Starting phenix.real_space_refine on Sat Jul 4 10:04:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu7_60892/07_2026/9iu7_60892.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu7_60892/07_2026/9iu7_60892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iu7_60892/07_2026/9iu7_60892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu7_60892/07_2026/9iu7_60892.map" model { file = "/net/cci-nas-00/data/ceres_data/9iu7_60892/07_2026/9iu7_60892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu7_60892/07_2026/9iu7_60892.cif" } resolution = 4.08 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= 0.026 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19472 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "C" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "D" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "E1" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "E2" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F1" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F2" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "G1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G2" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H2" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2429 SG CYS A 304 40.533 162.329 33.359 1.00362.59 S ATOM 2447 SG CYS A 307 42.545 159.225 33.242 1.00362.42 S ATOM 2598 SG CYS A 326 42.859 161.026 35.907 1.00362.59 S ATOM 2670 SG CYS A 335 44.226 162.694 32.713 1.00363.12 S ATOM 6292 SG CYS B 304 75.878 31.911 110.410 1.00265.33 S ATOM 6310 SG CYS B 307 76.056 33.593 107.139 1.00264.79 S ATOM 6461 SG CYS B 326 73.143 33.462 108.516 1.00264.57 S ATOM 6533 SG CYS B 335 74.487 30.003 107.434 1.00265.61 S ATOM 10155 SG CYS C 304 99.240 130.398 13.401 1.00248.86 S ATOM 10173 SG CYS C 307 99.825 126.752 13.298 1.00248.22 S ATOM 10324 SG CYS C 326 100.725 128.224 16.026 1.00243.88 S ATOM 10396 SG CYS C 335 102.829 129.266 13.039 1.00242.61 S ATOM 14018 SG CYS D 304 67.275 25.803 40.555 1.00202.82 S ATOM 14036 SG CYS D 307 68.041 28.278 37.947 1.00201.50 S ATOM 14187 SG CYS D 326 65.022 28.391 39.061 1.00198.32 S ATOM 14259 SG CYS D 335 65.795 25.234 37.089 1.00198.57 S Time building chain proxies: 5.00, per 1000 atoms: 0.26 Number of scatterers: 19472 At special positions: 0 Unit cell: (138.278, 196.129, 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: 2.17 Conformation dependent library (CDL) restraints added in 846.7 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 304 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 335 " 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 304 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 307 " 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 49.7% alpha, 13.8% beta 93 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.621A 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: 4.122A 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: 3.870A pdb=" N VAL A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.717A 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: 3.631A 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 285 removed outlier: 3.757A pdb=" N LYS B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR B 285 " --> pdb=" O GLU B 281 " (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: 3.630A pdb=" N LEU B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 423 removed outlier: 3.928A pdb=" N LEU B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) 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: 3.625A 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: 3.694A 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: 3.625A 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: 3.675A 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: 7.515A 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: 6.771A pdb=" N ILE A 7 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A 42 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU A 9 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU A 44 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG A 2 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL A 76 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.154A 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: 7.086A 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: 6.790A pdb=" N ALA B 3 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ALA B 41 " --> pdb=" O ALA B 3 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 5 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASP B 43 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE B 7 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG B 2 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL B 76 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.218A 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: 7.105A 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: 7.513A pdb=" N VAL C 5 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL C 40 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE C 7 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU C 42 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU C 9 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU C 44 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG C 2 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL C 76 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 6.163A 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: 7.099A 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: 7.373A pdb=" N VAL D 5 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL D 40 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE D 7 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU D 42 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU D 9 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU D 44 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG D 2 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL D 76 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 6.204A 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: 7.118A pdb=" N ARG D 362 " --> pdb=" O THR D 435 " (cutoff:3.500A) 811 hydrogen bonds defined for protein. 