m) cc_final: 0.6640 (m) REVERT: B 37 VAL cc_start: 0.8912 (t) cc_final: 0.8701 (p) REVERT: B 78 TYR cc_start: 0.8505 (t80) cc_final: 0.8170 (t80) REVERT: B 101 LYS cc_start: 0.8160 (mptt) cc_final: 0.7717 (mptt) REVERT: B 142 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7662 (ttp80) REVERT: B 177 ASP cc_start: 0.7767 (t0) cc_final: 0.7125 (t70) REVERT: B 186 GLU cc_start: 0.7827 (tt0) cc_final: 0.7466 (tm-30) REVERT: B 189 HIS cc_start: 0.7216 (m-70) cc_final: 0.6861 (m-70) REVERT: B 194 ASN cc_start: 0.8434 (m-40) cc_final: 0.7954 (m-40) REVERT: B 196 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7395 (mp0) REVERT: B 200 LEU cc_start: 0.8443 (mt) cc_final: 0.8125 (mt) REVERT: B 236 LYS cc_start: 0.8620 (tttp) cc_final: 0.8091 (tppt) REVERT: B 245 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8630 (tt) REVERT: B 263 LEU cc_start: 0.8289 (tp) cc_final: 0.7701 (pp) REVERT: B 276 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7744 (mt-10) REVERT: B 279 ARG cc_start: 0.7843 (ptp-170) cc_final: 0.7388 (ptp-170) REVERT: B 281 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: B 282 LEU cc_start: 0.8520 (mp) cc_final: 0.8256 (mt) REVERT: B 283 VAL cc_start: 0.7017 (OUTLIER) cc_final: 0.6729 (p) REVERT: B 344 GLU cc_start: 0.8619 (tt0) cc_final: 0.7934 (tm-30) REVERT: B 416 ARG cc_start: 0.8245 (mmm160) cc_final: 0.7869 (mmm160) REVERT: B 452 ASN cc_start: 0.8655 (t0) cc_final: 0.7680 (t0) REVERT: B 456 ARG cc_start: 0.8568 (ptp-110) cc_final: 0.8201 (ptp-110) REVERT: B 458 MET cc_start: 0.7791 (mmt) cc_final: 0.7501 (mmt) REVERT: C 27 GLN cc_start: 0.7932 (pp30) cc_final: 0.7603 (pp30) REVERT: C 43 ASP cc_start: 0.7514 (m-30) cc_final: 0.7179 (m-30) REVERT: C 45 ASP cc_start: 0.7133 (t0) cc_final: 0.6730 (t0) REVERT: C 56 LYS cc_start: 0.7825 (tppp) cc_final: 0.7209 (tppp) REVERT: C 70 GLN cc_start: 0.7844 (mt0) cc_final: 0.7506 (mt0) REVERT: C 79 ARG cc_start: 0.7658 (mtp-110) cc_final: 0.7373 (mtp-110) REVERT: C 142 ARG cc_start: 0.7772 (ttp-110) cc_final: 0.7527 (ttm-80) REVERT: C 147 PHE cc_start: 0.7396 (t80) cc_final: 0.7183 (t80) REVERT: C 149 ILE cc_start: 0.8574 (mm) cc_final: 0.8364 (mm) REVERT: C 174 LEU cc_start: 0.7434 (mt) cc_final: 0.7143 (mt) REVERT: C 181 ARG cc_start: 0.8285 (ttp80) cc_final: 0.8038 (tmm-80) REVERT: C 199 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.6872 (p-80) REVERT: C 228 ARG cc_start: 0.7520 (mtt90) cc_final: 0.6998 (mmm-85) REVERT: C 274 GLN cc_start: 0.8289 (mt0) cc_final: 0.7977 (mt0) REVERT: C 276 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8340 (mp0) REVERT: C 329 MET cc_start: 0.4372 (tmm) cc_final: 0.3862 (pmm) REVERT: C 342 MET cc_start: 0.5161 (OUTLIER) cc_final: 0.4837 (mmm) REVERT: D 17 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7396 (p) REVERT: D 20 GLU cc_start: 0.8264 (mp0) cc_final: 0.7881 (mp0) REVERT: D 22 GLN cc_start: 0.8419 (mt0) cc_final: 0.7913 (mt0) REVERT: D 25 SER cc_start: 0.7672 (m) cc_final: 0.7245 (p) REVERT: D 42 GLU cc_start: 0.7716 (tp30) cc_final: 0.7299 (tp30) REVERT: D 68 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7367 (mm-30) REVERT: D 72 PHE cc_start: 0.8108 (p90) cc_final: 0.7676 (p90) REVERT: D 73 ASP cc_start: 0.7708 (m-30) cc_final: 0.7330 (m-30) REVERT: D 135 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7161 (tp30) REVERT: D 140 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7091 (ttp-170) REVERT: D 158 LEU cc_start: 0.8749 (tp) cc_final: 0.8466 (tt) REVERT: D 181 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.6917 (ttm-80) REVERT: D 183 ARG cc_start: 0.8547 (tpp80) cc_final: 0.8304 (tpp80) REVERT: D 190 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7629 (tpp80) REVERT: D 224 GLU cc_start: 0.8283 (pm20) cc_final: 0.8012 (pm20) REVERT: D 235 LEU cc_start: 0.8853 (mt) cc_final: 0.8601 (mm) REVERT: D 237 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7522 (ttp-110) REVERT: D 242 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7905 (mt-10) REVERT: D 247 TYR cc_start: 0.7918 (m-10) cc_final: 0.7452 (m-10) REVERT: D 267 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7154 (tm-30) REVERT: D 269 ILE cc_start: 0.8127 (mm) cc_final: 0.7718 (mm) REVERT: D 278 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8179 (mm) REVERT: D 309 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6178 (mp0) REVERT: D 327 ARG cc_start: 0.8413 (ttt180) cc_final: 0.8123 (ttp80) REVERT: D 351 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: D 367 TRP cc_start: 0.6895 (t-100) cc_final: 0.6525 (t-100) REVERT: D 458 MET cc_start: 0.7869 (mmt) cc_final: 0.7636 (mmt) outliers start: 70 outliers final: 53 residues processed: 460 average time/residue: 0.1556 time to fit residues: 102.7306 Evaluate side-chains 478 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 414 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 251 ASN Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 60 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 46 optimal weight: 50.0000 chunk 207 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 160 optimal weight: 0.4980 chunk 18 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 GLN B 206 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.212759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.165604 restraints weight = 39513.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.165179 restraints weight = 17985.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.165691 restraints weight = 13300.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.166246 restraints weight = 11212.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166487 restraints weight = 9826.454| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20302 Z= 0.145 Angle : 0.676 17.159 28362 Z= 0.360 Chirality : 0.043 0.337 3108 Planarity : 0.005 0.065 3020 Dihedral : 23.705 84.703 4283 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.30 % Allowed : 20.07 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.19), residues: 1936 helix: 2.08 (0.17), residues: 916 sheet: -0.62 (0.28), residues: 292 loop : 0.40 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 237 TYR 0.022 0.002 TYR D 216 PHE 0.027 0.002 PHE C 303 TRP 0.058 0.002 TRP C 230 HIS 0.009 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (20286) covalent geometry : angle 0.66960 / 0.36 (28338) hydrogen bonds : bond 0.04450 / 3.05 ( 1054) hydrogen bonds : angle 3.88532 / 2.84 ( 2783) metal coordination : bond 0.00344 / 0.23 ( 16) metal coordination : angle 3.15522 / 2.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 417 time to evaluate : 0.622 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: 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: A 7 ILE cc_start: 0.8269 (mt) cc_final: 0.7945 (mm) REVERT: A 9 LEU cc_start: 0.8257 (tp) cc_final: 0.7692 (mt) REVERT: A 24 GLU cc_start: 0.6762 (tp30) cc_final: 0.6456 (tm-30) REVERT: A 33 ARG cc_start: 0.7711 (mmt90) cc_final: 0.7097 (tpp80) REVERT: A 42 GLU cc_start: 0.5910 (tp30) cc_final: 0.5321 (tp30) REVERT: A 72 PHE cc_start: 0.7647 (p90) cc_final: 