Starting phenix.real_space_refine on Mon Apr 6 15:39:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu6_60891/04_2026/9iu6_60891.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu6_60891/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/9iu6_60891/04_2026/9iu6_60891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu6_60891/04_2026/9iu6_60891.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iu6_60891/04_2026/9iu6_60891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu6_60891/04_2026/9iu6_60891.map" } 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-2.1rc1-6017/lib/python3.9/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: 4.35, 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 703.7 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: 2.69 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: 3.61 Time building geometry restraints manager: 2.21 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=" 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=" C LEU C 158 " pdb=" N PRO C 159 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.18e-02 7.18e+03 7.92e+00 bond pdb=" C LEU A 158 " pdb=" N PRO A 159 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.18e-02 7.18e+03 7.90e+00 ... (remaining 20281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 26415 3.44 - 6.88: 1805 6.88 - 10.32: 101 10.32 - 13.76: 12 13.76 - 17.20: 5 Bond angle restraints: 28338 Sorted by residual: 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 1.50e+00 4.44e-01 1.32e+02 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 1.50e+00 4.44e-01 1.01e+02 angle pdb=" O3' DAE1 20 " pdb=" P DCE1 21 " pdb=" O5' DCE1 21 " ideal model delta sigma weight residual 104.00 89.59 14.41 1.50e+00 4.44e-01 9.22e+01 angle pdb=" O3' DAF2 20 " pdb=" P DCF2 21 " pdb=" O5' DCF2 21 " ideal model delta sigma weight residual 104.00 89.71 14.29 1.50e+00 4.44e-01 9.08e+01 angle pdb=" O3' DCH1 25 " pdb=" P DGH1 26 " pdb=" O5' DGH1 26 " ideal model delta sigma weight residual 104.00 89.75 14.25 1.50e+00 4.44e-01 9.02e+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 - 0.128: 2763 0.128 - 0.256: 321 0.256 - 0.384: 18 0.384 - 0.512: 2 0.512 - 0.640: 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 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+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 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+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 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+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: 0.730 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 22.290 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 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= 0.567 Angle : 1.835 20.569 28362 Z= 1.174 Chirality : 0.086 0.640 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 covalent geometry : bond 0.00940 (20286) covalent geometry : angle 1.81483 (28338) hydrogen bonds : bond 0.16035 ( 1054) hydrogen bonds : angle 5.98674 ( 2783) metal coordination : bond 0.05815 ( 16) metal coordination : angle 9.49656 ( 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 : 0.443 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: 0.6716 (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: 0.5849 (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: 0.7021 (pp20) REVERT: A 137 ILE cc_start: 0.6687 (mt) cc_final: 0.6393 (mt) REVERT: A 146 HIS cc_start: 0.8065 (m170) cc_final: 0.7641 (m90) REVERT: A 148 ASN cc_start: 0.8752 (m-40) cc_final: 0.8545 (m-40) REVERT: A 150 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8053 (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: 0.6002 (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: 0.8446 (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: -0.3288 (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: 0.7359 (p0) REVERT: B 56 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7568 (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: 0.8193 (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: 0.6848 (mtm) REVERT: B 142 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.7031 (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: 0.5600 (t0) REVERT: B 186 GLU cc_start: 0.8825 (tt0) cc_final: 0.8175 (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: 0.7614 (t0) REVERT: B 206 ASN cc_start: 0.6878 (m-40) cc_final: 0.6603 (m110) REVERT: B 216 TYR cc_start: 0.6962 (t80) cc_final: 0.6671 (t80) REVERT: B 228 ARG cc_start: 0.6019 (mtm-85) cc_final: 0.5749 (mtm-85) 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: 0.7934 (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: 0.8830 (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: 0.4674 (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: 0.6699 (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: 0.6342 (ttm-80) REVERT: C 149 ILE cc_start: 0.7734 (mm) cc_final: 0.7347 (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: 0.6835 (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: 0.6560 (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: 0.6238 (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: 0.7409 (m-30) REVERT: D 216 TYR cc_start: 0.7877 (t80) cc_final: 0.7491 (t80) REVERT: D 230 TRP cc_start: 0.8025 (m100) cc_final: 0.6821 (m100) REVERT: D 235 LEU cc_start: 0.8493 (mt) cc_final: 0.8207 (mm) REVERT: D 242 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7947 (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 296 SER cc_start: 0.7677 (OUTLIER) cc_final: 0.7207 (t) REVERT: D 327 ARG cc_start: 0.8087 (ttt180) cc_final: 0.7782 (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: 0.1765 time to fit residues: 130.9256 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 : 0.369 ------------------------------------------------------------------------------- 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: 0.9980 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: 20.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 91 GLN A 194 ASN A 446 GLN B 22 GLN B 203 HIS ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 GLN D 22 GLN D 189 HIS ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN D 251 ASN D 452 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.214557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.166532 restraints weight = 40368.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.166511 restraints weight = 23200.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.168053 restraints weight = 13498.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.168546 restraints weight = 11456.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170129 restraints weight = 8998.675| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20302 Z= 0.174 Angle : 0.608 13.292 28362 Z= 0.336 Chirality : 0.039 0.186 3108 Planarity : 0.004 0.050 3020 Dihedral : 23.071 81.551 4344 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.24 % Allowed : 11.85 % Favored : 84.91 % 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: 2.28 (0.19), residues: 1936 helix: 2.60 (0.16), residues: 915 sheet: 0.12 (0.28), residues: 286 loop : 0.83 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 416 TYR 0.015 0.002 TYR A 324 PHE 0.020 0.002 PHE D 348 TRP 0.024 0.001 TRP C 230 HIS 0.007 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00366 (20286) covalent geometry : angle 0.59908 (28338) hydrogen bonds : bond 0.04530 ( 1054) hydrogen bonds : angle 3.73505 ( 2783) metal coordination : bond 0.00298 ( 16) metal coordination : angle 3.56074 ( 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 488 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 436 time to evaluate : 0.573 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: 0.8185 (mt) cc_final: 0.7743 (mm) REVERT: A 24 GLU cc_start: 0.7118 (tp30) cc_final: 0.6830 (tm-30) REVERT: A 70 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7453 (mm-40) REVERT: A 78 TYR cc_start: 0.8022 (t80) cc_final: 0.7496 (t80) REVERT: A 131 GLN cc_start: 0.7554 (tt0) cc_final: 0.7044 (tt0) REVERT: A 139 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7323 (mm-30) REVERT: A 150 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7534 (ttm-80) REVERT: A 164 LEU cc_start: 0.8505 (mm) cc_final: 0.8295 (mm) REVERT: A 174 LEU cc_start: 0.7279 (mt) cc_final: 0.7031 (mt) REVERT: A 182 GLU cc_start: 0.8505 (tt0) cc_final: 0.7885 (tm-30) REVERT: A 186 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8343 (tm-30) REVERT: A 221 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7878 (mp10) REVERT: A 239 MET cc_start: 0.7380 (mmm) cc_final: 0.7164 (mmm) REVERT: A 244 MET cc_start: 0.7640 (mmt) cc_final: 0.6861 (mmt) REVERT: A 276 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7616 (pt0) REVERT: A 481 GLU cc_start: -0.2270 (OUTLIER) cc_final: -0.2742 (mp0) REVERT: B 22 GLN cc_start: 0.8228 (mt0) cc_final: 0.7472 (mt0) REVERT: B 26 CYS cc_start: 0.8342 (m) cc_final: 0.8020 (m) REVERT: B 27 GLN cc_start: 0.7871 (mt0) cc_final: 0.7560 (mt0) REVERT: B 28 GLN cc_start: 0.7532 (tp-100) cc_final: 0.7115 (tm-30) REVERT: B 37 VAL cc_start: 0.8688 (t) cc_final: 0.8463 (p) REVERT: B 91 GLN cc_start: 0.7922 (mt0) cc_final: 0.7690 (mt0) REVERT: B 102 LYS cc_start: 0.8059 (mmtp) cc_final: 0.7433 (mmmm) REVERT: B 113 ASP cc_start: 0.6667 (t0) cc_final: 0.6229 (t0) REVERT: B 132 MET cc_start: 0.6971 (mtm) cc_final: 0.6749 (mtm) REVERT: B 142 ARG cc_start: 0.7736 (ttp-110) cc_final: 0.7333 (ttp80) REVERT: B 149 ILE cc_start: 0.7736 (mt) cc_final: 0.7383 (tp) REVERT: B 177 ASP cc_start: 0.7228 (t0) cc_final: 0.6879 (t0) REVERT: B 186 GLU cc_start: 0.7991 (tt0) cc_final: 0.7005 (tm-30) REVERT: B 189 HIS cc_start: 0.7132 (m-70) cc_final: 0.6746 (m-70) REVERT: B 196 GLU cc_start: 0.7704 (tt0) cc_final: 0.7451 (mt-10) REVERT: B 198 LEU cc_start: 0.8702 (pt) cc_final: 0.8251 (mt) REVERT: B 200 LEU cc_start: 0.8148 (mt) cc_final: 0.7766 (mt) REVERT: B 203 HIS cc_start: 0.8148 (t70) cc_final: 0.7846 (t70) REVERT: B 224 GLU cc_start: 0.7008 (pp20) cc_final: 0.6536 (pp20) REVERT: B 236 LYS cc_start: 0.8425 (tttt) cc_final: 0.7934 (ttpp) REVERT: B 240 ILE cc_start: 0.8211 (tt) cc_final: 0.7952 (tp) REVERT: B 242 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7549 (mt-10) REVERT: B 269 ILE cc_start: 0.8472 (mm) cc_final: 0.8223 (mm) REVERT: B 272 ARG cc_start: 0.6254 (tpp80) cc_final: 0.6017 (tpp80) REVERT: B 276 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7616 (mt-10) REVERT: B 279 ARG cc_start: 0.7751 (ptp90) cc_final: 0.7363 (ptp90) REVERT: B 281 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7094 (tp30) REVERT: B 344 GLU cc_start: 0.8338 (tt0) cc_final: 0.7741 (tm-30) REVERT: B 348 PHE cc_start: 0.8870 (t80) cc_final: 0.8568 (t80) REVERT: B 379 GLU cc_start: 0.8332 (pt0) cc_final: 0.7995 (mt-10) REVERT: B 456 ARG cc_start: 0.8348 (mtp180) cc_final: 0.8142 (ptp-110) REVERT: B 457 SER cc_start: 0.8361 (t) cc_final: 0.7493 (p) REVERT: B 458 MET cc_start: 0.8251 (mmt) cc_final: 0.7421 (mmt) REVERT: C 9 LEU cc_start: 0.7871 (tp) cc_final: 0.7621 (tp) REVERT: C 23 LEU cc_start: 0.8129 (tp) cc_final: 0.7915 (tt) REVERT: C 27 GLN cc_start: 0.8027 (pp30) cc_final: 0.7669 (pp30) REVERT: C 30 CYS cc_start: 0.7518 (m) cc_final: 0.7163 (p) REVERT: C 33 ARG cc_start: 0.7643 (tpp80) cc_final: 0.6942 (ttm110) REVERT: C 42 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6667 (mt-10) REVERT: C 56 LYS cc_start: 0.7721 (tppp) cc_final: 0.7064 (tppp) REVERT: C 70 GLN cc_start: 0.7656 (mt0) cc_final: 0.7402 (mt0) REVERT: C 78 TYR cc_start: 0.8023 (t80) cc_final: 0.7745 (t80) REVERT: C 79 ARG cc_start: 0.7726 (mtp85) cc_final: 0.7248 (mtp-110) REVERT: C 126 MET cc_start: 0.7527 (mmm) cc_final: 0.6407 (mtp) REVERT: C 132 MET cc_start: 0.7740 (tpp) cc_final: 0.7388 (tpp) REVERT: C 140 ARG cc_start: 0.6709 (mtm-85) cc_final: 0.6334 (ttm-80) REVERT: C 142 ARG cc_start: 0.7518 (ttp-110) cc_final: 0.7251 (ttm-80) REVERT: C 149 ILE cc_start: 0.8414 (mm) cc_final: 0.8207 (mm) REVERT: C 199 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.6825 (p-80) REVERT: C 212 SER cc_start: 0.6488 (p) cc_final: 0.5293 (m) REVERT: C 213 PRO cc_start: 0.7991 (Cg_exo) cc_final: 0.7305 (Cg_endo) REVERT: C 235 LEU cc_start: 0.8774 (mt) cc_final: 0.8342 (mt) REVERT: C 241 SER cc_start: 0.8326 (m) cc_final: 0.8080 (p) REVERT: C 274 GLN cc_start: 0.8307 (mt0) cc_final: 0.7778 (mt0) REVERT: C 342 MET cc_start: 0.5015 (OUTLIER) cc_final: 0.4759 (mmm) REVERT: D 7 ILE cc_start: 0.8551 (mt) cc_final: 0.7768 (mm) REVERT: D 22 GLN cc_start: 0.8219 (mt0) cc_final: 0.7574 (mt0) REVERT: D 25 SER cc_start: 0.7498 (m) cc_final: 0.7071 (p) REVERT: D 26 CYS cc_start: 0.8193 (m) cc_final: 0.7858 (t) REVERT: D 42 GLU cc_start: 0.7531 (tt0) cc_final: 0.7197 (tp30) REVERT: D 68 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7325 (mm-30) REVERT: D 72 PHE cc_start: 0.8137 (p90) cc_final: 0.7601 (p90) REVERT: D 102 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7432 (mmtp) REVERT: D 109 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7296 (mt-10) REVERT: D 113 ASP cc_start: 0.7525 (t0) cc_final: 0.7297 (t0) REVERT: D 135 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7490 (tp30) REVERT: D 163 TYR cc_start: 0.7223 (m-80) cc_final: 0.6977 (m-80) REVERT: D 190 ARG cc_start: 0.8199 (mtp180) cc_final: 0.7354 (ttp80) REVERT: D 221 GLN cc_start: 0.8557 (mm110) cc_final: 0.8241 (mm-40) REVERT: D 226 GLN cc_start: 0.7854 (mp10) cc_final: 0.7319 (mm110) REVERT: D 230 TRP cc_start: 0.8164 (m100) cc_final: 0.7810 (m100) REVERT: D 235 LEU cc_start: 0.8820 (mt) cc_final: 0.8435 (mm) REVERT: D 239 MET cc_start: 0.8484 (mmm) cc_final: 0.8241 (mmm) REVERT: D 276 GLU cc_start: 0.7939 (mm-30) cc_final: 0.6891 (pt0) REVERT: D 309 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6452 (mm-30) REVERT: D 327 ARG cc_start: 0.8420 (ttt180) cc_final: 0.7830 (ttp80) REVERT: D 328 SER cc_start: 0.8316 (t) cc_final: 0.6885 (p) REVERT: D 331 PHE cc_start: 0.6246 (m-10) cc_final: 0.5429 (m-80) REVERT: D 334 HIS cc_start: 0.5735 (p90) cc_final: 0.5248 (p90) REVERT: D 416 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7791 (ptp-110) REVERT: D 458 MET cc_start: 0.7508 (mmt) cc_final: 0.6708 (mmt) REVERT: D 459 ASN cc_start: 0.8270 (m110) cc_final: 0.7837 (p0) REVERT: D 463 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7858 (t) outliers start: 52 outliers final: 26 residues processed: 468 average time/residue: 0.1652 time to fit residues: 109.2974 Evaluate side-chains 439 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 409 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 13 THR 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 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 486 LEU 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 199 HIS 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 342 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 480 GLN 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 175 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 129 optimal weight: 0.0770 chunk 207 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 132 optimal weight: 50.0000 chunk 107 optimal weight: 0.0370 chunk 196 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN ** C 146 HIS ** 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 = 0.4529 r_free = 0.4529 target = 0.213419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.162479 restraints weight = 40351.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164891 restraints weight = 22231.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.165942 restraints weight = 11842.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166447 restraints weight = 11389.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.166785 restraints weight = 8693.393| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20302 Z= 0.138 Angle : 0.570 12.841 28362 Z= 0.308 Chirality : 0.037 0.179 3108 Planarity : 0.004 0.067 3020 Dihedral : 23.082 82.040 4299 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.24 % Allowed : 14.46 % Favored : 82.29 % 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: 2.44 (0.19), residues: 1936 helix: 2.65 (0.17), residues: 923 sheet: 0.08 (0.29), residues: 266 loop : 1.04 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 327 TYR 0.014 0.001 TYR B 188 PHE 0.015 0.001 PHE A 331 TRP 0.025 0.001 TRP C 230 HIS 0.007 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00293 (20286) covalent geometry : angle 0.56192 (28338) hydrogen bonds : bond 0.03629 ( 1054) hydrogen bonds : angle 3.58095 ( 2783) metal coordination : bond 0.00344 ( 16) metal coordination : angle 3.37488 ( 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 474 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 422 time to evaluate : 0.590 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: A 7 ILE cc_start: 0.8139 (mt) cc_final: 0.7812 (mm) REVERT: A 24 GLU cc_start: 0.7021 (tp30) cc_final: 0.6378 (tp30) REVERT: A 51 ASP cc_start: 0.8172 (t0) cc_final: 0.7899 (t0) REVERT: A 98 GLU cc_start: 0.6345 (tm-30) cc_final: 0.5927 (tm-30) REVERT: A 102 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7898 (mmtm) REVERT: A 131 GLN cc_start: 0.7601 (tt0) cc_final: 0.6978 (tt0) REVERT: A 139 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7295 (mm-30) REVERT: A 140 ARG cc_start: 0.6988 (tmm-80) cc_final: 0.6738 (ptm-80) REVERT: A 149 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 150 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7513 (ttm-80) REVERT: A 164 LEU cc_start: 0.8522 (mm) cc_final: 0.8273 (mm) REVERT: A 182 GLU cc_start: 0.8317 (tt0) cc_final: 0.7766 (tm-30) REVERT: A 183 ARG cc_start: 0.8640 (mmm160) cc_final: 0.8264 (mmm160) REVERT: A 221 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7892 (mp10) REVERT: A 244 MET cc_start: 0.7415 (mmt) cc_final: 0.6774 (mmt) REVERT: A 276 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7541 (pt0) REVERT: A 281 GLU cc_start: 0.7274 (tp30) cc_final: 0.6753 (tp30) REVERT: A 342 MET cc_start: 0.2512 (mtp) cc_final: 0.2099 (mtp) REVERT: A 377 LEU cc_start: 0.5393 (OUTLIER) cc_final: 0.4282 (mp) REVERT: A 481 GLU cc_start: -0.1831 (OUTLIER) cc_final: -0.2336 (mp0) REVERT: B 22 GLN cc_start: 0.8281 (mt0) cc_final: 0.7471 (mt0) REVERT: B 26 CYS cc_start: 0.8211 (m) cc_final: 0.7804 (m) REVERT: B 27 GLN cc_start: 0.7866 (mt0) cc_final: 0.7594 (mt0) REVERT: B 37 VAL cc_start: 0.8803 (t) cc_final: 0.8576 (p) REVERT: B 98 GLU cc_start: 0.7250 (tt0) cc_final: 0.7042 (tp30) REVERT: B 102 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7650 (mmmt) REVERT: B 113 ASP cc_start: 0.6552 (t0) cc_final: 0.6348 (t0) REVERT: B 131 GLN cc_start: 0.7832 (tp40) cc_final: 0.7380 (tp40) REVERT: B 142 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.7495 (ttp80) REVERT: B 149 ILE cc_start: 0.7801 (mt) cc_final: 0.7404 (tp) REVERT: B 173 ARG cc_start: 0.7943 (ttm110) cc_final: 0.7408 (mtp85) REVERT: B 177 ASP cc_start: 0.7443 (t0) cc_final: 0.6923 (t0) REVERT: B 183 ARG cc_start: 0.7643 (mmp80) cc_final: 0.7191 (mmp80) REVERT: B 186 GLU cc_start: 0.7707 (tt0) cc_final: 0.6937 (tt0) REVERT: B 189 HIS cc_start: 0.7004 (m-70) cc_final: 0.6641 (m-70) REVERT: B 196 GLU cc_start: 0.7885 (tt0) cc_final: 0.7418 (mt-10) REVERT: B 198 LEU cc_start: 0.8694 (pt) cc_final: 0.8371 (mt) REVERT: B 200 LEU cc_start: 0.8114 (mt) cc_final: 0.7658 (mt) REVERT: B 203 HIS cc_start: 0.8013 (t70) cc_final: 0.6596 (t70) REVERT: B 207 ARG cc_start: 0.7753 (tpp80) cc_final: 0.7142 (ttm110) REVERT: B 236 LYS cc_start: 0.8521 (tttt) cc_final: 0.8278 (ttpp) REVERT: B 270 LEU cc_start: 0.7643 (mm) cc_final: 0.7345 (mm) REVERT: B 276 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7543 (mt-10) REVERT: B 281 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7154 (tp30) REVERT: B 329 MET cc_start: 0.7368 (mmp) cc_final: 0.7123 (mmp) REVERT: B 344 GLU cc_start: 0.8281 (tt0) cc_final: 0.7672 (tm-30) REVERT: B 351 GLU cc_start: 0.8836 (pt0) cc_final: 0.8339 (pp20) REVERT: B 379 GLU cc_start: 0.8109 (pt0) cc_final: 0.7675 (mt-10) REVERT: B 406 LEU cc_start: 0.8610 (tp) cc_final: 0.8328 (mt) REVERT: B 416 ARG cc_start: 0.8297 (mmm160) cc_final: 0.7960 (mmm160) REVERT: B 452 ASN cc_start: 0.8108 (t0) cc_final: 0.7119 (t0) REVERT: B 457 SER cc_start: 0.8040 (t) cc_final: 0.7551 (p) REVERT: B 476 PHE cc_start: 0.7386 (m-10) cc_final: 0.7146 (m-10) REVERT: C 9 LEU cc_start: 0.7883 (tp) cc_final: 0.7643 (tp) REVERT: C 23 LEU cc_start: 0.7968 (tp) cc_final: 0.7644 (tt) REVERT: C 30 CYS cc_start: 0.7531 (m) cc_final: 0.7075 (p) REVERT: C 33 ARG cc_start: 0.7691 (tpp80) cc_final: 0.7005 (tpp80) REVERT: C 56 LYS cc_start: 0.7599 (tppp) cc_final: 0.6006 (tppp) REVERT: C 69 GLU cc_start: 0.7225 (mm-30) cc_final: 0.7024 (mm-30) REVERT: C 70 GLN cc_start: 0.7641 (mt0) cc_final: 0.7251 (mt0) REVERT: C 78 TYR cc_start: 0.8174 (t80) cc_final: 0.7888 (t80) REVERT: C 126 MET cc_start: 0.7328 (mmm) cc_final: 0.6150 (mtp) REVERT: C 128 THR cc_start: 0.8305 (p) cc_final: 0.7898 (p) REVERT: C 132 MET cc_start: 0.7709 (tpp) cc_final: 0.6924 (mpp) REVERT: C 149 ILE cc_start: 0.8488 (mm) cc_final: 0.8136 (mm) REVERT: C 150 ARG cc_start: 0.7517 (mmm-85) cc_final: 0.7261 (mmm-85) REVERT: C 181 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.8030 (tmm-80) REVERT: C 186 GLU cc_start: 0.8455 (tp30) cc_final: 0.8073 (tp30) REVERT: C 199 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.6721 (p-80) REVERT: C 212 SER cc_start: 0.6440 (p) cc_final: 0.5355 (m) REVERT: C 213 PRO cc_start: 0.8089 (Cg_exo) cc_final: 0.7591 (Cg_endo) REVERT: C 228 ARG cc_start: 