2295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 241 hydrogen bonds 482 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 2.77 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: 3764 1.34 - 1.46: 6029 1.46 - 1.58: 10017 1.58 - 1.69: 384 1.69 - 1.81: 92 Bond restraints: 20286 Sorted by residual: bond pdb=" C2 DGH2 20 " pdb=" N3 DGH2 20 " ideal model delta sigma weight residual 1.323 1.348 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" P DCH2 1 " pdb=" O5' DCH2 1 " ideal model delta sigma weight residual 1.593 1.623 -0.030 1.00e-02 1.00e+04 8.85e+00 bond pdb=" C ALA D 261 " pdb=" N PRO D 262 " ideal model delta sigma weight residual 1.331 1.366 -0.035 1.20e-02 6.94e+03 8.58e+00 bond pdb=" C ALA C 261 " pdb=" N PRO C 262 " ideal model delta sigma weight residual 1.331 1.366 -0.035 1.20e-02 6.94e+03 8.46e+00 bond pdb=" C HIS D 321 " pdb=" N PRO D 322 " ideal model delta sigma weight residual 1.330 1.365 -0.035 1.22e-02 6.72e+03 8.25e+00 ... (remaining 20281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 26459 3.44 - 6.89: 1751 6.89 - 10.33: 113 10.33 - 13.78: 11 13.78 - 17.22: 4 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 86.78 17.22 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 89.06 14.94 1.50e+00 4.44e-01 9.91e+01 angle pdb=" O3' DCH1 25 " pdb=" P DGH1 26 " pdb=" O5' DGH1 26 " ideal model delta sigma weight residual 104.00 89.27 14.73 1.50e+00 4.44e-01 9.64e+01 angle pdb=" O3' DAE1 20 " pdb=" P DCE1 21 " pdb=" O5' DCE1 21 " ideal model delta sigma weight residual 104.00 89.69 14.31 1.50e+00 4.44e-01 9.10e+01 angle pdb=" O4' DCE2 28 " pdb=" C4' DCE2 28 " pdb=" C3' DCE2 28 " ideal model delta sigma weight residual 106.00 100.51 5.49 6.00e-01 2.78e+00 8.37e+01 ... (remaining 28333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 9445 17.64 - 35.29: 1053 35.29 - 52.93: 855 52.93 - 70.58: 234 70.58 - 88.22: 29 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 -136.38 13.78 0 2.50e+00 1.60e-01 3.04e+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 -135.34 12.74 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C ASP D 407 " pdb=" N ASP D 407 " pdb=" CA ASP D 407 " pdb=" CB ASP D 407 " ideal model delta harmonic sigma weight residual -122.60 -134.85 12.25 0 2.50e+00 1.60e-01 2.40e+01 ... (remaining 11613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2764 0.131 - 0.263: 323 0.263 - 0.394: 15 0.394 - 0.525: 2 0.525 - 0.657: 4 Chirality restraints: 3108 Sorted by residual: chirality pdb=" P DCH2 1 " pdb=" OP1 DCH2 1 " pdb=" OP2 DCH2 1 " pdb=" O5' DCH2 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P DGE1 1 " pdb=" OP1 DGE1 1 " pdb=" OP2 DGE1 1 " pdb=" O5' DGE1 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DGG1 1 " pdb=" OP1 DGG1 1 " pdb=" OP2 DGG1 1 " pdb=" O5' DGG1 1 " both_signs ideal model delta sigma weight residual True 2.34 2.98 -0.65 2.00e-01 2.50e+01 1.04e+01 ... (remaining 3105 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DGF2 23 " -0.019 2.00e-02 2.50e+03 1.92e-02 1.11e+01 pdb=" N9 DGF2 23 " -0.009 2.00e-02 2.50e+03 pdb=" C8 DGF2 23 " 0.027 2.00e-02 2.50e+03 pdb=" N7 DGF2 23 " 0.028 2.00e-02 2.50e+03 pdb=" C5 DGF2 23 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DGF2 23 " -0.018 2.00e-02 2.50e+03 pdb=" O6 DGF2 23 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DGF2 23 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DGF2 23 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DGF2 23 " 0.034 2.00e-02 2.50e+03 pdb=" N3 DGF2 23 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DGF2 23 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCE2 30 " 0.031 2.00e-02 2.50e+03 2.02e-02 9.20e+00 pdb=" N1 DCE2 30 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DCE2 30 " -0.022 2.00e-02 2.50e+03 pdb=" O2 DCE2 30 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DCE2 30 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DCE2 30 " 0.009 2.00e-02 2.50e+03 pdb=" N4 DCE2 30 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DCE2 30 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DCE2 30 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DGF2 25 " -0.006 2.00e-02 2.50e+03 1.68e-02 8.46e+00 pdb=" N9 DGF2 25 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DGF2 25 " 0.019 2.00e-02 2.50e+03 pdb=" N7 DGF2 25 " 0.026 2.00e-02 2.50e+03 pdb=" C5 DGF2 25 " -0.018 2.00e-02 2.50e+03 pdb=" C6 DGF2 25 " -0.023 2.00e-02 2.50e+03 pdb=" O6 DGF2 25 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DGF2 25 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DGF2 25 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DGF2 25 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DGF2 25 " 0.023 2.00e-02 2.50e+03 pdb=" C4 DGF2 25 " -0.018 2.00e-02 2.50e+03 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 5 2.26 - 2.92: 6772 2.92 - 3.58: 28381 3.58 - 4.24: 47708 4.24 - 4.90: 77445 Nonbonded interactions: 160311 Sorted by model distance: nonbonded pdb=" OG SER B 10 " pdb=" P DCE2 28 " model vdw 1.603 3.400 nonbonded pdb=" OG SER A 10 " pdb=" P DCF1 28 " model vdw 1.605 3.400 nonbonded pdb=" OG SER C 10 " pdb=" P DCH1 25 " model vdw 1.606 3.400 nonbonded pdb=" OG SER D 10 " pdb=" P DCG2 25 " model vdw 1.610 3.400 nonbonded pdb=" NH1 ARG D 223 " pdb=" OP1 DGH2 20 " model vdw 2.161 3.120 ... (remaining 160306 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: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.040 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5743 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 0.077 20302 Z= 0.646 Angle : 1.830 19.798 28362 Z= 1.268 Chirality : 0.086 0.657 3108 Planarity : 0.006 0.068 3020 Dihedral : 21.333 88.220 7984 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.27 % Favored : 97.68 % Rotamer: Outliers : 4.18 % Allowed : 6.42 % Favored : 89.40 % Cbeta Deviations : 0.50 % 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: 0.51 (0.14), residues: 918 sheet: 0.21 (0.27), residues: 293 loop : 0.24 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.004 ARG A 142 TYR 0.029 0.005 TYR B 482 PHE 0.036 0.004 PHE D 118 TRP 0.030 0.004 TRP D 35 HIS 0.019 0.003 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00981 / 0.64 (20286) covalent geometry : angle 1.81041 / 1.27 (28338) hydrogen bonds : bond 0.16479 / 11.10 ( 1052) hydrogen bonds : angle 6.04880 / 4.40 ( 2777) metal coordination : bond 0.05785 / 3.59 ( 16) metal coordination : angle 9.33634 / 6.64 ( 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 535 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 468 time to evaluate : 0.605 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: 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 6 VAL cc_start: 0.7591 (t) cc_final: 0.7265 (m) REVERT: A 21 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6862 (tpm170) REVERT: A 24 GLU cc_start: 0.8754 (tp30) cc_final: 0.7533 (tp30) REVERT: A 30 CYS cc_start: 0.7694 (m) cc_final: 0.7292 (t) REVERT: A 59 PRO cc_start: 0.7955 (Cg_endo) cc_final: 0.7697 (Cg_exo) REVERT: A 61 LEU cc_start: 0.7510 (tp) cc_final: 0.7115 (tp) REVERT: A 85 ARG cc_start: 0.5246 (OUTLIER) cc_final: 0.4885 (mmt90) REVERT: A 92 GLN cc_start: 0.8298 (tt0) cc_final: 0.8069 (tt0) REVERT: A 100 HIS cc_start: 0.7309 (m90) cc_final: 0.6870 (m90) REVERT: A 125 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7597 (tt) REVERT: A 126 MET cc_start: 0.6698 (mmm) cc_final: 0.6429 (mmp) REVERT: A 131 GLN cc_start: 0.7522 (tp40) cc_final: 0.7147 (tp40) REVERT: A 132 MET cc_start: 0.8298 (mtm) cc_final: 0.7670 (mmm) REVERT: A 138 LYS cc_start: 0.8551 (mttm) cc_final: 0.8117 (mmtp) REVERT: A 185 LEU cc_start: 0.8951 (mp) cc_final: 0.8681 (pp) REVERT: A 239 MET cc_start: 0.4986 (mmm) cc_final: 0.4413 (ptp) REVERT: A 302 LEU cc_start: 0.2851 (tp) cc_final: 0.1958 (tp) REVERT: A 312 