0.6720 (p90) REVERT: A 102 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7587 (mmmm) REVERT: A 139 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7109 (tm-30) REVERT: A 142 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7354 (ttp80) REVERT: A 244 MET cc_start: 0.7831 (mmt) cc_final: 0.7299 (mmt) REVERT: A 276 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7678 (pt0) REVERT: A 342 MET cc_start: 0.2411 (mtp) cc_final: 0.2166 (mtp) REVERT: A 377 LEU cc_start: 0.5087 (OUTLIER) cc_final: 0.4072 (mp) REVERT: A 481 GLU cc_start: -0.1926 (OUTLIER) cc_final: -0.2366 (mp0) REVERT: B 26 CYS cc_start: 0.8441 (m) cc_final: 0.7876 (m) REVERT: B 27 GLN cc_start: 0.7987 (mt0) cc_final: 0.7656 (mt0) REVERT: B 28 GLN cc_start: 0.7639 (tp-100) cc_final: 0.7344 (tp-100) REVERT: B 32 GLN cc_start: 0.7679 (tp40) cc_final: 0.7445 (tm-30) REVERT: B 98 GLU cc_start: 0.7481 (tp30) cc_final: 0.7191 (tp30) REVERT: B 101 LYS cc_start: 0.8095 (mptt) cc_final: 0.7727 (mptt) REVERT: B 142 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7567 (ttp80) REVERT: B 149 ILE cc_start: 0.7723 (mt) cc_final: 0.7350 (tp) REVERT: B 173 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7234 (mtt-85) REVERT: B 177 ASP cc_start: 0.7860 (t0) cc_final: 0.7090 (t70) REVERT: B 186 GLU cc_start: 0.7994 (tt0) cc_final: 0.7585 (tt0) REVERT: B 189 HIS cc_start: 0.7221 (m-70) cc_final: 0.6742 (m-70) REVERT: B 190 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7698 (mmm-85) REVERT: B 196 GLU cc_start: 0.7808 (mt-10) cc_final: 0.6874 (mt-10) REVERT: B 245 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8529 (tt) REVERT: B 263 LEU cc_start: 0.8235 (tp) cc_final: 0.7630 (pp) REVERT: B 276 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7804 (mt-10) REVERT: B 281 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7203 (tm-30) REVERT: B 344 GLU cc_start: 0.8580 (tt0) cc_final: 0.7832 (tm-30) REVERT: B 348 PHE cc_start: 0.8719 (t80) cc_final: 0.8394 (t80) REVERT: B 351 GLU cc_start: 0.8831 (pt0) cc_final: 0.8340 (pt0) REVERT: B 376 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7252 (tp30) REVERT: B 383 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8186 (mt-10) REVERT: B 416 ARG cc_start: 0.8236 (mmm160) cc_final: 0.7880 (mmm160) REVERT: B 452 ASN cc_start: 0.8642 (t0) cc_final: 0.7690 (t0) REVERT: B 456 ARG cc_start: 0.8475 (ptp-110) cc_final: 0.7975 (mmm-85) REVERT: B 458 MET cc_start: 0.7560 (mmt) cc_final: 0.7268 (mmt) REVERT: C 27 GLN cc_start: 0.8049 (pp30) cc_final: 0.7582 (pp30) REVERT: C 45 ASP cc_start: 0.7077 (t0) cc_final: 0.6676 (t0) REVERT: C 56 LYS cc_start: 0.7836 (tppp) cc_final: 0.7164 (tppp) REVERT: C 70 GLN cc_start: 0.7735 (mt0) cc_final: 0.7343 (mt0) REVERT: C 132 MET cc_start: 0.7980 (tpp) cc_final: 0.7335 (mpp) REVERT: C 142 ARG cc_start: 0.7782 (ttp-110) cc_final: 0.7339 (mtp-110) REVERT: C 147 PHE cc_start: 0.7326 (t80) cc_final: 0.7067 (t80) REVERT: C 174 LEU cc_start: 0.7379 (mt) cc_final: 0.7110 (mt) REVERT: C 181 ARG cc_start: 0.8275 (ttp80) cc_final: 0.8047 (tmm-80) REVERT: C 185 LEU cc_start: 0.9112 (mm) cc_final: 0.8791 (mm) REVERT: C 199 HIS cc_start: 0.7440 (OUTLIER) cc_final: 0.6727 (p-80) REVERT: C 228 ARG cc_start: 0.7518 (mtt90) cc_final: 0.6965 (mmm-85) REVERT: C 274 GLN cc_start: 0.8303 (mt0) cc_final: 0.8013 (mt0) REVERT: C 329 MET cc_start: 0.4288 (tmm) cc_final: 0.3572 (pmm) REVERT: C 342 MET cc_start: 0.5163 (OUTLIER) cc_final: 0.4823 (mmm) REVERT: D 17 THR cc_start: 0.7921 (p) cc_final: 0.7207 (p) REVERT: D 20 GLU cc_start: 