0.7502 (mmm-85) cc_final: 0.6840 (ttm170) REVERT: C 235 LEU cc_start: 0.8758 (mt) cc_final: 0.8356 (mm) REVERT: C 253 LYS cc_start: 0.7559 (tppp) cc_final: 0.7330 (tppp) REVERT: C 274 GLN cc_start: 0.8220 (mt0) cc_final: 0.7763 (mt0) REVERT: C 342 MET cc_start: 0.5096 (OUTLIER) cc_final: 0.4771 (mmm) REVERT: D 17 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7401 (p) REVERT: D 20 GLU cc_start: 0.8209 (mp0) cc_final: 0.7747 (mm-30) REVERT: D 22 GLN cc_start: 0.8186 (mt0) cc_final: 0.7556 (mt0) REVERT: D 25 SER cc_start: 0.7461 (m) cc_final: 0.7068 (p) REVERT: D 68 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7328 (mm-30) REVERT: D 72 PHE cc_start: 0.8127 (p90) cc_final: 0.7670 (p90) REVERT: D 73 ASP cc_start: 0.7637 (m-30) cc_final: 0.7252 (m-30) REVERT: D 102 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7359 (mmtp) REVERT: D 113 ASP cc_start: 0.7485 (t0) cc_final: 0.7072 (t0) REVERT: D 115 THR cc_start: 0.7671 (t) cc_final: 0.7416 (m) REVERT: D 133 GLU cc_start: 0.6932 (tp30) cc_final: 0.6601 (tp30) REVERT: D 135 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7222 (tp30) REVERT: D 139 GLU cc_start: 0.7545 (tp30) cc_final: 0.7159 (tp30) REVERT: D 140 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7152 (ttp-170) REVERT: D 149 ILE cc_start: 0.8060 (mm) cc_final: 0.7854 (tt) REVERT: D 154 TYR cc_start: 0.7229 (t80) cc_final: 0.6966 (t80) REVERT: D 190 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7351 (mtm180) REVERT: D 206 ASN cc_start: 0.6728 (m-40) cc_final: 0.6417 (m110) REVERT: D 211 LEU cc_start: 0.7807 (mm) cc_final: 0.7403 (mm) REVERT: D 221 GLN cc_start: 0.8574 (mm110) cc_final: 0.8230 (mm-40) REVERT: D 230 TRP cc_start: 0.8192 (m100) cc_final: 0.7338 (m100) REVERT: D 235 LEU cc_start: 0.8753 (mt) cc_final: 0.8313 (mm) REVERT: D 267 GLU cc_start: 0.7669 (tp30) cc_final: 0.7262 (tm-30) REVERT: D 275 LEU cc_start: 0.8181 (tp) cc_final: 0.7895 (tp) REVERT: D 278 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7909 (mm) REVERT: D 327 ARG cc_start: 0.8337 (ttt180) cc_final: 0.7842 (ttp80) REVERT: D 331 PHE cc_start: 0.6299 (m-10) cc_final: 0.5242 (m-80) REVERT: D 334 HIS cc_start: 0.5954 (p90) cc_final: 0.5352 (p90) REVERT: D 351 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: D 416 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7755 (ptp-110) REVERT: D 458 MET cc_start: 0.7560 (mmt) cc_final: 0.6665 (mmt) REVERT: D 459 ASN cc_start: 0.8131 (m110) cc_final: 0.7677 (p0) outliers start: 52 outliers final: 33 residues processed: 451 average time/residue: 0.1623 time to fit residues: 103.7191 Evaluate side-chains 449 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 407 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 231 SER 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 153 LYS Chi-restraints excluded: chain B residue 249 THR 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 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 114 THR 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 D residue 17 THR Chi-restraints excluded: chain D residue 38 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 97 optimal weight: 7.9990 chunk 186 optimal weight: 0.0570 chunk 197 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 145 optimal weight: 0.0570 chunk 202 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 446 GLN B 194 ASN C 146 HIS ** C 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 70 GLN D 111 HIS ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.215443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.168650 restraints weight = 40351.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.167901 restraints weight = 18305.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.169707 restraints weight = 12125.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.170084 restraints weight = 10157.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.169991 restraints weight = 8951.593| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20302 Z= 0.134 Angle : 0.542 11.784 28362 Z= 0.294 Chirality : 0.037 0.168 3108 Planarity : 0.004 0.047 3020 Dihedral : 23.031 81.398 4295 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.49 % Allowed : 15.27 % Favored : 81.23 % 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: 2.51 (0.19), residues: 1936 helix: 2.71 (0.17), residues: 917 sheet: 0.07 (0.28), residues: 286 loop : 1.14 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.014 0.001 TYR D 247 PHE 0.020 0.001 PHE B 147 TRP 0.030 0.001 TRP C 230 HIS 0.009 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00283 (20286) covalent geometry : angle 0.53602 (28338) hydrogen bonds : bond 0.03378 ( 1054) hydrogen bonds : angle 3.46865 ( 2783) metal coordination : bond 0.00253 ( 16) metal coordination : angle 2.82447 ( 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 483 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 427 time to evaluate : 0.485 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 23 LEU cc_start: 0.8463 (mt) cc_final: 0.8214 (mm) REVERT: A 24 GLU cc_start: 0.6730 (tp30) cc_final: 0.6375 (tp30) REVERT: A 54 ASP cc_start: 0.7735 (t0) cc_final: 0.7523 (t0) REVERT: A 102 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7879 (mmmm) REVERT: A 131 GLN cc_start: 0.7663 (tt0) cc_final: 0.7081 (tp40) REVERT: A 140 ARG cc_start: 0.7018 (tmm-80) cc_final: 0.6714 (ptm-80) REVERT: A 149 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8132 (mp) REVERT: A 221 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7851 (mp10) REVERT: A 244 MET cc_start: 0.7452 (mmt) cc_final: 0.6906 (mmt) REVERT: A 276 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7443 (pt0) REVERT: A 342 MET cc_start: 0.2507 (mtp) cc_final: 0.2106 (mtp) REVERT: A 481 GLU cc_start: -0.1864 (OUTLIER) cc_final: -0.2313 (mp0) REVERT: B 25 SER cc_start: 0.8268 (m) cc_final: 0.7838 (p) REVERT: B 26 CYS cc_start: 0.8285 (m) cc_final: 0.7456 (m) REVERT: B 27 GLN cc_start: 0.7873 (mt0) cc_final: 0.7549 (mt0) REVERT: B 28 GLN cc_start: 0.7614 (tp40) cc_final: 0.7406 (tp-100) REVERT: B 37 VAL cc_start: 0.8805 (t) cc_final: 0.8602 (p) REVERT: B 65 LEU cc_start: 0.8564 (mt) cc_final: 0.8352 (mm) REVERT: B 102 LYS cc_start: 0.7996 (mmtp) cc_final: 0.7615 (mmmt) REVERT: B 109 GLU cc_start: 0.7423 (mp0) cc_final: 0.7215 (mp0) REVERT: B 113 ASP cc_start: 0.6609 (t0) cc_final: 0.6325 (t0) REVERT: B 131 GLN cc_start: 0.7835 (tp40) cc_final: 0.7321 (tp40) REVERT: B 142 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7505 (ttp80) REVERT: B 149 ILE cc_start: 0.7791 (mt) cc_final: 0.7371 (tp) REVERT: B 173 ARG cc_start: 0.7948 (ttm110) cc_final: 0.7242 (mtp85) REVERT: B 177 ASP cc_start: 0.7562 (t0) cc_final: 0.6843 (t70) REVERT: B 183 ARG cc_start: 0.7606 (mmp80) cc_final: 0.7397 (mmp80) REVERT: B 189 HIS cc_start: 0.7082 (m-70) cc_final: 0.6681 (m-70) REVERT: B 196 GLU cc_start: 0.7875 (tt0) cc_final: 0.7402 (mt-10) REVERT: B 198 LEU cc_start: 0.8738 (pt) cc_final: 0.8445 (mt) REVERT: B 200 LEU cc_start: 0.8139 (mt) cc_final: 0.7707 (mt) REVERT: B 270 LEU cc_start: 0.7639 (mm) cc_final: 0.7393 (mm) REVERT: B 276 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 279 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.7194 (ptp90) REVERT: B 281 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7263 (tp30) REVERT: B 329 MET cc_start: 0.7311 (mmp) cc_final: 0.7076 (mmp) REVERT: B 344 GLU cc_start: 0.8459 (tt0) cc_final: 0.7770 (tm-30) REVERT: B 348 PHE cc_start: 0.8815 (t80) cc_final: 0.8074 (t80) REVERT: B 351 GLU cc_start: 0.8823 (pt0) cc_final: 0.8282 (pt0) REVERT: B 379 GLU cc_start: 0.8136 (pt0) cc_final: 0.7578 (mt-10) REVERT: B 406 LEU cc_start: 0.8638 (tp) cc_final: 0.8346 (mt) REVERT: B 416 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7877 (mmm160) REVERT: B 476 PHE cc_start: 0.7218 (m-10) cc_final: 0.6931 (m-10) REVERT: C 9 LEU cc_start: 0.7995 (tp) cc_final: 0.7761 (tp) REVERT: C 23 LEU cc_start: 0.7819 (tp) cc_final: 0.7409 (tt) REVERT: C 27 GLN cc_start: 0.7996 (pp30) cc_final: 0.7569 (pp30) REVERT: C 29 LEU cc_start: 0.7368 (tp) cc_final: 0.7030 (tt) REVERT: C 30 CYS cc_start: 0.7522 (m) cc_final: 0.7140 (p) REVERT: C 33 ARG cc_start: 0.7633 (tpp80) cc_final: 0.6959 (tpp80) REVERT: C 56 LYS cc_start: 0.7470 (tppp) cc_final: 0.7255 (tppp) REVERT: C 69 GLU cc_start: 0.7242 (mm-30) cc_final: 0.7029 (mm-30) REVERT: C 70 GLN cc_start: 0.7719 (mt0) cc_final: 0.7337 (mt0) REVERT: C 78 TYR cc_start: 0.8242 (t80) cc_final: 0.7955 (t80) REVERT: C 126 MET cc_start: 0.7492 (mmm) cc_final: 0.6410 (mtp) REVERT: C 128 THR cc_start: 0.8377 (p) cc_final: 0.7361 (t) REVERT: C 132 MET cc_start: 0.7761 (tpp) cc_final: 0.6875 (mpp) REVERT: C 138 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7536 (mttt) REVERT: C 149 ILE cc_start: 0.8580 (mm) cc_final: 0.8052 (mm) REVERT: C 181 ARG cc_start: 0.8334 (tmm-80) cc_final: 0.8100 (ttp80) REVERT: C 186 GLU cc_start: 0.8419 (tp30) cc_final: 0.8048 (tp30) REVERT: C 199 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6862 (p-80) REVERT: C 213 PRO cc_start: 0.8062 (Cg_exo) cc_final: 0.7773 (Cg_endo) REVERT: C 228 ARG cc_start: 0.7539 (mmm-85) cc_final: 0.7275 (mmm-85) REVERT: C 235 LEU cc_start: 0.8680 (mt) cc_final: 0.8439 (mm) REVERT: C 253 LYS cc_start: 0.7565 (tppp) cc_final: 0.7277 (tppp) REVERT: C 274 GLN cc_start: 0.8239 (mt0) cc_final: 0.7800 (mt0) REVERT: C 342 MET cc_start: 0.5076 (OUTLIER) cc_final: 0.4777 (mmm) REVERT: D 17 THR cc_start: 0.7947 (p) cc_final: 0.7401 (p) REVERT: D 20 GLU cc_start: 0.8218 (mp0) cc_final: 0.7955 (mp0) REVERT: D 22 GLN cc_start: 0.8297 (mt0) cc_final: 0.7736 (mt0) REVERT: D 25 SER cc_start: 0.7615 (m) cc_final: 0.7266 (p) REVERT: D 42 GLU cc_start: 0.7316 (tp30) cc_final: 0.6832 (tm-30) REVERT: D 44 LEU cc_start: 0.8232 (mt) cc_final: 0.7786 (mt) REVERT: D 68 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7346 (mm-30) REVERT: D 72 PHE cc_start: 0.8133 (p90) cc_final: 0.7716 (p90) REVERT: D 73 ASP cc_start: 0.7689 (m-30) cc_final: 0.7377 (m-30) REVERT: D 101 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7698 (mmtt) REVERT: D 102 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7427 (mmtp) REVERT: D 113 ASP cc_start: 0.7566 (t0) cc_final: 0.7040 (t0) REVERT: D 115 THR cc_start: 0.7801 (t) cc_final: 0.7571 (m) REVERT: D 133 GLU cc_start: 0.7008 (tp30) cc_final: 0.6590 (tp30) REVERT: D 135 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7123 (tp30) REVERT: D 140 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7435 (ttp-170) REVERT: D 149 ILE cc_start: 0.8119 (mm) cc_final: 0.7780 (tt) REVERT: D 158 LEU cc_start: 0.8807 (tp) cc_final: 0.8542 (tp) REVERT: D 206 ASN cc_start: 0.6720 (m-40) cc_final: 0.6511 (m110) REVERT: D 216 TYR cc_start: 0.8005 (t80) cc_final: 0.7782 (t80) REVERT: D 235 LEU cc_start: 0.8744 (mt) cc_final: 0.8434 (mm) REVERT: D 267 GLU cc_start: 0.7692 (tp30) cc_final: 0.7139 (tm-30) REVERT: D 327 ARG cc_start: 0.8326 (ttt180) cc_final: 0.7835 (ttp80) REVERT: D 331 PHE cc_start: 0.6445 (m-10) cc_final: 0.5440 (m-80) REVERT: D 334 HIS cc_start: 0.6201 (p90) cc_final: 0.5805 (p90) REVERT: D 350 GLU cc_start: 0.8199 (pt0) cc_final: 0.7861 (mt-10) REVERT: D 351 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8285 (pt0) outliers start: 56 outliers final: 42 residues processed: 458 average time/residue: 0.1622 time to fit residues: 105.7638 Evaluate side-chains 470 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 423 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 21 ARG Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 231 SER 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 84 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 153 LYS 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 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 146 HIS 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 D residue 9 LEU Chi-restraints excluded: chain D residue 38 VAL 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 250 LEU Chi-restraints excluded: chain D residue 251 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 159 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 0.0040 chunk 84 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 142 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.210493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.159208 restraints weight = 39846.