TYR cc_start: 0.2977 (m-10) cc_final: 0.2386 (m-10) REVERT: A 329 MET cc_start: 0.0091 (mtp) cc_final: -0.1063 (tpt) REVERT: A 397 ARG cc_start: -0.1032 (OUTLIER) cc_final: -0.2543 (ttm170) REVERT: B 9 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7566 (mm) REVERT: B 11 ARG cc_start: 0.6936 (tpp80) cc_final: 0.6706 (ttm-80) REVERT: B 23 LEU cc_start: 0.7873 (tp) cc_final: 0.7658 (mt) REVERT: B 43 ASP cc_start: 0.5973 (m-30) cc_final: 0.5239 (m-30) REVERT: B 50 VAL cc_start: 0.8410 (t) cc_final: 0.8159 (m) REVERT: B 51 ASP cc_start: 0.8393 (t0) cc_final: 0.8187 (t0) REVERT: B 54 ASP cc_start: 0.5786 (t0) cc_final: 0.5415 (t0) REVERT: B 56 LYS cc_start: 0.7842 (mtmm) cc_final: 0.7574 (mtmm) REVERT: B 60 ASN cc_start: 0.7405 (m-40) cc_final: 0.6978 (m110) REVERT: B 69 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7044 (mm-30) REVERT: B 88 ARG cc_start: 0.7991 (ttt180) cc_final: 0.7647 (tpp80) REVERT: B 94 VAL cc_start: 0.7842 (t) cc_final: 0.7585 (m) REVERT: B 95 HIS cc_start: 0.7336 (m90) cc_final: 0.6462 (m90) REVERT: B 98 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7213 (mt-10) REVERT: B 99 ASP cc_start: 0.7928 (m-30) cc_final: 0.7588 (m-30) REVERT: B 100 HIS cc_start: 0.8003 (m90) cc_final: 0.7708 (m-70) REVERT: B 101 LYS cc_start: 0.8705 (mptt) cc_final: 0.8498 (mptt) REVERT: B 125 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8325 (tt) REVERT: B 133 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7400 (tp30) REVERT: B 134 LEU cc_start: 0.7640 (tp) cc_final: 0.7254 (tt) REVERT: B 148 ASN cc_start: 0.8272 (m-40) cc_final: 0.7385 (t0) REVERT: B 149 ILE cc_start: 0.8457 (mt) cc_final: 0.8133 (mm) REVERT: B 153 LYS cc_start: 0.7802 (mtmp) cc_final: 0.7136 (mtmp) REVERT: B 174 LEU cc_start: 0.7745 (mt) cc_final: 0.7340 (mt) REVERT: B 175 VAL cc_start: 0.7686 (OUTLIER) cc_final: 0.7314 (p) REVERT: B 177 ASP cc_start: 0.5827 (t0) cc_final: 0.5285 (t0) REVERT: B 187 VAL cc_start: 0.7941 (t) cc_final: 0.7738 (p) REVERT: B 188 TYR cc_start: 0.6974 (t80) cc_final: 0.6617 (t80) REVERT: B 189 HIS cc_start: 0.7189 (m-70) cc_final: 0.6842 (t-90) REVERT: B 207 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7249 (mtm-85) REVERT: B 211 LEU cc_start: 0.7658 (mt) cc_final: 0.7337 (tp) REVERT: B 214 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7832 (ttmt) REVERT: B 220 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7451 (mt) REVERT: B 236 LYS cc_start: 0.7831 (tttt) cc_final: 0.7600 (tptm) REVERT: B 257 ASP cc_start: 0.7813 (t70) cc_final: 0.6810 (p0) REVERT: B 274 GLN cc_start: 0.7257 (mt0) cc_final: 0.6832 (mt0) REVERT: B 299 LEU cc_start: 0.7297 (tp) cc_final: 0.7080 (tp) REVERT: B 302 LEU cc_start: 0.8144 (tp) cc_final: 0.7637 (tp) REVERT: B 329 MET cc_start: 0.7537 (mmt) cc_final: 0.6959 (mmt) REVERT: B 344 GLU cc_start: 0.8508 (tt0) cc_final: 0.8073 (tt0) REVERT: B 345 TRP cc_start: 0.7160 (m100) cc_final: 0.6827 (m100) REVERT: B 350 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8601 (tm-30) REVERT: B 367 TRP cc_start: 0.8016 (t-100) cc_final: 0.7373 (t-100) REVERT: B 376 GLU cc_start: 0.8782 (tt0) cc_final: 0.8273 (tt0) REVERT: B 386 ASP cc_start: 0.7591 (t70) cc_final: 0.7262 (t70) REVERT: B 416 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7786 (mtm-85) REVERT: B 441 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8197 (p0) REVERT: B 442 TRP cc_start: 0.8605 (t60) cc_final: 0.8085 (t60) REVERT: B 447 ASP cc_start: 0.8562 (t0) cc_final: 0.8185 (p0) REVERT: B 454 TRP cc_start: 0.8562 (t60) cc_final: 0.7986 (t60) REVERT: B 456 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7338 (ttm110) REVERT: C 30 CYS cc_start: 0.8242 (m) cc_final: 0.7454 (m) REVERT: C 44 LEU cc_start: 0.6765 (mp) cc_final: 0.5921 (mp) REVERT: C 90 LEU cc_start: 0.7437 (tp) cc_final: 0.7133 (tp) REVERT: C 164 LEU cc_start: 0.1281 (OUTLIER) cc_final: 0.0462 (tp) REVERT: C 199 HIS cc_start: 0.1949 (OUTLIER) cc_final: 0.1234 (m90) REVERT: C 229 GLU cc_start: 0.7621 (pt0) cc_final: 0.7056 (tt0) REVERT: C 273 GLU cc_start: 0.8380 (pt0) cc_final: 0.8171 (tp30) REVERT: D 9 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6984 (mp) REVERT: D 11 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7216 (mtp85) REVERT: D 20 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: D 24 GLU cc_start: 0.8397 (tt0) cc_final: 0.8169 (tm-30) REVERT: D 26 CYS cc_start: 0.7905 (m) cc_final: 0.6851 (p) REVERT: D 27 GLN cc_start: 0.7471 (mt0) cc_final: 0.6621 (pt0) REVERT: D 28 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7119 (tm-30) REVERT: D 33 ARG cc_start: 0.8014 (mtp180) cc_final: 0.6859 (ttm-80) REVERT: D 42 GLU cc_start: 0.6878 (tt0) cc_final: 0.6455 (tt0) REVERT: D 60 ASN cc_start: 0.8097 (m-40) cc_final: 0.7666 (m110) REVERT: D 74 VAL cc_start: 0.7716 (p) cc_final: 0.7436 (m) REVERT: D 79 ARG cc_start: 0.7059 (mtp180) cc_final: 0.6684 (mtm110) REVERT: D 81 ASP cc_start: 0.7910 (p0) cc_final: 0.7440 (p0) REVERT: D 82 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8168 (mmp80) REVERT: D 93 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7829 (mm) REVERT: D 98 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6076 (pt0) REVERT: D 125 LEU cc_start: 0.8350 (pp) cc_final: 0.8073 (pp) REVERT: D 131 GLN cc_start: 0.8079 (tt0) cc_final: 0.7604 (tt0) REVERT: D 135 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7829 (mm-30) REVERT: D 138 LYS cc_start: 0.8626 (mttt) cc_final: 0.8064 (mmmt) REVERT: D 142 ARG cc_start: 0.7596 (ttm110) cc_final: 0.7084 (ttm-80) REVERT: D 146 HIS cc_start: 0.8195 (m170) cc_final: 0.7580 (m-70) REVERT: D 153 LYS cc_start: 0.7959 (mttt) cc_final: 0.7451 (mttt) REVERT: D 182 GLU cc_start: 0.8309 (tt0) cc_final: 0.8049 (tt0) REVERT: D 193 ASP cc_start: 0.7275 (m-30) cc_final: 0.6687 (m-30) REVERT: D 214 LYS cc_start: 0.7550 (ttmt) cc_final: 0.7276 (ttmt) REVERT: D 220 LEU cc_start: 0.7889 (tt) cc_final: 0.7431 (mm) REVERT: D 225 PRO cc_start: 0.8019 (Cg_exo) cc_final: 0.7648 (Cg_endo) REVERT: D 228 ARG cc_start: 0.7275 (mtt-85) cc_final: 0.6803 (mtt-85) REVERT: D 236 LYS cc_start: 0.8556 (tttt) cc_final: 0.8160 (ttmm) REVERT: D 242 GLU cc_start: 0.8674 (mt-10) cc_final: 0.7690 (mt-10) REVERT: D 244 MET cc_start: 0.7940 (mmt) cc_final: 0.7513 (mmm) REVERT: D 245 LEU cc_start: 0.8275 (mt) cc_final: 0.7915 (mt) REVERT: D 247 TYR cc_start: 0.6348 (m-10) cc_final: 0.5853 (m-10) REVERT: D 269 ILE cc_start: 0.8204 (mm) cc_final: 0.7791 (mm) REVERT: D 270 LEU cc_start: 0.8260 (mt) cc_final: 0.8048 (mp) REVERT: D 272 ARG cc_start: 0.8110 (tpt170) cc_final: 0.7894 (mmm160) REVERT: D 278 LEU cc_start: 0.8632 (mt) cc_final: 0.8413 (mt) REVERT: D 312 TYR cc_start: 0.4065 (m-10) cc_final: 0.3779 (m-80) REVERT: D 328 SER cc_start: 0.7251 (t) cc_final: 0.6928 (p) REVERT: D 345 TRP cc_start: 0.6805 (m100) cc_final: 0.5128 (m100) REVERT: D 387 LEU cc_start: 0.9042 (mt) cc_final: 0.8701 (pp) REVERT: D 410 ILE cc_start: 0.8725 (mt) cc_final: 0.8398 (pt) REVERT: D 442 TRP cc_start: 0.7121 (t60) cc_final: 0.6697 (t60) REVERT: D 452 ASN cc_start: 0.6698 (t0) cc_final: 0.6084 (t0) REVERT: D 456 ARG cc_start: 0.8306 (mtp180) cc_final: 0.7726 (tpp80) REVERT: D 461 ARG cc_start: 0.6596 (ttm-80) cc_final: 0.6371 (ttp80) outliers start: 67 outliers final: 15 residues processed: 511 average time/residue: 0.1848 time to fit residues: 133.1694 Evaluate side-chains 429 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 396 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 ASN B 27 GLN B 32 GLN B 131 GLN C 60 ASN C 111 HIS C 148 ASN D 27 GLN D 111 HIS D 189 HIS D 199 HIS ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 HIS D 381 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.229835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.169439 restraints weight = 46040.