0.8244 (mp0) cc_final: 0.7882 (mp0) REVERT: D 22 GLN cc_start: 0.8298 (mt0) cc_final: 0.7748 (mt0) REVERT: D 25 SER cc_start: 0.7537 (m) cc_final: 0.7165 (p) REVERT: D 42 GLU cc_start: 0.7638 (tp30) cc_final: 0.6925 (tp30) REVERT: D 43 ASP cc_start: 0.7815 (t0) cc_final: 0.7410 (t0) REVERT: D 44 LEU cc_start: 0.8258 (mt) cc_final: 0.7764 (mt) REVERT: D 68 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7028 (mm-30) REVERT: D 72 PHE cc_start: 0.8065 (p90) cc_final: 0.7542 (p90) REVERT: D 73 ASP cc_start: 0.7723 (m-30) cc_final: 0.7330 (m-30) REVERT: D 135 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7112 (tp30) REVERT: D 140 ARG cc_start: 0.7826 (ttp-110) cc_final: 0.7221 (ttp-170) REVERT: D 158 LEU cc_start: 0.8684 (tp) cc_final: 0.8354 (tt) REVERT: D 183 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8396 (tpp80) REVERT: D 190 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7515 (tpp80) REVERT: D 203 HIS cc_start: 0.7348 (t70) cc_final: 0.7127 (t-90) REVERT: D 235 LEU cc_start: 0.8862 (mt) cc_final: 0.8544 (mm) REVERT: D 237 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7238 (ptm160) REVERT: D 247 TYR cc_start: 0.7957 (m-10) cc_final: 0.7485 (m-10) REVERT: D 267 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7065 (tm-30) REVERT: D 269 ILE cc_start: 0.7968 (mm) cc_final: 0.7568 (mm) REVERT: D 278 LEU cc_start: 0.8381 (mt) cc_final: 0.8115 (mm) REVERT: D 309 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6169 (mp0) REVERT: D 327 ARG cc_start: 0.8400 (ttt180) cc_final: 0.8095 (ttp80) REVERT: D 351 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: D 367 TRP cc_start: 0.6722 (t-100) cc_final: 0.6232 (t-100) REVERT: D 458 MET cc_start: 0.7730 (mmt) cc_final: 0.7480 (mmt) outliers start: 53 outliers final: 36 residues processed: 445 average time/residue: 0.1565 time to fit residues: 100.4468 Evaluate side-chains 460 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 416 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 71 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 40.0000 chunk 51 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 159 optimal weight: 0.0170 chunk 205 optimal weight: 30.0000 chunk 43 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.210328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161671 restraints weight = 39357.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.162946 restraints weight = 17538.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.163864 restraints weight = 10740.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.164185 restraints weight = 9834.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.164332 restraints weight = 8590.160| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 20302 Z= 0.218 Angle : 0.694 14.502 28362 Z= 0.373 Chirality : 0.044 0.294 3108 Planarity : 0.005 0.071 3020 Dihedral : 23.671 85.391 4283 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.05 % Allowed : 21.01 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.19), residues: 1936 helix: 1.98 (0.17), residues: 917 sheet: -0.78 (0.28), residues: 282 loop : 0.34 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 183 TYR 0.025 0.002 TYR B 78 PHE 0.027 0.002 PHE D 217 TRP 0.064 0.002 TRP C 230 HIS 0.008 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.22 (20286) covalent geometry : angle 0.68850 / 0.37 (28338) hydrogen bonds : bond 0.04932 / 3.35 ( 1054) hydrogen bonds : angle 3.98607 / 2.92 ( 2783) metal coordination : bond 0.00531 / 0.33 ( 16) metal coordination : angle 