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.160215 restraints weight = 24907.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161507 restraints weight = 13099.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.162524 restraints weight = 11394.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.162629 restraints weight = 9398.902| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20302 Z= 0.165 Angle : 0.558 11.336 28362 Z= 0.303 Chirality : 0.038 0.214 3108 Planarity : 0.004 0.080 3020 Dihedral : 23.075 82.129 4295 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.87 % Allowed : 15.90 % Favored : 80.24 % 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: 2.42 (0.19), residues: 1936 helix: 2.61 (0.17), residues: 922 sheet: 0.06 (0.28), residues: 295 loop : 1.11 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 150 TYR 0.020 0.001 TYR B 188 PHE 0.017 0.001 PHE C 72 TRP 0.038 0.001 TRP C 230 HIS 0.026 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00352 (20286) covalent geometry : angle 0.55275 (28338) hydrogen bonds : bond 0.03784 ( 1054) hydrogen bonds : angle 3.48740 ( 2783) metal coordination : bond 0.00376 ( 16) metal coordination : angle 2.68871 ( 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 488 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 426 time to evaluate : 0.602 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 24 GLU cc_start: 0.6793 (tp30) cc_final: 0.6548 (tm-30) REVERT: A 29 LEU cc_start: 0.7551 (tp) cc_final: 0.7148 (tp) REVERT: A 102 LYS cc_start: 0.8179 (mmtm) cc_final: 0.7805 (mmmm) REVERT: A 131 GLN cc_start: 0.7762 (tt0) cc_final: 0.7303 (tp40) REVERT: A 182 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 244 MET cc_start: 0.7533 (mmt) cc_final: 0.7136 (mmt) REVERT: A 276 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7567 (pt0) REVERT: A 342 MET cc_start: 0.2527 (mtp) cc_final: 0.2135 (mtp) REVERT: A 481 GLU cc_start: -0.1813 (OUTLIER) cc_final: -0.2252 (mp0) REVERT: B 22 GLN cc_start: 0.8316 (mt0) cc_final: 0.7552 (mt0) REVERT: B 26 CYS cc_start: 0.8399 (m) cc_final: 0.7714 (m) REVERT: B 27 GLN cc_start: 0.7892 (mt0) cc_final: 0.7616 (mt0) REVERT: B 28 GLN cc_start: 0.7677 (tp40) cc_final: 0.7477 (tp-100) REVERT: B 65 LEU cc_start: 0.8572 (mt) cc_final: 0.8285 (mm) REVERT: B 86 SER cc_start: 0.8303 (t) cc_final: 0.7631 (p) REVERT: B 102 LYS cc_start: 0.7909 (mmtp) cc_final: 0.7691 (mmmt) REVERT: B 142 ARG cc_start: 0.7856 (ttp-110) cc_final: 0.7598 (ttp80) REVERT: B 149 ILE cc_start: 0.7773 (mt) cc_final: 0.7389 (tp) REVERT: B 177 ASP cc_start: 0.7776 (t0) cc_final: 0.7034 (t70) REVERT: B 183 ARG cc_start: 0.7607 (mmp80) cc_final: 0.7397 (mmp80) REVERT: B 189 HIS cc_start: 0.7182 (m-70) cc_final: 0.6711 (m-70) REVERT: B 196 GLU cc_start: 0.7961 (tt0) cc_final: 0.7403 (mt-10) REVERT: B 198 LEU cc_start: 0.8741 (pt) cc_final: 0.8473 (mt) REVERT: B 200 LEU cc_start: 0.8211 (mt) cc_final: 0.7972 (mp) REVERT: B 210 VAL cc_start: 0.7780 (t) cc_final: 0.7547 (p) REVERT: B 236 LYS cc_start: 0.8498 (tttp) cc_final: 0.8009 (tppt) REVERT: B 270 LEU cc_start: 0.7637 (mm) cc_final: 0.7352 (mm) REVERT: B 276 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7720 (mt-10) REVERT: B 279 ARG cc_start: 0.7854 (ptp-170) cc_final: 0.7216 (ptp90) REVERT: B 281 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7059 (tm-30) REVERT: B 323 ARG cc_start: 0.7030 (mmp80) cc_final: 0.6797 (mmp80) REVERT: B 329 MET cc_start: 0.7470 (mmp) cc_final: 0.7144 (mmp) REVERT: B 344 GLU cc_start: 0.8475 (tt0) cc_final: 0.7859 (tm-30) REVERT: B 351 GLU cc_start: 0.8810 (pt0) cc_final: 0.8208 (pp20) REVERT: B 376 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7043 (tp30) REVERT: B 379 GLU cc_start: 0.8134 (pt0) cc_final: 0.7562 (mt-10) REVERT: B 416 ARG cc_start: 0.8257 (mmm160) cc_final: 0.7849 (mmm160) REVERT: B 474 ILE cc_start: 0.8812 (tt) cc_final: 0.8578 (mm) REVERT: B 476 PHE cc_start: 0.7140 (m-10) cc_final: 0.6910 (m-10) REVERT: B 483 GLU cc_start: 0.8921 (pp20) cc_final: 0.8697 (pp20) REVERT: C 23 LEU cc_start: 0.7882 (tp) cc_final: 0.7405 (tt) REVERT: C 27 GLN cc_start: 0.7960 (pp30) cc_final: 0.7700 (pp30) REVERT: C 56 LYS cc_start: 0.7578 (tppp) cc_final: 0.7363 (tppp) REVERT: C 69 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6872 (mm-30) REVERT: C 70 GLN cc_start: 0.7587 (mt0) cc_final: 0.7257 (mt0) REVERT: C 108 THR cc_start: 0.8143 (m) cc_final: 0.7868 (t) REVERT: C 113 ASP cc_start: 0.7231 (t0) cc_final: 0.6844 (t70) REVERT: C 126 MET cc_start: 0.7457 (mmm) cc_final: 0.6506 (mtp) REVERT: C 128 THR cc_start: 0.8220 (p) cc_final: 0.7257 (t) REVERT: C 132 MET cc_start: 0.7743 (tpp) cc_final: 0.6973 (mpp) REVERT: C 149 ILE cc_start: 0.8428 (mm) cc_final: 0.8081 (mm) REVERT: C 181 ARG cc_start: 0.8357 (tmm-80) cc_final: 0.8102 (ttp80) REVERT: C 199 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.6630 (p-80) REVERT: C 235 LEU cc_start: 0.8662 (mt) cc_final: 0.8402 (mt) REVERT: C 274 GLN cc_start: 0.8261 (mt0) cc_final: 0.7837 (mt0) REVERT: C 342 MET cc_start: 0.4964 (OUTLIER) cc_final: 0.4659 (mmm) REVERT: D 9 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7938 (tp) REVERT: D 17 THR cc_start: 0.7919 (OUTLIER) cc_final: 0.7423 (p) REVERT: D 22 GLN cc_start: 0.8281 (mt0) cc_final: 0.7738 (mt0) REVERT: D 25 SER cc_start: 0.7764 (m) cc_final: 0.7356 (p) REVERT: D 72 PHE cc_start: 0.8095 (p90) cc_final: 0.7720 (p90) REVERT: D 73 ASP cc_start: 0.7693 (m-30) cc_final: 0.7366 (m-30) REVERT: D 74 VAL cc_start: 0.8233 (m) cc_final: 0.7999 (m) REVERT: D 113 ASP cc_start: 0.7618 (t0) cc_final: 0.6721 (p0) REVERT: D 133 GLU cc_start: 0.7205 (tp30) cc_final: 0.6340 (tp30) REVERT: D 140 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7413 (ttp-170) REVERT: D 149 ILE cc_start: 0.8175 (mm) cc_final: 0.7966 (tt) REVERT: D 154 TYR cc_start: 0.7352 (t80) cc_final: 0.7082 (t80) REVERT: D 158 LEU cc_start: 0.8665 (tp) cc_final: 0.8293 (tt) REVERT: D 164 LEU cc_start: 0.7671 (mt) cc_final: 0.7410 (mt) REVERT: D 190 ARG cc_start: 0.8030 (mtp85) cc_final: 0.7152 (ttp80) REVERT: D 216 TYR cc_start: 0.8197 (t80) cc_final: 0.7922 (t80) REVERT: D 226 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8110 (mp10) REVERT: D 229 GLU cc_start: 0.7425 (pt0) cc_final: 0.7158 (pt0) REVERT: D 235 LEU cc_start: 0.8578 (mt) cc_final: 0.8310 (mm) REVERT: D 327 ARG cc_start: 0.8294 (ttt180) cc_final: 0.7794 (ttp80) REVERT: D 331 PHE cc_start: 0.6631 (m-10) cc_final: 0.5514 (m-80) REVERT: D 334 HIS cc_start: 0.6161 (p90) cc_final: 0.5675 (p90) REVERT: D 351 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8281 (pt0) outliers start: 62 outliers final: 47 residues processed: 462 average time/residue: 0.1608 time to fit residues: 106.4712 Evaluate side-chains 464 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 411 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 231 SER 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 153 LYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 SER 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 10 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 135 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 254 THR 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 35 TRP Chi-restraints excluded: chain D residue 38 VAL 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 231 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 263 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 99 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 50.0000 chunk 163 optimal weight: 6.9990 chunk 38 optimal weight: 40.0000 chunk 161 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 206 ASN D 27 GLN D 100 HIS ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.210448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.163820 restraints weight = 39539.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.162484 restraints weight = 18165.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.163658 restraints weight = 12667.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.164703 restraints weight = 10180.