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.174854 restraints weight = 21162.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.178172 restraints weight = 12552.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.180169 restraints weight = 8875.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.181409 restraints weight = 7147.304| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20302 Z= 0.218 Angle : 0.827 15.127 28362 Z= 0.454 Chirality : 0.057 0.291 3108 Planarity : 0.006 0.075 3020 Dihedral : 23.409 88.551 4268 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.88 % 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: 1.66 (0.18), residues: 1936 helix: 1.91 (0.16), residues: 915 sheet: -0.42 (0.29), residues: 243 loop : 0.82 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 63 TYR 0.016 0.002 TYR D 396 PHE 0.030 0.003 PHE B 476 TRP 0.025 0.002 TRP A 64 HIS 0.012 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.22 (20286) covalent geometry : angle 0.80527 / 0.45 (28338) hydrogen bonds : bond 0.06215 / 4.29 ( 1052) hydrogen bonds : angle 4.22713 / 3.09 ( 2777) metal coordination : bond 0.00826 / 0.41 ( 16) metal coordination : angle 6.50620 / 4.58 ( 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 410 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 409 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7740 (t) cc_final: 0.7430 (m) REVERT: A 21 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7286 (tpm170) REVERT: A 24 GLU cc_start: 0.8561 (tp30) cc_final: 0.7899 (tp30) REVERT: A 30 CYS cc_start: 0.7743 (m) cc_final: 0.7365 (t) REVERT: A 58 ARG cc_start: 0.7917 (ttt180) cc_final: 0.7387 (ttm110) REVERT: A 59 PRO cc_start: 0.8104 (Cg_endo) cc_final: 0.7803 (Cg_exo) REVERT: A 60 ASN cc_start: 0.7726 (t160) cc_final: 0.7269 (t0) REVERT: A 61 LEU cc_start: 0.7562 (tp) cc_final: 0.7103 (tp) REVERT: A 92 GLN cc_start: 0.8358 (tt0) cc_final: 0.8152 (tt0) REVERT: A 96 TRP cc_start: 0.6569 (t60) cc_final: 0.6276 (t60) REVERT: A 100 HIS cc_start: 0.7595 (m90) cc_final: 0.7332 (m90) REVERT: A 131 GLN cc_start: 0.7737 (tp40) cc_final: 0.7314 (tp40) REVERT: A 132 MET cc_start: 0.8091 (mtm) cc_final: 0.7770 (mtm) REVERT: A 138 LYS cc_start: 0.8699 (mttm) cc_final: 0.8154 (mmtt) REVERT: A 185 LEU cc_start: 0.8938 (mp) cc_final: 0.8587 (pp) REVERT: A 228 ARG cc_start: 0.7085 (mtt90) cc_final: 0.6762 (mtm110) REVERT: A 237 ARG cc_start: 0.4146 (ttp-170) cc_final: 0.2606 (ptm160) REVERT: A 239 MET cc_start: 0.4882 (mmm) cc_final: 0.4300 (ptp) REVERT: A 329 MET cc_start: 0.0406 (mtp) cc_final: -0.0158 (mmm) REVERT: B 21 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7324 (ptm-80) REVERT: B 28 GLN cc_start: 0.7613 (tp-100) cc_final: 0.7155 (tp-100) REVERT: B 32 GLN cc_start: 0.8177 (mp10) cc_final: 0.7480 (mp10) REVERT: B 43 ASP cc_start: 0.6416 (m-30) cc_final: 0.5911 (m-30) REVERT: B 50 VAL cc_start: 0.8472 (t) cc_final: 0.8262 (m) REVERT: B 56 LYS cc_start: 0.7917 (mtmm) cc_final: 0.7362 (mtmm) REVERT: B 60 ASN cc_start: 0.7518 (m-40) cc_final: 0.7266 (m-40) REVERT: B 68 GLU cc_start: 0.6718 (pt0) cc_final: 0.6453 (pt0) REVERT: B 88 ARG cc_start: 0.7960 (ttt180) cc_final: 0.7741 (tpp80) REVERT: B 94 VAL cc_start: 0.8120 (t) cc_final: 0.7782 (m) REVERT: B 101 LYS cc_start: 0.8688 (mptt) cc_final: 0.8287 (mptt) REVERT: B 102 LYS cc_start: 0.8045 (mptt) cc_final: 0.7771 (mptt) REVERT: B 109 GLU cc_start: 0.6238 (mt-10) cc_final: 0.5975 (mp0) REVERT: B 138 LYS cc_start: 0.7772 (mttt) cc_final: 0.7269 (ttmm) REVERT: B 142 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7255 (tmm-80) REVERT: B 148 ASN cc_start: 0.8387 (m-40) cc_final: 0.7730 (t0) REVERT: B 149 ILE cc_start: 0.8501 (mt) cc_final: 0.8065 (mm) REVERT: B 174 LEU cc_start: 0.7637 (mt) cc_final: 0.7298 (mt) REVERT: B 182 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: B 187 VAL cc_start: 0.8260 (t) cc_final: 0.7997 (p) REVERT: B 204 ASP cc_start: 0.7636 (t70) cc_final: 0.7011 (m-30) REVERT: B 242 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7608 (mt-10) REVERT: B 282 LEU cc_start: 0.7838 (mt) cc_final: 0.7563 (mm) REVERT: B 289 LYS cc_start: 0.8698 (mppt) cc_final: 0.8440 (mppt) REVERT: B 298 LEU cc_start: 0.8041 (mt) cc_final: 0.7728 (mm) REVERT: B 299 LEU cc_start: 0.7360 (tp) cc_final: 0.7135 (tp) REVERT: B 302 LEU cc_start: 0.8267 (tp) cc_final: 0.7519 (tp) REVERT: B 329 MET cc_start: 0.7491 (mmt) cc_final: 0.6948 (mmt) REVERT: B 334 HIS cc_start: 0.6720 (p90) cc_final: 0.6099 (p90) REVERT: B 342 MET cc_start: 0.6460 (ttp) cc_final: 0.5937 (mmt) REVERT: B 344 GLU cc_start: 0.7952 (tt0) cc_final: 0.7391 (tm-30) REVERT: B 367 TRP cc_start: 0.7734 (t-100) cc_final: 0.7383 (t-100) REVERT: B 386 ASP cc_start: 0.7667 (t70) cc_final: 0.7238 (t70) REVERT: B 454 TRP cc_start: 0.8097 (t60) cc_final: 0.7735 (t60) REVERT: B 456 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7526 (ttm110) REVERT: B 459 ASN cc_start: 0.8559 (m-40) cc_final: 0.8229 (m-40) REVERT: B 475 ASP cc_start: 0.6858 (t0) cc_final: 0.6544 (p0) REVERT: C 28 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7584 (tm-30) REVERT: C 42 GLU cc_start: 0.7573 (tp30) cc_final: 0.7133 (tp30) REVERT: C 90 LEU cc_start: 0.7874 (tp) cc_final: 0.7667 (tp) REVERT: C 98 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7683 (tm-30) REVERT: C 173 ARG cc_start: 0.7128 (mmm-85) cc_final: 0.6923 (mmm160) REVERT: C 174 LEU cc_start: 0.8632 (tp) cc_final: 0.7636 (tp) REVERT: C 229 GLU cc_start: 0.7577 (pt0) cc_final: 0.7114 (tt0) REVERT: C 273 GLU cc_start: 0.8620 (pt0) cc_final: 0.8231 (tp30) REVERT: D 24 GLU cc_start: 0.8256 (tt0) cc_final: 0.8002 (tm-30) REVERT: D 26 CYS cc_start: 0.7928 (m) cc_final: 0.7191 (p) REVERT: D 27 GLN cc_start: 0.7369 (mt0) cc_final: 0.6821 (pt0) REVERT: D 28 GLN cc_start: 0.7529 (tm-30) cc_final: 0.7069 (tm-30) REVERT: D 33 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7520 (mtm-85) REVERT: D 35 TRP cc_start: 0.6316 (p90) cc_final: 0.5744 (p90) REVERT: D 60 ASN cc_start: 0.8257 (m-40) cc_final: 0.7897 (m110) REVERT: D 74 VAL cc_start: 0.7956 (p) cc_final: 0.7726 (m) REVERT: D 82 ARG cc_start: 0.8106 (mmp-170) cc_final: 0.7905 (mmp80) REVERT: D 92 GLN cc_start: 0.7757 (tt0) cc_final: 0.7463 (mt0) REVERT: D 102 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7030 (mmtt) REVERT: D 131 GLN cc_start: 0.8121 (tt0) cc_final: 0.7788 (tt0) REVERT: D 135 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7647 (mm-30) REVERT: D 138 LYS cc_start: 0.8815 (mttt) cc_final: 0.8190 (mtpp) REVERT: D 139 GLU cc_start: 0.7451 (tp30) cc_final: 0.6908 (tp30) REVERT: D 140 ARG cc_start: 0.7474 (ttp-110) cc_final: 0.7196 (ttt90) REVERT: D 142 ARG cc_start: 0.7521 (ttm110) cc_final: 0.6955 (ttm-80) REVERT: D 146 HIS cc_start: 0.8184 (m170) cc_final: 0.7805 (m-70) REVERT: D 153 LYS cc_start: 0.8289 (mttt) cc_final: 0.7676 (mttt) REVERT: D 182 GLU cc_start: 0.8012 (tt0) cc_final: 0.7734 (tt0) REVERT: D 186 GLU cc_start: 0.7338 (tt0) cc_final: 0.7109 (tp30) REVERT: D 220 LEU cc_start: 0.7985 (tt) cc_final: 0.7612 (mm) REVERT: D 226 GLN cc_start: 0.7702 (mp10) cc_final: 0.7091 (mp10) REVERT: D 242 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7644 (mt-10) REVERT: D 244 MET cc_start: 0.7644 (mmt) cc_final: 0.7228 (mmm) REVERT: D 245 LEU cc_start: 0.8434 (mt) cc_final: 0.7924 (mt) REVERT: D 247 TYR cc_start: 0.6698 (m-10) cc_final: 0.6259 (m-10) REVERT: D 269 ILE cc_start: 0.8005 (mm) cc_final: 0.7622 (mm) REVERT: D 278 LEU cc_start: 0.8416 (mt) cc_final: 0.8116 (mt) REVERT: D 328 SER cc_start: 0.7822 (t) cc_final: 0.7240 (p) REVERT: D 345 TRP cc_start: 0.6592 (m100) cc_final: 0.5009 (m100) REVERT: D 410 ILE cc_start: 0.8684 (mt) cc_final: 0.8427 (pt) REVERT: D 416 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.7978 (ptp-110) outliers start: 1 outliers final: 0 residues processed: 409 average time/residue: 0.1748 time to fit residues: 101.1818 Evaluate side-chains 367 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 366 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 129 optimal weight: 0.0670 chunk 207 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 132 optimal weight: 50.0000 chunk 107 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 ASN ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN A 251 ASN B 131 GLN B 203 HIS B 274 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN C 60 ASN C 274 GLN C 484 GLN C 485 HIS D 141 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.229783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.170691 restraints weight = 45974.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.176068 restraints weight = 20891.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.179335 restraints weight = 12258.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.181232 restraints weight = 8608.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.182466 restraints weight = 6951.267| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20302 Z= 0.170 Angle : 0.687 13.601 28362 Z= 0.389 Chirality : 0.047 0.457 3108 Planarity : 0.005 0.060 3020 Dihedral : 23.333 89.396 4268 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.12 % Allowed : 2.31 % Favored : 97.57 % 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: 1.78 (0.19), residues: 1936 helix: 2.01 (0.16), residues: 914 sheet: -0.42 (0.30), residues: 237 loop : 0.88 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 79 TYR 0.039 0.002 TYR D 312 PHE 0.022 0.002 PHE B 348 TRP 0.034 0.002 TRP D 35 HIS 0.014 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.17 (20286) covalent geometry : angle 0.67232 / 0.39 (28338) hydrogen bonds : bond 0.05337 / 3.66 ( 1052) hydrogen bonds : angle 4.05092 / 2.96 ( 2777) metal coordination : bond 0.00663 / 0.34 ( 16) metal coordination : angle 4.81981 / 3.48 ( 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 411 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 409 time to evaluate : 0.481 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7319 (tpm170) REVERT: A 24 GLU cc_start: 0.8556 (tp30) cc_final: 0.7503 (tp30) REVERT: A 30 CYS cc_start: 0.7717 (m) cc_final: 0.7268 (t) REVERT: A 56 LYS cc_start: 0.8009 (pttp) cc_final: 0.7686 (pttm) REVERT: A 58 ARG cc_start: 0.7749 (ttt180) cc_final: 0.7293 (ttm170) REVERT: A 59 PRO cc_start: 0.8068 (Cg_endo) cc_final: 0.7802 (Cg_exo) REVERT: A 60 ASN cc_start: 0.7696 (t160) cc_final: 0.7184 (t0) REVERT: A 61 LEU cc_start: 0.7687 (tp) cc_final: 0.7226 (tp) REVERT: A 79 ARG cc_start: 0.6809 (tpp-160) cc_final: 0.6514 (tpp80) REVERT: A 92 GLN cc_start: 0.8338 (tt0) cc_final: 0.7954 (tt0) REVERT: A 96 TRP cc_start: 0.6587 (t60) cc_final: 0.6337 (t60) REVERT: A 100 HIS cc_start: 0.7458 (m90) cc_final: 0.6987 (m90) REVERT: A 132 MET cc_start: 0.8265 (mtm) cc_final: 0.7863 (mtm) REVERT: A 138 LYS cc_start: 0.8523 (mttm) cc_final: 0.8051 (mmmt) REVERT: A 185 LEU cc_start: 0.8914 (mp) cc_final: 0.8639 (pp) REVERT: A 237 ARG cc_start: 0.3616 (ttp-170) cc_final: 0.2156 (ptm160) REVERT: A 239 MET cc_start: 0.4623 (mmm) cc_final: 0.4089 (ptm) REVERT: A 329 MET cc_start: 0.0021 (mtp) cc_final: -0.0516 (mmm) REVERT: A 342 MET cc_start: -0.1696 (mtp) cc_final: -0.2758 (mtp) REVERT: B 11 ARG cc_start: 0.6176 (pmt-80) cc_final: 0.5896 (ttp80) REVERT: B 21 ARG cc_start: 0.7685 (ttt-90) cc_final: 0.7314 (ptm-80) REVERT: B 50 VAL cc_start: 0.8472 (t) cc_final: 0.8249 (m) REVERT: B 56 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7337 (mtmm) REVERT: B 88 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7524 (tpp80) REVERT: B 95 HIS cc_start: 0.7141 (m90) cc_final: 0.6550 (m90) REVERT: B 96 TRP cc_start: 0.7839 (t60) cc_final: 0.7186 (t60) REVERT: B 98 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6871 (mt-10) REVERT: B 101 LYS cc_start: 0.8745 (mptt) cc_final: 0.8272 (mptt) REVERT: B 102 LYS cc_start: 0.8002 (mptt) cc_final: 0.7766 (mptt) REVERT: B 131 GLN cc_start: 0.7586 (tt0) cc_final: 0.7371 (tt0) REVERT: B 138 LYS cc_start: 0.7845 (mttt) cc_final: 0.7313 (ttmm) REVERT: B 142 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7515 (tmm-80) REVERT: B 148 ASN cc_start: 0.8167 (m-40) cc_final: 0.7746 (t0) REVERT: B 149 ILE cc_start: 0.8462 (mt) cc_final: 0.8050 (mm) REVERT: B 174 LEU cc_start: 0.7659 (mt) cc_final: 0.7366 (mt) REVERT: B 187 VAL cc_start: 0.8342 (t) cc_final: 0.8097 (p) REVERT: B 189 HIS cc_start: 0.6973 (t-90) cc_final: 0.6763 (t-90) REVERT: B 204 ASP cc_start: 0.7408 (t70) cc_final: 0.7066 (m-30) REVERT: B 242 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 289 LYS cc_start: 0.8642 (mppt) cc_final: 0.8408 (mppt) REVERT: B 298 LEU cc_start: 0.8078 (mt) cc_final: 0.7791 (mm) REVERT: B 302 LEU cc_start: 0.8024 (tp) cc_final: 0.7342 (tp) REVERT: B 329 MET cc_start: 0.7413 (mmt) cc_final: 0.6882 (mmt) REVERT: B 334 HIS cc_start: 0.6788 (p90) cc_final: 0.6175 (p90) REVERT: B 344 GLU cc_start: 0.8008 (tt0) cc_final: 0.7563 (tm-30) REVERT: B 351 GLU cc_start: 0.8215 (tt0) cc_final: 0.7745 (tt0) REVERT: B 367 TRP cc_start: 0.7841 (t-100) cc_final: 0.7456 (t-100) REVERT: B 376 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7899 (pt0) REVERT: B 383 GLU cc_start: 0.8280 (pt0) cc_final: 0.7670 (pp20) REVERT: B 386 ASP cc_start: 0.7566 (t70) cc_final: 0.7124 (t70) REVERT: B 416 ARG cc_start: 0.7677 (mpp-170) cc_final: 0.7284 (mtm-85) REVERT: B 454 TRP cc_start: 0.8201 (t60) cc_final: 0.7724 (t60) REVERT: B 456 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7624 (ttm110) REVERT: B 475 ASP cc_start: 0.6798 (t0) cc_final: 0.6461 (p0) REVERT: C 28 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 42 GLU cc_start: 0.7194 (tp30) cc_final: 0.6735 (tp30) REVERT: C 67 PHE cc_start: 0.7568 (m-80) cc_final: 0.7018 (m-80) REVERT: C 90 LEU cc_start: 0.7834 (tp) cc_final: 0.7596 (tp) REVERT: C 98 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7585 (tm-30) REVERT: C 229 GLU cc_start: 0.7675 (pt0) cc_final: 0.7191 (tt0) REVERT: C 273 GLU cc_start: 0.8711 (pt0) cc_final: 0.8371 (tm-30) REVERT: C 364 GLU cc_start: 0.7635 (pm20) cc_final: 0.7284 (pm20) REVERT: D 26 CYS cc_start: 0.7847 (m) cc_final: 0.7086 (p) REVERT: D 27 GLN cc_start: 0.7479 (mt0) cc_final: 0.6620 (mt0) REVERT: D 28 GLN cc_start: 0.7302 (tm-30) cc_final: 0.6809 (tm-30) REVERT: D 30 CYS cc_start: 0.7355 (p) cc_final: 0.7089 (p) REVERT: D 33 ARG cc_start: 0.7905 (mtp180) cc_final: 0.7486 (mtm-85) REVERT: D 35 TRP cc_start: 0.6196 (p90) cc_final: 0.5931 (p90) REVERT: D 36 ASP cc_start: 0.7923 (m-30) cc_final: 0.7528 (m-30) REVERT: D 42 GLU cc_start: 0.7080 (tt0) cc_final: 0.6775 (tt0) REVERT: D 44 LEU cc_start: 0.8960 (mp) cc_final: 0.8712 (mp) REVERT: D 60 ASN cc_start: 0.8223 (m-40) cc_final: 0.7805 (m110) REVERT: D 69 GLU cc_start: 0.6464 (mt-10) cc_final: 0.5485 (mt-10) REVERT: D 92 GLN cc_start: 0.7694 (tt0) cc_final: 0.7439 (mt0) REVERT: D 102 LYS cc_start: 0.7556 (mmtt) cc_final: 0.7087 (mmtt) REVERT: D 131 GLN cc_start: 0.8057 (tt0) cc_final: 0.7766 (tt0) REVERT: D 132 MET cc_start: 0.7175 (mmm) cc_final: 0.6842 (mmt) REVERT: D 133 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7172 (mt-10) REVERT: D 135 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7604 (mm-30) REVERT: D 138 LYS cc_start: 0.8834 (mttt) cc_final: 0.8210 (mtpp) REVERT: D 139 GLU cc_start: 0.7345 (tp30) cc_final: 0.6768 (tp30) REVERT: D 140 ARG cc_start: 0.7471 (ttp-110) cc_final: 0.7172 (ttt90) REVERT: D 142 ARG cc_start: 0.7451 (ttm110) cc_final: 0.6968 (ttm110) REVERT: D 146 HIS cc_start: 0.8223 (m170) cc_final: 0.7855 (m-70) REVERT: D 153 LYS cc_start: 0.8247 (mttt) cc_final: 0.7898 (mttt) REVERT: D 182 GLU cc_start: 0.7972 (tt0) cc_final: 0.7699 (tt0) REVERT: D 186 GLU cc_start: 0.7357 (tt0) cc_final: 0.7085 (tp30) REVERT: D 226 GLN cc_start: 0.7610 (mp10) cc_final: 0.7065 (mp10) REVERT: D 242 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7601 (mt-10) REVERT: D 245 LEU cc_start: 0.8476 (mt) cc_final: 0.7612 (mt) REVERT: D 247 TYR cc_start: 0.6708 (m-10) cc_final: 0.6247 (m-10) REVERT: D 278 LEU cc_start: 0.8305 (mt) cc_final: 0.8080 (mt) REVERT: D 328 SER cc_start: 0.7634 (t) cc_final: 0.7094 (p) REVERT: D 345 TRP cc_start: 0.6384 (m100) cc_final: 0.4824 (m100) REVERT: D 381 ASN cc_start: 0.7565 (m110) cc_final: 0.7290 (m-40) REVERT: D 404 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7998 (mm-30) REVERT: D 416 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7665 (ptp-110) REVERT: D 461 ARG cc_start: 0.6613 (ttm-80) cc_final: 0.6060 (tpt170) outliers start: 2 outliers final: 0 residues processed: 410 average time/residue: 0.1711 time to fit residues: 99.5871 Evaluate side-chains 378 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 97 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 197 optimal weight: 30.0000 chunk 169 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 60 ASN B 111 HIS B 274 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.223265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.162577 restraints weight = 44747.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.167783 restraints weight = 20893.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.170939 restraints weight = 12549.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.172880 restraints weight = 8965.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.174030 restraints weight = 7261.339| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20302 Z= 0.295 Angle : 0.754 11.139 28362 Z= 0.425 Chirality : 0.049 0.300 3108 Planarity : 0.006 0.054 3020 Dihedral : 23.299 87.860 4268 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.91 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: 1.19 (0.19), residues: 1936 helix: 1.44 (0.16), residues: 920 sheet: -0.64 (0.28), residues: 265 loop : 0.74 (0.25), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 21 TYR 0.019 0.002 TYR D 312 PHE 0.024 0.002 PHE B 476 TRP 0.028 0.002 TRP D 161 HIS 0.010 0.002 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.30 (20286) covalent geometry : angle 0.74646 / 0.43 (28338) hydrogen bonds : bond 0.06686 / 4.58 ( 1052) hydrogen bonds : angle 4.40555 / 3.24 ( 2777) metal coordination : bond 0.01124 / 0.65 ( 16) metal coordination : angle 3.76747 / 2.54 ( 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 391 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.634 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: A 21 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7303 (tpm170) REVERT: A 24 GLU cc_start: 0.8618 (tp30) cc_final: 0.7648 (tp30) REVERT: A 30 CYS cc_start: 0.7811 (m) cc_final: 0.7396 (t) REVERT: A 52 PRO cc_start: 0.7354 (Cg_endo) cc_final: 0.6293 (Cg_exo) REVERT: A 58 ARG cc_start: 0.7936 (ttt180) cc_final: 0.7490 (ttm110) REVERT: A 59 PRO cc_start: 0.8141 (Cg_endo) cc_final: 0.7852 (Cg_exo) REVERT: A 60 ASN cc_start: 0.8051 (t0) cc_final: 0.7491 (t0) REVERT: A 61 LEU cc_start: 0.7927 (tp) cc_final: 0.7448 (tp) REVERT: A 79 ARG cc_start: 0.7029 (tpp-160) cc_final: 0.6629 (tpp-160) REVERT: A 96 TRP cc_start: 0.6719 (t60) cc_final: 0.6495 (t60) REVERT: A 100 HIS cc_start: 0.7609 (m90) cc_final: 0.7284 (m90) REVERT: A 132 MET cc_start: 0.8311 (mtm) cc_final: 0.7766 (mtm) REVERT: A 134 LEU cc_start: 0.8733 (tp) cc_final: 0.8511 (tp) REVERT: A 138 LYS cc_start: 0.8560 (mttm) cc_final: 0.8194 (mmmt) REVERT: A 185 LEU cc_start: 0.8901 (mp) cc_final: 0.8603 (pp) REVERT: A 237 ARG cc_start: 0.3443 (ttp-110) cc_final: 0.1781 (ptm160) REVERT: A 239 MET cc_start: 0.4827 (mmm) cc_final: 0.4269 (ptm) REVERT: A 329 MET cc_start: -0.0176 (mtp) cc_final: -0.0918 (mmm) REVERT: B 8 ARG cc_start: 0.7372 (ttp80) cc_final: 0.6867 (ttp80) REVERT: B 21 ARG cc_start: 0.7752 (ttt-90) cc_final: 0.7413 (mmm160) REVERT: B 28 GLN cc_start: 0.7731 (tp-100) cc_final: 0.7209 (tp-100) REVERT: B 32 GLN cc_start: 0.8168 (mp10) cc_final: 0.7507 (mp10) REVERT: B 50 VAL cc_start: 0.8591 (t) cc_final: 0.8362 (m) REVERT: B 56 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7499 (mtmm) REVERT: B 67 PHE cc_start: 0.8042 (m-80) cc_final: 0.7600 (m-10) REVERT: B 71 PRO cc_start: 0.7767 (Cg_exo) cc_final: 0.7566 (Cg_endo) REVERT: B 95 HIS cc_start: 0.7196 (m90) cc_final: 0.6470 (m90) REVERT: B 98 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6849 (mt-10) REVERT: B 101 