3.05005 / 1.94 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 416 time to evaluate : 0.581 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: 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: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8116 (mt) cc_final: 0.7846 (mm) REVERT: A 9 LEU cc_start: 0.8319 (tp) cc_final: 0.7740 (mt) REVERT: A 24 GLU cc_start: 0.6725 (tp30) cc_final: 0.6414 (tm-30) REVERT: A 72 PHE cc_start: 0.7643 (p90) cc_final: 0.6840 (p90) REVERT: A 139 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7276 (tm-30) REVERT: A 164 LEU cc_start: 0.8592 (mm) cc_final: 0.8236 (mm) REVERT: A 221 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7851 (mp10) REVERT: A 244 MET cc_start: 0.7841 (mmt) cc_final: 0.7301 (mmt) REVERT: A 276 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7687 (pt0) REVERT: A 342 MET cc_start: 0.2417 (mtp) cc_final: 0.2162 (mtp) REVERT: A 377 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4087 (mp) REVERT: A 481 GLU cc_start: -0.1847 (OUTLIER) cc_final: -0.2307 (mp0) REVERT: B 26 CYS cc_start: 0.8412 (m) cc_final: 0.7912 (m) REVERT: B 27 GLN cc_start: 0.7893 (mt0) cc_final: 0.7671 (mt0) REVERT: B 28 GLN cc_start: 0.7664 (tp-100) cc_final: 0.7372 (tp-100) REVERT: B 32 GLN cc_start: 0.7764 (tp40) cc_final: 0.7528 (tm-30) REVERT: B 98 GLU cc_start: 0.7451 (tp30) cc_final: 0.7168 (tp30) REVERT: B 101 LYS cc_start: 0.8043 (mptt) cc_final: 0.7722 (mptt) REVERT: B 142 ARG cc_start: 0.7930 (ttp-110) cc_final: 0.7492 (ttp80) REVERT: B 149 ILE cc_start: 0.7781 (mt) cc_final: 0.7389 (tp) REVERT: B 164 LEU cc_start: 0.7698 (tp) cc_final: 0.7480 (tp) REVERT: B 177 ASP cc_start: 0.7855 (t0) cc_final: 0.7184 (t70) REVERT: B 183 ARG cc_start: 0.8034 (mmm160) cc_final: 0.7746 (mmp80) REVERT: B 189 HIS cc_start: 0.7207 (m-70) cc_final: 0.6784 (m-70) REVERT: B 196 GLU cc_start: 0.7850 (mt-10) cc_final: 0.6879 (mt-10) REVERT: B 199 HIS cc_start: 0.7946 (p-80) cc_final: 0.7699 (p-80) REVERT: B 200 LEU cc_start: 0.8481 (mp) cc_final: 0.8262 (mp) REVERT: B 247 TYR cc_start: 0.7061 (m-10) cc_final: 0.6396 (m-80) REVERT: B 263 LEU cc_start: 0.8264 (tp) cc_final: 0.7588 (pp) REVERT: B 276 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7826 (mt-10) REVERT: B 281 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7150 (tm-30) REVERT: B 299 LEU cc_start: 0.8339 (tt) cc_final: 0.7766 (mt) REVERT: B 344 GLU cc_start: 0.8527 (tt0) cc_final: 0.7784 (tm-30) REVERT: B 351 GLU cc_start: 0.8733 (pt0) cc_final: 0.8284 (pp20) REVERT: B 376 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7305 (mm-30) REVERT: B 416 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7855 (mmm160) REVERT: B 452 ASN cc_start: 0.8641 (t0) cc_final: 0.7814 (t0) REVERT: B 456 ARG cc_start: 0.8438 (ptp-110) cc_final: 0.7920 (mmm-85) REVERT: B 458 MET cc_start: 0.7605 (mmt) cc_final: 0.7294 (mmt) REVERT: C 27 GLN cc_start: 0.7977 (pp30) cc_final: 0.7634 (pp30) REVERT: C 45 ASP cc_start: 0.7107 (t0) cc_final: 0.6716 (t0) REVERT: C 56 LYS cc_start: 0.7822 (tppp) cc_final: 0.7211 (tppp) REVERT: C 70 GLN cc_start: 0.7882 (mt0) cc_final: 0.7542 (mt0) REVERT: C 132 MET cc_start: 0.7939 (tpp) cc_final: 0.7286 (mpp) REVERT: C 142 ARG cc_start: 0.7774 (ttp-110) cc_final: 0.7340 (mtp-110) REVERT: C 147 PHE cc_start: 0.7280 (t80) cc_final: 0.7057 (t80) REVERT: C 174 LEU cc_start: 0.7460 (mt) cc_final: 0.7136 (mt) REVERT: C 181 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8103 (tmm-80) REVERT: C 185 LEU cc_start: 0.9126 (mm) cc_final: 0.8823 (mm) REVERT: C 199 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.6788 (p-80) REVERT: C 228 ARG cc_start: 0.7465 (mtt90) cc_final: 0.6967 (mmm-85) REVERT: C 274 GLN cc_start: 0.8336 (mt0) cc_final: 0.7959 (mt0) REVERT: C 276 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8314 (mp0) REVERT: C 329 MET cc_start: 0.4527 (tmm) cc_final: 0.3898 (pmm) REVERT: C 342 MET cc_start: 0.5228 (OUTLIER) cc_final: 0.4858 (mmm) REVERT: D 17 THR cc_start: 0.7924 (p) cc_final: 0.7268 (p) REVERT: D 22 GLN cc_start: 0.8373 (mt0) cc_final: 0.7882 (mt0) REVERT: D 25 SER cc_start: 0.7512 (m) cc_final: 0.7250 (p) REVERT: D 42 GLU cc_start: 0.7703 (tp30) cc_final: 0.7229 (tp30) REVERT: D 44 LEU cc_start: 0.8302 (mt) cc_final: 0.8075 (mt) REVERT: D 72 PHE cc_start: 0.8106 (p90) cc_final: 0.7655 (p90) REVERT: D 73 ASP cc_start: 0.7673 (m-30) cc_final: 0.7374 (m-30) REVERT: D 133 GLU cc_start: 0.7104 (tp30) cc_final: 0.6776 (tp30) REVERT: D 140 ARG cc_start: 0.7731 (ttp-110) cc_final: 0.7109 (ttp-170) REVERT: D 183 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8398 (tpp80) REVERT: D 190 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7638 (tpp80) REVERT: D 229 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7311 (mt-10) REVERT: D 235 LEU cc_start: 0.8802 (mt) cc_final: 0.8502 (mm) REVERT: D 267 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7581 (tm-30) REVERT: D 269 ILE cc_start: 0.8082 (mm) cc_final: 0.7661 (mm) REVERT: D 278 LEU cc_start: 0.8405 (mt) cc_final: 0.8156 (mm) REVERT: D 327 ARG cc_start: 0.8450 (ttt180) cc_final: 0.8074 (ttp80) REVERT: D 351 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: D 458 MET cc_start: 0.7757 (mmt) cc_final: 0.7530 (mmt) outliers start: 49 outliers final: 40 residues processed: 440 average time/residue: 0.1594 time to fit residues: 100.9217 Evaluate side-chains 450 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 405 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 115 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 147 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 97 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.213524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166528 restraints weight = 39611.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.166520 restraints weight = 17848.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.167163 restraints weight = 13343.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.167549 restraints weight = 10843.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.167778 restraints weight = 9401.892| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20302 Z= 0.141 Angle : 0.671 15.121 28362 Z= 0.358 Chirality : 0.042 0.301 3108 Planarity : 0.005 0.060 3020 Dihedral : 23.614 84.055 4283 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.99 % Allowed : 21.57 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 1936 helix: 2.13 (0.17), residues: 918 sheet: -0.67 (0.29), residues: 288 loop : 0.42 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 416 TYR 0.020 0.002 TYR D 216 PHE 0.025 0.002 PHE C 303 TRP 0.071 0.002 TRP C 230 HIS 0.007 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (20286) covalent geometry : angle 0.66618 / 0.36 (28338) hydrogen bonds : bond 0.04260 / 2.92 ( 1054) hydrogen bonds : angle 3.80956 / 2.80 ( 2783) metal coordination : bond 0.00295 / 0.20 ( 16) metal coordination : angle 2.84956 / 1.83 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3468.64 seconds wall clock time: 60 minutes 10.99 seconds (3610.99 seconds total)