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.164680 restraints weight = 9170.346| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 20302 Z= 0.241 Angle : 0.615 11.035 28362 Z= 0.333 Chirality : 0.041 0.232 3108 Planarity : 0.005 0.085 3020 Dihedral : 23.190 83.294 4295 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.43 % Allowed : 16.71 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.01 (0.19), residues: 1936 helix: 2.33 (0.17), residues: 916 sheet: -0.07 (0.27), residues: 302 loop : 0.81 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 150 TYR 0.020 0.002 TYR B 188 PHE 0.025 0.002 PHE D 217 TRP 0.051 0.002 TRP C 230 HIS 0.008 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00514 (20286) covalent geometry : angle 0.60738 (28338) hydrogen bonds : bond 0.04508 ( 1054) hydrogen bonds : angle 3.78686 ( 2783) metal coordination : bond 0.00540 ( 16) metal coordination : angle 3.26561 ( 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 503 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 432 time to evaluate : 0.427 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 128 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8334 (t) REVERT: A 131 GLN cc_start: 0.8067 (tt0) cc_final: 0.7740 (tp40) REVERT: A 132 MET cc_start: 0.8007 (tpp) cc_final: 0.7691 (mpp) REVERT: A 141 ASN cc_start: 0.8166 (m-40) cc_final: 0.7666 (t0) REVERT: A 164 LEU cc_start: 0.8567 (mm) cc_final: 0.8232 (mm) REVERT: A 177 ASP cc_start: 0.8077 (t70) cc_final: 0.7781 (t0) REVERT: A 183 ARG cc_start: 0.8592 (mmm160) cc_final: 0.8334 (mmm160) REVERT: A 186 GLU cc_start: 0.8452 (tp30) cc_final: 0.8170 (tm-30) REVERT: A 244 MET cc_start: 0.7731 (mmt) cc_final: 0.7260 (mmt) REVERT: A 276 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7660 (pt0) REVERT: A 342 MET cc_start: 0.2694 (mtp) cc_final: 0.2336 (mtp) REVERT: A 481 GLU cc_start: -0.1568 (OUTLIER) cc_final: -0.2014 (mp0) REVERT: B 22 GLN cc_start: 0.8375 (mt0) cc_final: 0.7595 (mt0) REVERT: B 26 CYS cc_start: 0.8627 (m) cc_final: 0.7927 (m) REVERT: B 28 GLN cc_start: 0.7706 (tp40) cc_final: 0.7146 (tp40) REVERT: B 64 TRP cc_start: 0.8063 (m100) cc_final: 0.7711 (m100) REVERT: B 65 LEU cc_start: 0.8440 (mt) cc_final: 0.8056 (mm) REVERT: B 86 SER cc_start: 0.8445 (t) cc_final: 0.8198 (t) REVERT: B 98 GLU cc_start: 0.7653 (tp30) cc_final: 0.7403 (tp30) REVERT: B 142 ARG cc_start: 0.7928 (ttp-110) cc_final: 0.7604 (ttp80) REVERT: B 149 ILE cc_start: 0.7753 (mt) cc_final: 0.7378 (tp) REVERT: B 173 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7333 (mtp85) REVERT: B 177 ASP cc_start: 0.7861 (t0) cc_final: 0.7153 (t70) REVERT: B 189 HIS cc_start: 0.7167 (m-70) cc_final: 0.6625 (m-70) REVERT: B 190 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7650 (mtm-85) REVERT: B 196 GLU cc_start: 0.8114 (tt0) cc_final: 0.7768 (mt-10) REVERT: B 203 HIS cc_start: 0.8139 (t70) cc_final: 0.7040 (t70) REVERT: B 207 ARG cc_start: 0.7923 (tpp80) cc_final: 0.7574 (ttm110) REVERT: B 210 VAL cc_start: 0.7991 (t) cc_final: 0.7780 (p) REVERT: B 236 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8095 (tppp) REVERT: B 247 TYR cc_start: 0.7108 (m-10) cc_final: 0.6163 (m-80) REVERT: B 265 ARG cc_start: 0.8260 (ptt180) cc_final: 0.7348 (ptt180) REVERT: B 276 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 279 ARG cc_start: 0.7925 (ptp-170) cc_final: 0.7660 (ptp-170) REVERT: B 281 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7099 (tp30) REVERT: B 297 LEU cc_start: 0.8761 (tp) cc_final: 0.8108 (pp) REVERT: B 329 MET cc_start: 0.7546 (mmp) cc_final: 0.7183 (mmp) REVERT: B 351 GLU cc_start: 0.8826 (pt0) cc_final: 0.8254 (pp20) REVERT: B 379 GLU cc_start: 0.7998 (pt0) cc_final: 0.7468 (mt-10) REVERT: B 383 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8017 (mt-10) REVERT: B 416 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7865 (mmm160) REVERT: B 474 ILE cc_start: 0.8782 (tt) cc_final: 0.8551 (mm) REVERT: C 23 LEU cc_start: 0.8048 (tp) cc_final: 0.7556 (tt) REVERT: C 42 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6868 (mt-10) REVERT: C 56 LYS cc_start: 0.7693 (tppp) cc_final: 0.7402 (tppp) REVERT: C 69 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6963 (mm-30) REVERT: C 70 GLN cc_start: 0.7859 (mt0) cc_final: 0.7586 (mt0) REVERT: C 108 THR cc_start: 0.8155 (m) cc_final: 0.7916 (t) REVERT: C 113 ASP cc_start: 0.7089 (t0) cc_final: 0.6668 (t70) REVERT: C 128 THR cc_start: 0.8066 (p) cc_final: 0.7725 (t) REVERT: C 132 MET cc_start: 0.7964 (tpp) cc_final: 0.7449 (mpp) REVERT: C 149 ILE cc_start: 0.8418 (mm) cc_final: 0.8190 (mm) REVERT: C 181 ARG cc_start: 0.8314 (tmm-80) cc_final: 0.8068 (ttp80) REVERT: C 185 LEU cc_start: 0.9103 (mm) cc_final: 0.8879 (mm) REVERT: C 199 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6673 (p-80) REVERT: C 228 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.7279 (mmm-85) REVERT: C 253 LYS cc_start: 0.7298 (tppp) cc_final: 0.7074 (tppp) REVERT: C 274 GLN cc_start: 0.8331 (mt0) cc_final: 0.7927 (mt0) REVERT: C 342 MET cc_start: 0.5416 (OUTLIER) cc_final: 0.5066 (mmm) REVERT: D 17 THR cc_start: 0.7744 (OUTLIER) cc_final: 0.7270 (p) REVERT: D 20 GLU cc_start: 0.8359 (mp0) cc_final: 0.7999 (mp0) REVERT: D 22 GLN cc_start: 0.8389 (mt0) cc_final: 0.7966 (mt0) REVERT: D 25 SER cc_start: 0.7886 (m) cc_final: 0.7450 (p) REVERT: D 42 GLU cc_start: 0.7301 (tp30) cc_final: 0.7098 (tp30) REVERT: D 68 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7160 (mm-30) REVERT: D 72 PHE cc_start: 0.8107 (p90) cc_final: 0.7699 (p90) REVERT: D 73 ASP cc_start: 0.7681 (m-30) cc_final: 0.7437 (m-30) REVERT: D 113 ASP cc_start: 0.7747 (t0) cc_final: 0.6825 (p0) REVERT: D 116 THR cc_start: 0.7896 (p) cc_final: 0.6709 (p) REVERT: D 133 GLU cc_start: 0.7266 (tp30) cc_final: 0.6523 (tm-30) REVERT: D 135 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7112 (tp30) REVERT: D 140 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7269 (ttp-170) REVERT: D 154 TYR cc_start: 0.7497 (t80) cc_final: 0.7232 (t80) REVERT: D 164 LEU cc_start: 0.7843 (mt) cc_final: 0.7217 (mt) REVERT: D 177 ASP cc_start: 0.6402 (t0) cc_final: 0.5441 (t0) REVERT: D 190 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7597 (mtm180) REVERT: D 216 TYR cc_start: 0.8189 (t80) cc_final: 0.7950 (t80) REVERT: D 226 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8211 (mp10) REVERT: D 229 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: D 235 LEU cc_start: 0.8528 (mt) cc_final: 0.8209 (mm) REVERT: D 267 GLU cc_start: 0.7805 (tp30) cc_final: 0.6963 (tm-30) REVERT: D 309 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6189 (mp0) REVERT: D 327 ARG cc_start: 0.8422 (ttt180) cc_final: 0.8065 (ttp80) REVERT: D 334 HIS cc_start: 0.6395 (p90) cc_final: 0.5884 (p90) REVERT: D 351 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8054 (tm-30) outliers start: 71 outliers final: 49 residues processed: 467 average time/residue: 0.1626 time to fit residues: 108.4260 Evaluate side-chains 482 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 425 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 84 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 231 SER 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 36 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 457 SER 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 21 ARG Chi-restraints excluded: chain C residue 45 ASP 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 135 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 241 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 17 THR 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 212 SER Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 231 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 146 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 126 optimal weight: 40.0000 chunk 158 optimal weight: 0.8980 chunk 200 optimal weight: 30.0000 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 chunk 117 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS B 206 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.212232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.164619 restraints weight = 39858.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.164508 restraints weight = 24384.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.165672 restraints weight = 13995.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.166178 restraints weight = 12513.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166737 restraints weight = 9838.532| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20302 Z= 0.173 Angle : 0.604 12.813 28362 Z= 0.322 Chirality : 0.039 0.238 3108 Planarity : 0.005 0.097 3020 Dihedral : 23.180 84.115 4295 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.74 % Allowed : 19.33 % Favored : 76.93 % 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: 2.01 (0.19), residues: 1936 helix: 2.32 (0.17), residues: 916 sheet: -0.04 (0.27), residues: 310 loop : 0.82 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.020 0.002 TYR B 188 PHE 0.021 0.001 PHE D 217 TRP 0.050 0.001 TRP C 230 HIS 0.006 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00368 (20286) covalent geometry : angle 0.59734 (28338) hydrogen bonds : bond 0.03948 ( 1054) hydrogen bonds : angle 3.63851 ( 2783) metal coordination : bond 0.00394 ( 16) metal coordination : angle 3.12292 ( 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 475 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 415 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: A 9 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7413 (mt) REVERT: A 27 GLN cc_start: 0.8077 (mt0) cc_final: 0.7816 (mt0) REVERT: A 72 PHE cc_start: 0.7646 (p90) cc_final: 0.6721 (p90) REVERT: A 73 ASP cc_start: 0.7261 (m-30) cc_final: 0.6522 (m-30) REVERT: A 102 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7801 (mmmm) REVERT: A 113 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6915 (m-30) REVERT: A 131 GLN cc_start: 0.8061 (tt0) cc_final: 0.7756 (tp40) REVERT: A 132 MET cc_start: 0.8042 (tpp) cc_final: 0.7706 (mpp) REVERT: A 135 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7092 (mm-30) REVERT: A 139 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7582 (mm-30) REVERT: A 164 LEU cc_start: 0.8587 (mm) cc_final: 0.8238 (mm) REVERT: A 177 ASP cc_start: 0.8076 (t70) cc_final: 0.7799 (t0) REVERT: A 182 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A 183 ARG cc_start: 0.8585 (mmm160) cc_final: 0.8248 (mmm160) REVERT: A 186 GLU cc_start: 0.8434 (tp30) cc_final: 0.8113 (tp30) REVERT: A 244 MET cc_start: 0.7726 (mmt) cc_final: 0.7188 (mmt) REVERT: A 276 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7558 (pt0) REVERT: A 342 MET cc_start: 0.2372 (mtp) cc_final: 0.2030 (mtp) REVERT: A 397 ARG cc_start: -0.1245 (OUTLIER) cc_final: -0.1551 (ttm170) REVERT: A 481 GLU cc_start: -0.1508 (OUTLIER) cc_final: -0.1953 (mp0) REVERT: B 22 GLN cc_start: 0.8258 (mt0) cc_final: 0.7617 (mt0) REVERT: B 25 SER cc_start: 0.8613 (m) cc_final: 0.8045 (p) REVERT: B 26 CYS cc_start: 0.8615 (m) cc_final: 0.7926 (m) REVERT: B 28 GLN cc_start: 0.7846 (tp40) cc_final: 0.7530 (tp-100) REVERT: B 64 TRP cc_start: 0.7987 (m100) cc_final: 0.7678 (m100) REVERT: B 65 LEU cc_start: 0.8398 (mt) cc_final: 0.8053 (mm) REVERT: B 86 SER cc_start: 0.8325 (t) cc_final: 0.7629 (p) REVERT: B 98 GLU cc_start: 0.7602 (tp30) cc_final: 0.7314 (tp30) REVERT: B 142 ARG cc_start: 0.7793 (ttp-110) cc_final: 0.7557 (ttp80) REVERT: B 149 ILE cc_start: 0.7741 (mt) cc_final: 0.7413 (tp) REVERT: B 177 ASP cc_start: 0.7859 (t0) cc_final: 0.7074 (t70) REVERT: B 186 GLU cc_start: 0.8075 (tt0) cc_final: 0.7151 (tm-30) REVERT: B 189 HIS cc_start: 0.7271 (m-70) cc_final: 0.6785 (m-70) REVERT: B 190 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7380 (mtm-85) REVERT: B 196 GLU cc_start: 0.8095 (tt0) cc_final: 0.7750 (mt-10) REVERT: B 200 LEU cc_start: 0.8451 (mp) cc_final: 0.8228 (mp) REVERT: B 203 HIS cc_start: 0.8187 (t70) cc_final: 0.7032 (t70) REVERT: B 207 ARG cc_start: 0.7937 (tpp80) cc_final: 0.7597 (ttm110) REVERT: B 210 VAL cc_start: 0.7853 (t) cc_final: 0.7647 (p) REVERT: B 236 LYS cc_start: 0.8493 (tttp) cc_final: 0.7909 (tppt) REVERT: B 247 TYR cc_start: 0.6723 (m-10) cc_final: 0.6105 (m-80) REVERT: B 263 LEU cc_start: 0.8247 (tp) cc_final: 0.7583 (pp) REVERT: B 265 ARG cc_start: 0.8219 (ptt180) cc_final: 0.7079 (ptt90) REVERT: B 276 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7701 (mt-10) REVERT: B 279 ARG cc_start: 0.8020 (ptp-170) cc_final: 0.7315 (ptp90) REVERT: B 281 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6921 (tm-30) REVERT: B 297 LEU cc_start: 0.8544 (tp) cc_final: 0.8339 (pp) REVERT: B 329 MET cc_start: 0.7570 (mmp) cc_final: 0.7138 (mmp) REVERT: B 342 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6717 (mmp) REVERT: B 345 TRP cc_start: 0.7566 (m100) cc_final: 0.7227 (m100) REVERT: B 351 GLU cc_start: 0.8744 (pt0) cc_final: 0.8291 (pt0) REVERT: B 376 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7308 (mm-30) REVERT: B 379 GLU cc_start: 0.8077 (pt0) cc_final: 0.7461 (mt-10) REVERT: B 383 GLU cc_start: 0.8210 (mt-10) cc_final: 0.8004 (mt-10) REVERT: B 416 ARG cc_start: 0.8280 (mmm160) cc_final: 0.7869 (mmm160) REVERT: B 461 ARG cc_start: 0.7027 (mmt180) cc_final: 0.6811 (mmt180) REVERT: B 474 ILE cc_start: 0.8827 (tt) cc_final: 0.8547 (mm) REVERT: C 23 LEU cc_start: 0.7891 (tp) cc_final: 0.7564 (tt) REVERT: C 56 LYS cc_start: 0.7752 (tppp) cc_final: 0.7431 (tppp) REVERT: C 70 GLN cc_start: 0.7859 (mt0) cc_final: 0.7569 (mt0) REVERT: C 108 THR cc_start: 0.8168 (m) cc_final: 0.7951 (t) REVERT: C 113 ASP cc_start: 0.7254 (t0) cc_final: 0.6894 (t70) REVERT: C 126 MET cc_start: 0.7602 (mmm) cc_final: 0.6575 (mtp) REVERT: C 128 THR cc_start: 0.8020 (p) cc_final: 0.7711 (t) REVERT: C 131 GLN cc_start: 0.8318 (tt0) cc_final: 0.8086 (tt0) REVERT: C 132 MET cc_start: 0.8002 (tpp) cc_final: 0.7459 (mpp) REVERT: C 140 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6642 (ptm-80) REVERT: C 149 ILE cc_start: 0.8613 (mm) cc_final: 0.8278 (mm) REVERT: C 181 ARG cc_start: 0.8343 (tmm-80) cc_final: 0.8019 (tmm-80) REVERT: C 199 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.6696 (p-80) REVERT: C 228 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.6985 (mtp85) REVERT: C 235 LEU cc_start: 0.8687 (mt) cc_final: 0.8130 (pp) REVERT: C 240 ILE cc_start: 0.8655 (pt) cc_final: 0.8288 (mp) REVERT: C 253 LYS cc_start: 0.7401 (tppp) cc_final: 0.7090 (tppp) REVERT: C 274 GLN cc_start: 0.8404 (mt0) cc_final: 0.7976 (mt0) REVERT: C 342 MET cc_start: 0.5446 (OUTLIER) cc_final: 0.5050 (mmm) REVERT: D 17 THR cc_start: 0.7694 (OUTLIER) cc_final: 0.7145 (p) REVERT: D 20 GLU cc_start: 0.8317 (mp0) cc_final: 0.8032 (mp0) REVERT: D 22 GLN cc_start: 0.8372 (mt0) cc_final: 0.7894 (mt0) REVERT: D 25 SER cc_start: 0.7775 (m) cc_final: 0.7318 (p) REVERT: D 68 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7031 (mm-30) REVERT: D 72 PHE cc_start: 0.8084 (p90) cc_final: 0.7739 (p90) REVERT: D 73 ASP cc_start: 0.7737 (m-30) cc_final: 0.7482 (m-30) REVERT: D 102 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7620 (mmtp) REVERT: D 113 ASP cc_start: 0.7571 (t0) cc_final: 0.6683 (p0) REVERT: D 116 THR cc_start: 0.7762 (p) cc_final: 0.6489 (p) REVERT: D 133 GLU cc_start: 0.7344 (tp30) cc_final: 0.6442 (tm-30) REVERT: D 135 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7155 (tp30) REVERT: D 140 ARG cc_start: 0.7931 (ttp-110) cc_final: 0.7326 (ttp-170) REVERT: D 154 TYR cc_start: 0.7369 (t80) cc_final: 0.7101 (t80) REVERT: D 158 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8071 (pt) REVERT: D 164 LEU cc_start: 0.7683 (mt) cc_final: 0.6943 (mt) REVERT: D 177 ASP cc_start: 0.6538 (t0) cc_final: 0.5448 (t70) REVERT: D 183 ARG cc_start: 0.8652 (tpp80) cc_final: 0.8334 (tpp80) REVERT: D 216 TYR cc_start: 0.8147 (t80) cc_final: 0.7922 (t80) REVERT: D 226 GLN cc_start: 0.8501 (mm-40) cc_final: 0.7893 (mp10) REVERT: D 229 GLU cc_start: 0.7645 (pt0) cc_final: 0.7368 (pt0) REVERT: D 235 LEU cc_start: 0.8505 (mt) cc_final: 0.8182 (mm) REVERT: D 267 GLU cc_start: 0.7707 (tp30) cc_final: 0.7002 (tm-30) REVERT: D 309 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6330 (mp0) REVERT: D 327 ARG cc_start: 0.8437 (ttt180) cc_final: 0.7974 (ttp80) REVERT: D 334 HIS cc_start: 0.6510 (p90) cc_final: 0.5941 (p90) REVERT: D 351 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: D 409 ARG cc_start: 0.8244 (ttt180) cc_final: 0.7971 (ttp-170) outliers start: 60 outliers final: 45 residues processed: 448 average time/residue: 0.1632 time to fit residues: 104.2231 Evaluate side-chains 466 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 410 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 231 SER 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 80 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 457 SER 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 45 ASP 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 140 ARG Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 198 LEU 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 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 26 CYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 175 VAL 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 351 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 25 optimal weight: 0.0870 chunk 97 optimal weight: 0.0870 chunk 148 optimal weight: 0.0170 chunk 40 optimal weight: 40.0000 chunk 172 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN B 146 HIS B 206 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.210700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161441 restraints weight = 39611.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161179 restraints weight = 23243.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.162526 restraints weight = 13376.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.163407 restraints weight = 11617.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163532 restraints weight = 9355.820| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20302 Z= 0.134 Angle : 0.580 11.992 28362 Z= 0.307 Chirality : 0.038 0.203 3108 Planarity : 0.004 0.048 3020 Dihedral : 23.108 81.978 4295 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.43 % Allowed : 20.07 % Favored : 76.50 % 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: 2.04 (0.19), residues: 1936 helix: 2.33 (0.17), residues: 917 sheet: -0.05 (0.28), residues: 311 loop : 0.87 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 237 TYR 0.022 0.001 TYR B 188 PHE 0.021 0.001 PHE D 147 TRP 0.037 0.001 TRP C 230 HIS 0.005 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00287 (20286) covalent geometry : angle 0.57451 (28338) hydrogen bonds : bond 0.03530 ( 1054) hydrogen bonds : angle 3.54084 ( 2783) metal coordination : bond 0.00287 ( 16) metal coordination : angle 2.77174 ( 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 482 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 427 time to evaluate : 0.589 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: A 9 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 23 LEU cc_start: 0.8270 (mp) cc_final: 0.7782 (mt) REVERT: A 27 GLN cc_start: 0.7979 (mt0) cc_final: 0.7735 (mt0) REVERT: A 72 PHE cc_start: 0.7636 (p90) cc_final: 0.6831 (p90) REVERT: A 102 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7891 (mmmm) REVERT: A 115 THR cc_start: 0.8027 (p) cc_final: 0.7782 (m) REVERT: A 131 GLN cc_start: 0.7946 (tt0) cc_final: 0.7591 (tp40) REVERT: A 132 MET cc_start: 0.7920 (tpp) cc_final: 0.7521 (mpp) REVERT: A 139 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7487 (mm-30) REVERT: A 142 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7415 (ttp80) REVERT: A 164 LEU cc_start: 0.8574 (mm) cc_final: 0.8078 (mm) REVERT: A 182 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7643 (tm-30) REVERT: A 183 ARG cc_start: 0.8520 (mmm160) cc_final: 0.8087 (mmm160) REVERT: A 186 GLU cc_start: 0.8282 (tp30) cc_final: 0.8072 (tm-30) REVERT: A 244 MET cc_start: 0.7656 (mmt) cc_final: 0.7145 (mmt) REVERT: A 276 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7531 (pt0) REVERT: A 342 MET cc_start: 0.2383 (mtp) cc_final: 0.2042 (mtp) REVERT: A 397 ARG cc_start: -0.1253 (OUTLIER) cc_final: -0.1529 (ttm170) REVERT: A 481 GLU cc_start: -0.1466 (OUTLIER) cc_final: -0.1913 (mp0) REVERT: B 25 SER cc_start: 0.8594 (m) cc_final: 0.8054 (p) REVERT: B 26 CYS cc_start: 0.8353 (m) cc_final: 0.7506 (m) REVERT: B 28 GLN cc_start: 0.7827 (tp40) cc_final: 0.7484 (tp-100) REVERT: B 64 TRP cc_start: 0.8030 (m100) cc_final: 0.7672 (m100) REVERT: B 65 LEU cc_start: 0.8521 (mt) cc_final: 0.8161 (mm) REVERT: B 98 GLU cc_start: 0.7497 (tp30) cc_final: 0.7186 (tp30) REVERT: B 142 ARG cc_start: 0.7864 (ttp-110) cc_final: 0.7518 (ttp80) REVERT: B 149 ILE cc_start: 0.7740 (mt) cc_final: 0.7357 (tp) REVERT: B 173 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7189 (mtp85) REVERT: B 177 ASP cc_start: 0.7837 (t0) cc_final: 0.7038 (t70) REVERT: B 186 GLU cc_start: 0.7771 (tt0) cc_final: 0.7343 (tt0) REVERT: B 189 HIS cc_start: 0.7126 (m-70) cc_final: 0.6656 (m-70) REVERT: B 196 GLU cc_start: 0.8062 (tt0) cc_final: 0.6457 (tt0) REVERT: B 200 LEU cc_start: 0.8360 (mp) cc_final: 0.8018 (mp) REVERT: B 203 HIS cc_start: 0.8008 (t70) cc_final: 0.7798 (t70) REVERT: B 210 VAL cc_start: 0.7813 (t) cc_final: 0.7562 (p) REVERT: B 247 TYR cc_start: 0.6629 (m-10) cc_final: 0.6301 (m-80) REVERT: B 263 LEU cc_start: 0.8227 (tp) cc_final: 0.7734 (pp) REVERT: B 265 ARG cc_start: 0.8249 (ptt180) cc_final: 0.7112 (ptt180) REVERT: B 276 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7643 (mt-10) REVERT: B 279 ARG cc_start: 0.7894 (ptp-170) cc_final: 0.7216 (ptp90) REVERT: B 297 LEU cc_start: 0.8693 (tp) cc_final: 0.8292 (pp) REVERT: B 310 PRO cc_start: 0.7142 (Cg_exo) cc_final: 0.6756 (Cg_endo) REVERT: B 329 MET cc_start: 0.7452 (mmp) cc_final: 0.7000 (mmp) REVERT: B 342 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6689 (mmp) REVERT: B 345 TRP cc_start: 0.7405 (m100) cc_final: 0.7109 (m100) REVERT: B 416 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7817 (mmm160) REVERT: B 454 TRP cc_start: 0.8017 (t60) cc_final: 0.7802 (t60) REVERT: B 474 ILE cc_start: 0.8892 (tt) cc_final: 0.8580 (mm) REVERT: C 23 LEU cc_start: 0.7858 (tp) cc_final: 0.7574 (tt) REVERT: C 56 LYS cc_start: 0.7663 (tppp) cc_final: 0.7325 (tppp) REVERT: C 68 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7308 (tm-30) REVERT: C 108 THR cc_start: 0.8123 (m) cc_final: 0.7008 (t) REVERT: C 113 ASP cc_start: 0.7120 (t0) cc_final: 0.6905 (t70) REVERT: C 126 MET cc_start: 0.7566 (mmm) cc_final: 0.6741 (mtp) REVERT: C 128 THR cc_start: 0.8057 (p) cc_final: 0.7804 (t) REVERT: C 132 MET cc_start: 0.7832 (tpp) cc_final: 0.7505 (mmm) REVERT: C 142 ARG cc_start: 0.7633 (ptm160) cc_final: 0.7334 (ptm-80) REVERT: C 181 ARG cc_start: 0.8310 (tmm-80) cc_final: 0.7928 (tmm-80) REVERT: C 199 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.6696 (p-80) REVERT: C 228 ARG cc_start: 0.7605 (mmm-85) cc_final: 0.7050 (mtp85) REVERT: C 235 LEU cc_start: 0.8735 (mt) cc_final: 0.8220 (pp) REVERT: C 253 LYS cc_start: 0.7319 (tppp) cc_final: 0.7069 (tppp) REVERT: C 274 GLN cc_start: 0.8291 (mt0) cc_final: 0.7805 (mt0) REVERT: C 342 MET cc_start: 0.5443 (OUTLIER) cc_final: 0.5039 (mmm) REVERT: D 9 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8153 (tp) REVERT: D 17 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.6896 (p) REVERT: D 20 GLU cc_start: 0.8257 (mp0) cc_final: 0.8029 (mp0) REVERT: D 22 GLN cc_start: 0.8193 (mt0) cc_final: 0.7619 (mt0) REVERT: D 25 SER cc_start: 0.7695 (m) cc_final: 0.7449 (p) REVERT: D 30 CYS cc_start: 0.7909 (m) cc_final: 0.7653 (m) REVERT: D 68 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7040 (mm-30) REVERT: D 72 PHE cc_start: 0.8087 (p90) cc_final: 0.7687 (p90) REVERT: D 73 ASP cc_start: 0.7716 (m-30) cc_final: 0.7508 (m-30) REVERT: D 113 ASP cc_start: 0.7460 (t0) cc_final: 0.6639 (p0) REVERT: D 116 THR cc_start: 0.7506 (p) cc_final: 0.6243 (p) REVERT: D 133 GLU cc_start: 0.7344 (tp30) cc_final: 0.6761 (tm-30) REVERT: D 135 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7152 (tp30) REVERT: D 140 ARG cc_start: 0.7738 (ttp-110) cc_final: 0.7374 (ttp-110) REVERT: D 154 TYR cc_start: 0.7277 (t80) cc_final: 0.7001 (t80) REVERT: D 158 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8091 (pp) REVERT: D 164 LEU cc_start: 0.7914 (mt) cc_final: 0.7133 (mt) REVERT: D 177 ASP cc_start: 0.6506 (t0) cc_final: 0.5420 (t70) REVERT: D 183 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8214 (tpp80) REVERT: D 226 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8040 (mp10) REVERT: D 229 GLU cc_start: 0.7580 (pt0) cc_final: 0.7328 (pt0) REVERT: D 235 LEU cc_start: 0.8542 (mt) cc_final: 0.8164 (mm) REVERT: D 267 GLU cc_start: 0.7732 (tp30) cc_final: 0.7105 (tm-30) REVERT: D 309 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6297 (mp0) REVERT: D 327 ARG cc_start: 0.8357 (ttt180) cc_final: 0.7916 (ttp80) REVERT: D 334 HIS cc_start: 0.6238 (p90) cc_final: 0.5903 (p90) REVERT: D 409 ARG cc_start: 0.8325 (ttt180) cc_final: 0.7787 (ttm170) REVERT: D 452 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7459 (t0) outliers start: 55 outliers final: 40 residues processed: 457 average time/residue: 0.1630 time to fit residues: 106.6584 Evaluate side-chains 471 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 421 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 231 SER 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 249 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 457 SER 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 45 ASP 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 199 HIS 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 115 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 158 LEU 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 271 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 452 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 60 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 50.0000 chunk 207 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 160 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.212369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.164618 restraints weight = 39677.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164710 restraints weight = 25971.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.165654 restraints weight = 14863.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.166320 restraints weight = 13163.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.167419 restraints weight = 10138.568| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20302 Z= 0.162 Angle : 0.598 10.956 28362 Z= 0.319 Chirality : 0.039 0.190 3108 Planarity : 0.004 0.048 3020 Dihedral : 23.130 80.563 4295 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.43 % Allowed : 20.51 % Favored : 76.06 % 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: 1.94 (0.19), residues: 1936 helix: 2.26 (0.17), residues: 916 sheet: -0.10 (0.27), residues: 310 loop : 0.80 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 456 TYR 0.025 0.002 TYR D 216 PHE 0.018 0.001 PHE D 217 TRP 0.032 0.001 TRP C 230 HIS 0.005 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00349 (20286) covalent geometry : angle 0.59153 (28338) hydrogen bonds : bond 0.03819 ( 1054) hydrogen bonds : angle 3.64426 ( 2783) metal coordination : bond 0.00339 ( 16) metal coordination : angle 2.98123 ( 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 478 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 423 time to evaluate : 0.452 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: A 9 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7431 (mt) REVERT: A 23 LEU cc_start: 0.8294 (mp) cc_final: 0.7824 (mt) REVERT: A 72 PHE cc_start: 0.7663 (p90) cc_final: 0.6797 (p90) REVERT: A 102 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7878 (mmmm) REVERT: A 113 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6996 (m-30) REVERT: A 115 THR cc_start: 0.8054 (p) cc_final: 0.7739 (m) REVERT: A 131 GLN cc_start: 0.8009 (tt0) cc_final: 0.7685 (tp40) REVERT: A 132 MET cc_start: 0.8014 (tpp) cc_final: 0.7648 (mpp) REVERT: A 135 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7110 (mm-30) REVERT: A 139 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7429 (mm-30) REVERT: A 140 ARG cc_start: 0.7395 (tmm-80) cc_final: 0.7099 (tmm-80) REVERT: A 164 LEU cc_start: 0.8581 (mm) cc_final: 0.8207 (mm) REVERT: A 177 ASP cc_start: 0.7958 (t70) cc_final: 0.7639 (t0) REVERT: A 182 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 183 ARG cc_start: 0.8529 (mmm160) cc_final: 0.8102 (mmm160) REVERT: A 244 MET cc_start: 0.7729 (mmt) cc_final: 0.7220 (mmt) REVERT: A 342 MET cc_start: 0.2733 (mtp) cc_final: 0.2376 (mtp) REVERT: A 377 LEU cc_start: 0.5458 (OUTLIER) cc_final: 0.4379 (mp) REVERT: A 397 ARG cc_start: -0.1303 (OUTLIER) cc_final: -0.1530 (ttm170) REVERT: A 481 GLU cc_start: -0.1405 (OUTLIER) cc_final: -0.1817 (mp0) REVERT: B 22 GLN cc_start: 0.8290 (mt0) cc_final: 0.7694 (mt0) REVERT: B 25 SER cc_start: 0.8646 (m) cc_final: 0.8090 (p) REVERT: B 26 CYS cc_start: 0.8226 (m) cc_final: 0.7864 (m) REVERT: B 28 GLN cc_start: 0.7933 (tp40) cc_final: 0.7452 (tp-100) REVERT: B 64 TRP cc_start: 0.8009 (m100) cc_final: 0.7644 (m100) REVERT: B 65 LEU cc_start: 0.8417 (mt) cc_final: 0.8028 (mm) REVERT: B 98 GLU cc_start: 0.7527 (tp30) cc_final: 0.7201 (tp30) REVERT: B 109 GLU cc_start: 0.7983 (mp0) cc_final: 0.7716 (mp0) REVERT: B 142 ARG cc_start: 0.7826 (ttp-110) cc_final: 0.7470 (ttp80) REVERT: B 149 ILE cc_start: 0.7707 (mt) cc_final: 0.7364 (tp) REVERT: B 173 ARG cc_start: 0.7936 (ttm110) cc_final: 0.7036 (mtp85) REVERT: B 177 ASP cc_start: 0.7842 (t0) cc_final: 0.7047 (t70) REVERT: B 183 ARG cc_start: 0.7808 (mmm160) cc_final: 0.6975 (mmp80) REVERT: B 186 GLU cc_start: 0.7886 (tt0) cc_final: 0.6811 (tt0) REVERT: B 189 HIS cc_start: 0.7316 (m-70) cc_final: 0.6810 (m-70) REVERT: B 196 GLU cc_start: 0.7957 (tt0) cc_final: 0.7622 (mt-10) REVERT: B 203 HIS cc_start: 0.8126 (t70) cc_final: 0.6865 (t70) REVERT: B 207 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7522 (ttm110) REVERT: B 229 GLU cc_start: 0.7186 (mp0) cc_final: 0.6936 (mp0) REVERT: B 236 LYS cc_start: 0.8521 (tptm) cc_final: 0.8119 (tptp) REVERT: B 247 TYR cc_start: 0.6758 (m-10) cc_final: 0.6340 (m-80) REVERT: B 263 LEU cc_start: 0.8246 (tp) cc_final: 0.7684 (pp) REVERT: B 265 ARG cc_start: 0.8191 (ptt180) cc_final: 0.7195 (ptt180) REVERT: B 276 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7704 (mt-10) REVERT: B 297 LEU cc_start: 0.8682 (tp) cc_final: 0.8318 (pp) REVERT: B 310 PRO cc_start: 0.7090 (Cg_exo) cc_final: 0.6708 (Cg_endo) REVERT: B 329 MET cc_start: 0.7456 (mmp) cc_final: 0.7020 (mmp) REVERT: B 342 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6854 (mmp) REVERT: B 345 TRP cc_start: 0.7603 (m100) cc_final: 0.7219 (m100) REVERT: B 351 GLU cc_start: 0.8758 (pt0) cc_final: 0.8212 (pp20) REVERT: B 379 GLU cc_start: 0.8131 (pt0) cc_final: 0.7511 (mt-10) REVERT: B 416 ARG cc_start: 0.8268 (mmm160) cc_final: 0.7945 (mmm160) REVERT: B 474 ILE cc_start: 0.8900 (tt) cc_final: 0.8586 (mm) REVERT: B 483 GLU cc_start: 0.8876 (pt0) cc_final: 0.8648 (pp20) REVERT: C 56 LYS cc_start: 0.7765 (tppp) cc_final: 0.7533 (tppp) REVERT: C 68 GLU cc_start: 0.7665 (tm-30) cc_final: 0.6646 (tm-30) REVERT: C 69 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6065 (mm-30) REVERT: C 108 THR cc_start: 0.7993 (m) cc_final: 0.7516 (t) REVERT: C 113 ASP cc_start: 0.6986 (t0) cc_final: 0.6587 (t70) REVERT: C 126 MET cc_start: 0.7693 (mmm) cc_final: 0.6764 (mtp) REVERT: C 128 THR cc_start: 0.8011 (p) cc_final: 0.7787 (t) REVERT: C 132 MET cc_start: 0.7901 (tpp) cc_final: 0.7562 (mmm) REVERT: C 134 LEU cc_start: 0.7738 (tp) cc_final: 0.7420 (tt) REVERT: C 140 ARG cc_start: 0.7258 (ttp80) cc_final: 0.6886 (ptm-80) REVERT: C 149 ILE cc_start: 0.8555 (mm) cc_final: 0.7858 (mm) REVERT: C 181 ARG cc_start: 0.8448 (tmm-80) cc_final: 0.8163 (tmm-80) REVERT: C 199 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.6715 (p-80) REVERT: C 228 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.7380 (mmt180) REVERT: C 231 SER cc_start: 0.8394 (t) cc_final: 0.8123 (p) REVERT: C 253 LYS cc_start: 0.7401 (tppp) cc_final: 0.7110 (tppp) REVERT: C 342 MET cc_start: 0.5469 (OUTLIER) cc_final: 0.5072 (mmm) REVERT: D 17 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7002 (p) REVERT: D 20 GLU cc_start: 0.8330 (mp0) cc_final: 0.8017 (mp0) REVERT: D 22 GLN cc_start: 0.8268 (mt0) cc_final: 0.7697 (mt0) REVERT: D 30 CYS cc_start: 0.7999 (m) cc_final: 0.7673 (m) REVERT: D 68 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7044 (mm-30) REVERT: D 72 PHE cc_start: 0.8142 (p90) cc_final: 0.7715 (p90) REVERT: D 73 ASP cc_start: 0.7722 (m-30) cc_final: 0.7438 (m-30) REVERT: D 113 ASP cc_start: 0.7463 (t0) cc_final: 0.6642 (p0) REVERT: D 116 THR cc_start: 0.7546 (p) cc_final: 0.6341 (p) REVERT: D 133 GLU cc_start: 0.7419 (tp30) cc_final: 0.6622 (tp30) REVERT: D 135 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7215 (tp30) REVERT: D 140 ARG cc_start: 0.7742 (ttp-110) cc_final: 0.7423 (ttp-110) REVERT: D 154 TYR cc_start: 0.7355 (t80) cc_final: 0.7121 (t80) REVERT: D 158 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8061 (pt) REVERT: D 164 LEU cc_start: 0.7777 (mt) cc_final: 0.7556 (mt) REVERT: D 183 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8276 (tpp80) REVERT: D 226 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7908 (mp10) REVERT: D 229 GLU cc_start: 0.7663 (pt0) cc_final: 0.7374 (pt0) REVERT: D 235 LEU cc_start: 0.8521 (mt) cc_final: 0.8182 (mm) REVERT: D 267 GLU cc_start: 0.7688 (tp30) cc_final: 0.7101 (tm-30) REVERT: D 309 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6262 (mp0) REVERT: D 327 ARG cc_start: 0.8407 (ttt180) cc_final: 0.7927 (ttp80) REVERT: D 334 HIS cc_start: 0.6350 (p90) cc_final: 0.5965 (p90) REVERT: D 409 ARG cc_start: 0.8347 (ttt180) cc_final: 0.7961 (ttp-170) outliers start: 55 outliers final: 40 residues processed: 454 average time/residue: 0.1627 time to fit residues: 104.7436 Evaluate side-chains 468 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 418 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 231 SER 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 80 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 457 SER 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 45 ASP 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 198 LEU 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 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 69 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 158 LEU 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 271 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 71 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.211288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.164446 restraints weight = 39435.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163888 restraints weight = 18040.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164899 restraints weight = 12260.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.165581 restraints weight = 9920.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165707 restraints weight = 8961.200| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20302 Z= 0.203 Angle : 0.639 13.527 28362 Z= 0.339 Chirality : 0.040 0.187 3108 Planarity : 0.005 0.049 3020 Dihedral : 23.193 81.773 4291 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.55 % Allowed : 20.64 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.74 (0.19), residues: 1936 helix: 2.12 (0.17), residues: 913 sheet: -0.24 (0.27), residues: 314 loop : 0.71 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 456 TYR 0.024 0.002 TYR B 188 PHE 0.023 0.002 PHE D 217 TRP 0.046 0.002 TRP C 230 HIS 0.006 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00435 (20286) covalent geometry : angle 0.63364 (28338) hydrogen bonds : bond 0.04208 ( 1054) hydrogen bonds : angle 3.76947 ( 2783) metal coordination : bond 0.00449 ( 16) metal coordination : angle 2.86308 ( 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 463 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 406 time to evaluate : 0.544 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: A 1 MET cc_start: 0.7535 (tpp) cc_final: 0.7291 (mmm) REVERT: A 23 LEU cc_start: 0.8262 (mp) cc_final: 0.7954 (mt) REVERT: A 24 GLU cc_start: 0.6480 (tm-30) cc_final: 0.6231 (tm-30) REVERT: A 72 PHE cc_start: 0.7629 (p90) cc_final: 0.6864 (p90) REVERT: A 115 THR cc_start: 0.8004 (p) cc_final: 0.7697 (m) REVERT: A 128 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8309 (m) REVERT: A 131 GLN cc_start: 0.8015 (tt0) cc_final: 0.7724 (tp40) REVERT: A 139 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7606 (mm-30) REVERT: A 164 LEU cc_start: 0.8615 (mm) cc_final: 0.8246 (mm) REVERT: A 177 ASP cc_start: 0.7927 (t70) cc_final: 0.7615 (t0) REVERT: A 182 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 244 MET cc_start: 0.7732 (mmt) cc_final: 0.7256 (mmt) REVERT: A 276 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7613 (pt0) REVERT: A 342 MET cc_start: 0.2725 (mtp) cc_final: 0.2377 (mtp) REVERT: A 377 LEU cc_start: 0.5470 (OUTLIER) cc_final: 0.4399 (mp) REVERT: A 481 GLU cc_start: -0.1354 (OUTLIER) cc_final: -0.1765 (mp0) REVERT: B 22 GLN cc_start: 0.8366 (mt0) cc_final: 0.7759 (mt0) REVERT: B 25 SER cc_start: 0.8636 (m) cc_final: 0.8087 (p) REVERT: B 26 CYS cc_start: 0.8123 (m) cc_final: 0.7755 (m) REVERT: B 28 GLN cc_start: 0.7833 (tp40) cc_final: 0.7375 (tp-100) REVERT: B 64 TRP cc_start: 0.7971 (m100) cc_final: 0.7643 (m100) REVERT: B 98 GLU cc_start: 0.7488 (tp30) cc_final: 0.7217 (tp30) REVERT: B 142 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7514 (ttp80) REVERT: B 149 ILE cc_start: 0.7734 (mt) cc_final: 0.7377 (tp) REVERT: B 161 TRP cc_start: 0.8340 (t60) cc_final: 0.7976 (t60) REVERT: B 173 ARG cc_start: 0.8013 (ttm110) cc_final: 0.7282 (mtt-85) REVERT: B 177 ASP cc_start: 0.7903 (t0) cc_final: 0.7173 (t70) REVERT: B 186 GLU cc_start: 0.7737 (tt0) cc_final: 0.7354 (tm-30) REVERT: B 189 HIS cc_start: 0.7159 (m-70) cc_final: 0.6757 (m-70) REVERT: B 203 HIS cc_start: 0.7936 (t70) cc_final: 0.6663 (t70) REVERT: B 207 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7519 (ttm110) REVERT: B 247 TYR cc_start: 0.6868 (m-10) cc_final: 0.6542 (m-80) REVERT: B 263 LEU cc_start: 0.8273 (tp) cc_final: 0.7739 (pp) REVERT: B 265 ARG cc_start: 0.8220 (ptt180) cc_final: 0.7218 (ptt180) REVERT: B 276 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7639 (mt-10) REVERT: B 279 ARG cc_start: 0.7905 (ptp-170) cc_final: 0.7057 (mtt-85) REVERT: B 297 LEU cc_start: 0.8727 (tp) cc_final: 0.8361 (pp) REVERT: B 310 PRO cc_start: 0.7038 (Cg_exo) cc_final: 0.6688 (Cg_endo) REVERT: B 329 MET cc_start: 0.7454 (mmp) cc_final: 0.6913 (mmp) REVERT: B 342 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6964 (mmp) REVERT: B 345 TRP cc_start: 0.7612 (m100) cc_final: 0.7225 (m100) REVERT: B 351 GLU cc_start: 0.8705 (pt0) cc_final: 0.7847 (tm-30) REVERT: B 379 GLU cc_start: 0.8126 (pt0) cc_final: 0.7224 (mt-10) REVERT: B 383 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7552 (mp0) REVERT: B 416 ARG cc_start: 0.8153 (mmm160) cc_final: 0.7814 (mmm160) REVERT: B 474 ILE cc_start: 0.8868 (tt) cc_final: 0.8572 (mm) REVERT: B 483 GLU cc_start: 0.8888 (pt0) cc_final: 0.8595 (pp20) REVERT: C 17 THR cc_start: 0.5978 (p) cc_final: 0.5616 (t) REVERT: C 68 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7262 (tm-30) REVERT: C 108 THR cc_start: 0.8094 (m) cc_final: 0.7579 (t) REVERT: C 113 ASP cc_start: 0.6844 (t0) cc_final: 0.6515 (t70) REVERT: C 126 MET cc_start: 0.7592 (mmm) cc_final: 0.7051 (mtm) REVERT: C 132 MET cc_start: 0.7840 (tpp) cc_final: 0.7615 (mmm) REVERT: C 181 ARG cc_start: 0.8396 (tmm-80) cc_final: 0.8159 (tmm-80) REVERT: C 199 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.6411 (p-80) REVERT: C 231 SER cc_start: 0.8282 (t) cc_final: 0.8051 (p) REVERT: C 242 GLU cc_start: 0.8142 (mp0) cc_final: 0.7927 (mp0) REVERT: C 253 LYS cc_start: 0.6974 (tppp) cc_final: 0.6691 (tppp) REVERT: C 274 GLN cc_start: 0.8275 (mt0) cc_final: 0.7970 (mt0) REVERT: C 329 MET cc_start: 0.6036 (tmm) cc_final: 0.5586 (pmm) REVERT: C 342 MET cc_start: 0.5525 (OUTLIER) cc_final: 0.5139 (mmm) REVERT: D 17 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7025 (p) REVERT: D 20 GLU cc_start: 0.8231 (mp0) cc_final: 0.7943 (mp0) REVERT: D 22 GLN cc_start: 0.8288 (mt0) cc_final: 0.7804 (mt0) REVERT: D 30 CYS cc_start: 0.7765 (m) cc_final: 0.7534 (m) REVERT: D 68 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7032 (mm-30) REVERT: D 72 PHE cc_start: 0.8153 (p90) cc_final: 0.7761 (p90) REVERT: D 73 ASP cc_start: 0.7651 (m-30) cc_final: 0.7368 (m-30) REVERT: D 113 ASP cc_start: 0.7523 (t0) cc_final: 0.7015 (p0) REVERT: D 116 THR cc_start: 0.7725 (p) cc_final: 0.7345 (t) REVERT: D 133 GLU cc_start: 0.7324 (tp30) cc_final: 0.6800 (tm-30) REVERT: D 135 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7212 (tp30) REVERT: D 140 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.7412 (ttp-110) REVERT: D 154 TYR cc_start: 0.7403 (t80) cc_final: 0.7141 (t80) REVERT: D 158 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8157 (pt) REVERT: D 173 ARG cc_start: 0.7177 (mmt90) cc_final: 0.6886 (tpp80) REVERT: D 183 ARG cc_start: 0.8457 (tpp80) cc_final: 0.8212 (tpp80) REVERT: D 226 GLN cc_start: 0.8395 (mm-40) cc_final: 0.7922 (mp10) REVERT: D 229 GLU cc_start: 0.7613 (pt0) cc_final: 0.7375 (pt0) REVERT: D 235 LEU cc_start: 0.8420 (mt) cc_final: 0.8065 (mm) REVERT: D 267 GLU cc_start: 0.7461 (tp30) cc_final: 0.7084 (tm-30) REVERT: D 309 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6757 (mm-30) REVERT: D 327 ARG cc_start: 0.8486 (ttt180) cc_final: 0.8027 (ttp80) REVERT: D 334 HIS cc_start: 0.6399 (p90) cc_final: 0.5860 (p90) outliers start: 57 outliers final: 42 residues processed: 438 average time/residue: 0.1628 time to fit residues: 102.2030 Evaluate side-chains 454 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 404 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 21 ARG Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 231 SER 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 80 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 452 ASN 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 21 ARG 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 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 69 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 271 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 115 optimal weight: 0.4980 chunk 32 optimal weight: 40.0000 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.212829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165689 restraints weight = 39810.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.165018 restraints weight = 17326.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.166126 restraints weight = 11692.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.167759 restraints weight = 9574.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.167353 restraints weight = 8501.435| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20302 Z= 0.148 Angle : 0.622 11.804 28362 Z= 0.328 Chirality : 0.039 0.188 3108 Planarity : 0.004 0.048 3020 Dihedral : 23.176 81.195 4291 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.24 % Allowed : 21.38 % Favored : 75.37 % 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: 1.80 (0.19), residues: 1936 helix: 2.16 (0.17), residues: 917 sheet: -0.19 (0.28), residues: 314 loop : 0.72 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 456 TYR 0.025 0.001 TYR B 188 PHE 0.017 0.001 PHE D 217 TRP 0.051 0.001 TRP C 230 HIS 0.004 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00318 (20286) covalent geometry : angle 0.61749 (28338) hydrogen bonds : bond 0.03683 ( 1054) hydrogen bonds : angle 3.69576 ( 2783) metal coordination : bond 0.00307 ( 16) metal coordination : angle 2.69633 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3475.45 seconds wall clock time: 60 minutes 21.23 seconds (3621.23 seconds total)