LYS cc_start: 0.8793 (mptt) cc_final: 0.8296 (mptt) REVERT: B 102 LYS cc_start: 0.8183 (mptt) cc_final: 0.7849 (mptt) REVERT: B 109 GLU cc_start: 0.6531 (mm-30) cc_final: 0.6240 (mp0) REVERT: B 131 GLN cc_start: 0.7596 (tt0) cc_final: 0.7378 (tt0) REVERT: B 138 LYS cc_start: 0.8066 (mttt) cc_final: 0.7589 (ttmm) REVERT: B 143 SER cc_start: 0.8491 (t) cc_final: 0.7973 (p) REVERT: B 148 ASN cc_start: 0.8303 (m-40) cc_final: 0.7843 (t0) REVERT: B 204 ASP cc_start: 0.7488 (t70) cc_final: 0.7171 (m-30) REVERT: B 236 LYS cc_start: 0.8159 (tptm) cc_final: 0.7958 (tptm) REVERT: B 242 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7603 (mt-10) REVERT: B 245 LEU cc_start: 0.8099 (mt) cc_final: 0.7859 (tp) REVERT: B 247 TYR cc_start: 0.7185 (m-10) cc_final: 0.6452 (m-80) REVERT: B 282 LEU cc_start: 0.8056 (mt) cc_final: 0.7778 (mt) REVERT: B 297 LEU cc_start: 0.8113 (tp) cc_final: 0.7854 (tp) REVERT: B 298 LEU cc_start: 0.8139 (mt) cc_final: 0.7932 (mt) REVERT: B 302 LEU cc_start: 0.7850 (tp) cc_final: 0.7358 (tp) REVERT: B 329 MET cc_start: 0.7648 (mmt) cc_final: 0.7067 (mmt) REVERT: B 334 HIS cc_start: 0.7303 (p90) cc_final: 0.6586 (p90) REVERT: B 335 CYS cc_start: 0.3795 (p) cc_final: 0.3418 (p) REVERT: B 342 MET cc_start: 0.7198 (ttp) cc_final: 0.6309 (mmt) REVERT: B 344 GLU cc_start: 0.8232 (tt0) cc_final: 0.7406 (tm-30) REVERT: B 351 GLU cc_start: 0.8451 (tt0) cc_final: 0.7653 (tt0) REVERT: B 367 TRP cc_start: 0.8272 (t-100) cc_final: 0.7715 (t-100) REVERT: B 376 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7727 (mm-30) REVERT: B 386 ASP cc_start: 0.7812 (t70) cc_final: 0.7407 (t70) REVERT: B 391 ILE cc_start: 0.7888 (mt) cc_final: 0.7294 (mt) REVERT: B 409 ARG cc_start: 0.8273 (mtm180) cc_final: 0.8002 (mtm180) REVERT: B 416 ARG cc_start: 0.7834 (mpp-170) cc_final: 0.7403 (mtm-85) REVERT: B 442 TRP cc_start: 0.7995 (t60) cc_final: 0.7689 (t60) REVERT: B 454 TRP cc_start: 0.8182 (t60) cc_final: 0.7834 (t60) REVERT: B 456 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7759 (ttm110) REVERT: B 475 ASP cc_start: 0.6716 (t0) cc_final: 0.6444 (p0) REVERT: C 28 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7644 (tm-30) REVERT: C 90 LEU cc_start: 0.8142 (tp) cc_final: 0.7930 (tp) REVERT: C 229 GLU cc_start: 0.7847 (pt0) cc_final: 0.7445 (tt0) REVERT: C 273 GLU cc_start: 0.8842 (pt0) cc_final: 0.8342 (pm20) REVERT: C 364 GLU cc_start: 0.7984 (pm20) cc_final: 0.7590 (pm20) REVERT: D 7 ILE cc_start: 0.8450 (mt) cc_final: 0.8217 (mm) REVERT: D 9 LEU cc_start: 0.8099 (tt) cc_final: 0.7821 (mt) REVERT: D 24 GLU cc_start: 0.8228 (tp30) cc_final: 0.7926 (tm-30) REVERT: D 26 CYS cc_start: 0.8016 (m) cc_final: 0.7301 (m) REVERT: D 27 GLN cc_start: 0.7512 (mt0) cc_final: 0.6839 (mt0) REVERT: D 28 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7185 (tm-30) REVERT: D 36 ASP cc_start: 0.7967 (m-30) cc_final: 0.7372 (t0) REVERT: D 88 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7472 (ttm-80) REVERT: D 92 GLN cc_start: 0.7751 (tt0) cc_final: 0.7520 (mt0) REVERT: D 131 GLN cc_start: 0.8115 (tt0) cc_final: 0.7874 (tt0) REVERT: D 135 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7666 (mm-30) REVERT: D 138 LYS cc_start: 0.8970 (mttt) cc_final: 0.8342 (mmmt) REVERT: D 142 ARG cc_start: 0.7609 (ttm110) cc_final: 0.7337 (ttm-80) REVERT: D 146 HIS cc_start: 0.8367 (m170) cc_final: 0.8021 (m-70) REVERT: D 153 LYS cc_start: 0.8411 (mttt) cc_final: 0.7829 (mttt) REVERT: D 182 GLU cc_start: 0.8092 (tt0) cc_final: 0.7810 (tt0) REVERT: D 186 GLU cc_start: 0.7533 (tt0) cc_final: 0.7197 (tp30) REVERT: D 226 GLN cc_start: 0.7753 (mp10) cc_final: 0.7316 (mp10) REVERT: D 242 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7636 (mt-10) REVERT: D 245 LEU cc_start: 0.8399 (mt) cc_final: 0.7592 (mt) REVERT: D 247 TYR cc_start: 0.6850 (m-10) cc_final: 0.6269 (m-10) REVERT: D 272 ARG cc_start: 0.7509 (mmm160) cc_final: 0.7047 (mmm160) REVERT: D 278 LEU cc_start: 0.8306 (mt) cc_final: 0.8073 (mt) REVERT: D 302 LEU cc_start: 0.8160 (tp) cc_final: 0.7784 (mt) REVERT: D 328 SER cc_start: 0.7830 (t) cc_final: 0.7284 (p) REVERT: D 404 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8133 (mm-30) REVERT: D 409 ARG cc_start: 0.8308 (tpt-90) cc_final: 0.7712 (mtp85) REVERT: D 443 TRP cc_start: 0.8434 (t60) cc_final: 0.7165 (t60) REVERT: D 459 ASN cc_start: 0.8041 (m-40) cc_final: 0.7777 (m110) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.1702 time to fit residues: 95.0203 Evaluate side-chains 362 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 159 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 142 optimal weight: 50.0000 chunk 20 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 HIS B 274 GLN B 352 GLN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN C 274 GLN C 484 GLN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.226087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.167884 restraints weight = 44442.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.172937 restraints weight = 20500.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.176002 restraints weight = 12292.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177892 restraints weight = 8799.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.178978 restraints weight = 7163.930| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20302 Z= 0.230 Angle : 0.662 9.759 28362 Z= 0.381 Chirality : 0.045 0.240 3108 Planarity : 0.006 0.069 3020 Dihedral : 23.357 86.736 4268 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.06 % Allowed : 1.81 % Favored : 98.13 % 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: 1.22 (0.19), residues: 1936 helix: 1.52 (0.17), residues: 917 sheet: -0.59 (0.29), residues: 271 loop : 0.66 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 2 TYR 0.030 0.002 TYR D 312 PHE 0.015 0.002 PHE B 476 TRP 0.030 0.002 TRP B 443 HIS 0.012 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.23 (20286) covalent geometry : angle 0.65467 / 0.38 (28338) hydrogen bonds : bond 0.05479 / 3.74 ( 1052) hydrogen bonds : angle 4.28065 / 3.14 ( 2777) metal coordination : bond 0.00825 / 0.47 ( 16) metal coordination : angle 3.53882 / 2.47 ( 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 382 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 0.580 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: A 21 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7288 (tpm170) REVERT: A 24 GLU cc_start: 0.8537 (tp30) cc_final: 0.7686 (tp30) REVERT: A 30 CYS cc_start: 0.7723 (m) cc_final: 0.7441 (t) REVERT: A 58 ARG cc_start: 0.7878 (ttt180) cc_final: 0.7476 (ttm110) REVERT: A 59 PRO cc_start: 0.8088 (Cg_endo) cc_final: 0.7813 (Cg_exo) REVERT: A 60 ASN cc_start: 0.8055 (t0) cc_final: 0.7600 (t0) REVERT: A 61 LEU cc_start: 0.7931 (tp) cc_final: 0.7443 (tp) REVERT: A 100 HIS cc_start: 0.7276 (m90) cc_final: 0.7037 (m90) REVERT: A 132 MET cc_start: 0.8296 (mtm) cc_final: 0.7666 (mtm) REVERT: A 135 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8165 (mt-10) REVERT: A 138 LYS cc_start: 0.8574 (mttm) cc_final: 0.8182 (mmmt) REVERT: A 185 LEU cc_start: 0.8960 (mp) cc_final: 0.8671 (pp) REVERT: A 237 ARG cc_start: 0.3378 (ttp-110) cc_final: 0.1563 (ptm160) REVERT: A 239 MET cc_start: 0.4791 (mmm) cc_final: 0.4328 (ptp) REVERT: A 329 MET cc_start: -0.0464 (mtp) cc_final: -0.1100 (mmm) REVERT: A 337 ASN cc_start: -0.0315 (p0) cc_final: -0.1133 (p0) REVERT: B 8 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7044 (ttp80) REVERT: B 21 ARG cc_start: 0.7829 (ttt-90) cc_final: 0.7471 (mmm160) REVERT: B 28 GLN cc_start: 0.7635 (tp-100) cc_final: 0.7098 (tp-100) REVERT: B 56 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7503 (mtmm) REVERT: B 67 PHE cc_start: 0.8031 (m-80) cc_final: 0.7811 (m-10) REVERT: B 71 PRO cc_start: 0.7752 (Cg_exo) cc_final: 0.7544 (Cg_endo) REVERT: B 95 HIS cc_start: 0.7106 (m90) cc_final: 0.6457 (m90) REVERT: B 98 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6831 (mt-10) REVERT: B 101 LYS cc_start: 0.8798 (mptt) cc_final: 0.8364 (mptt) REVERT: B 102 LYS cc_start: 0.8236 (mptt) cc_final: 0.7821 (mptt) REVERT: B 131 GLN cc_start: 0.7569 (tt0) cc_final: 0.7357 (tt0) REVERT: B 138 LYS cc_start: 0.7947 (mttt) cc_final: 0.7461 (ttmm) REVERT: B 148 ASN cc_start: 0.8258 (m-40) cc_final: 0.7807 (t0) REVERT: B 149 ILE cc_start: 0.8561 (mt) cc_final: 0.8208 (mm) REVERT: B 199 HIS cc_start: 0.7739 (p-80) cc_final: 0.7505 (p-80) REVERT: B 204 ASP cc_start: 0.7560 (t70) cc_final: 0.7208 (m-30) REVERT: B 214 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7607 (ttpp) REVERT: B 245 LEU cc_start: 0.8050 (mt) cc_final: 0.7841 (tp) REVERT: B 247 TYR cc_start: 0.7157 (m-10) cc_final: 0.6357 (m-80) REVERT: B 297 LEU cc_start: 0.8203 (tp) cc_final: 0.7952 (tp) REVERT: B 302 LEU cc_start: 0.7924 (tp) cc_final: 0.7306 (tp) REVERT: B 325 ARG cc_start: 0.6666 (mtm110) cc_final: 0.6436 (mtp85) REVERT: B 329 MET cc_start: 0.7494 (mmt) cc_final: 0.6830 (mmt) REVERT: B 334 HIS cc_start: 0.7264 (p90) cc_final: 0.6567 (p90) REVERT: B 344 GLU cc_start: 0.8174 (tt0) cc_final: 0.7576 (tm-30) REVERT: B 351 GLU cc_start: 0.8225 (tt0) cc_final: 0.7628 (tt0) REVERT: B 367 TRP cc_start: 0.8274 (t-100) cc_final: 0.7676 (t-100) REVERT: B 376 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7614 (mm-30) REVERT: B 383 GLU cc_start: 0.8259 (pt0) cc_final: 0.7762 (pp20) REVERT: B 384 LEU cc_start: 0.8905 (mt) cc_final: 0.8690 (mt) REVERT: B 386 ASP cc_start: 0.7746 (t70) cc_final: 0.7267 (t70) REVERT: B 389 SER cc_start: 0.9175 (m) cc_final: 0.8719 (p) REVERT: B 409 ARG cc_start: 0.8240 (mtm180) cc_final: 0.7924 (mmp80) REVERT: B 413 LEU cc_start: 0.8581 (mm) cc_final: 0.7965 (mm) REVERT: B 416 ARG cc_start: 0.7806 (mpp-170) cc_final: 0.7249 (mtm110) REVERT: B 442 TRP cc_start: 0.7918 (t60) cc_final: 0.7607 (t60) REVERT: B 454 TRP cc_start: 0.8116 (t60) cc_final: 0.7669 (t60) REVERT: B 456 ARG cc_start: 0.7930 (mtp180) cc_final: 0.7565 (ttm110) REVERT: B 475 ASP cc_start: 0.6769 (t0) cc_final: 0.6448 (p0) REVERT: C 14 ASP cc_start: 0.2376 (p0) cc_final: 0.2100 (p0) REVERT: C 28 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7571 (tm-30) REVERT: C 229 GLU cc_start: 0.7731 (pt0) cc_final: 0.7346 (tt0) REVERT: C 273 GLU cc_start: 0.8828 (pt0) cc_final: 0.8350 (tm-30) REVERT: C 274 GLN cc_start: 0.6471 (pt0) cc_final: 0.6030 (pt0) REVERT: D 9 LEU cc_start: 0.8380 (tt) cc_final: 0.8029 (mt) REVERT: D 24 GLU cc_start: 0.8120 (tp30) cc_final: 0.7895 (tp30) REVERT: D 26 CYS cc_start: 0.7985 (m) cc_final: 0.7310 (m) REVERT: D 27 GLN cc_start: 0.7420 (mt0) cc_final: 0.6874 (mt0) REVERT: D 28 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7093 (tm-30) REVERT: D 36 ASP cc_start: 0.7964 (m-30) cc_final: 0.7417 (t0) REVERT: D 45 ASP cc_start: 0.7898 (m-30) cc_final: 0.7658 (m-30) REVERT: D 56 LYS cc_start: 0.8247 (tttt) cc_final: 0.7860 (ttpp) REVERT: D 57 ARG cc_start: 0.7150 (mtt90) cc_final: 0.6838 (ttm110) REVERT: D 92 GLN cc_start: 0.7815 (tt0) cc_final: 0.7504 (mt0) REVERT: D 109 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6851 (mm-30) REVERT: D 129 VAL cc_start: 0.8546 (m) cc_final: 0.7709 (p) REVERT: D 132 MET cc_start: 0.7470 (mmm) cc_final: 0.7130 (mmm) REVERT: D 133 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6942 (mp0) REVERT: D 135 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7701 (mm-30) REVERT: D 138 LYS cc_start: 0.8960 (mttt) cc_final: 0.8341 (mmmt) REVERT: D 153 LYS cc_start: 0.8459 (mttt) cc_final: 0.7845 (mttt) REVERT: D 182 GLU cc_start: 0.8090 (tt0) cc_final: 0.7811 (tt0) REVERT: D 186 GLU cc_start: 0.7558 (tt0) cc_final: 0.7200 (tp30) REVERT: D 215 ASP cc_start: 0.7568 (m-30) cc_final: 0.7191 (m-30) REVERT: D 226 GLN cc_start: 0.7834 (mp10) cc_final: 0.7306 (mp10) REVERT: D 242 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7590 (mt-10) REVERT: D 245 LEU cc_start: 0.8380 (mt) cc_final: 0.7597 (mt) REVERT: D 247 TYR cc_start: 0.6798 (m-10) cc_final: 0.6037 (m-10) REVERT: D 272 ARG cc_start: 0.7466 (mmm160) cc_final: 0.7108 (mmm160) REVERT: D 278 LEU cc_start: 0.8239 (mt) cc_final: 0.8031 (mt) REVERT: D 302 LEU cc_start: 0.8138 (tp) cc_final: 0.7786 (mt) REVERT: D 328 SER cc_start: 0.7684 (t) cc_final: 0.7086 (p) REVERT: D 404 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8070 (mm-30) REVERT: D 419 GLU cc_start: 0.8559 (tt0) cc_final: 0.8308 (tm-30) REVERT: D 459 ASN cc_start: 0.7973 (m-40) cc_final: 0.7750 (m110) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.1731 time to fit residues: 94.2821 Evaluate side-chains 355 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 99 optimal weight: 0.0000 chunk 73 optimal weight: 0.0270 chunk 76 optimal weight: 0.0670 chunk 105 optimal weight: 0.6980 chunk 44 optimal weight: 50.0000 chunk 163 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN B 274 GLN C 60 ASN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.228470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.171998 restraints weight = 44436.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177187 restraints weight = 19961.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.180393 restraints weight = 11747.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.182301 restraints weight = 8246.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.183500 restraints weight = 6632.154| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 20302 Z= 0.133 Angle : 0.594 7.415 28362 Z= 0.342 Chirality : 0.041 0.176 3108 Planarity : 0.005 0.100 3020 Dihedral : 23.429 85.517 4268 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.19), residues: 1936 helix: 1.86 (0.17), residues: 918 sheet: -0.45 (0.29), residues: 271 loop : 0.91 (0.25), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 416 TYR 0.021 0.002 TYR B 188 PHE 0.014 0.001 PHE A 53 TRP 0.048 0.002 TRP D 35 HIS 0.006 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (20286) covalent geometry : angle 0.58800 / 0.34 (28338) hydrogen bonds : bond 0.04472 / 3.09 ( 1052) hydrogen bonds : angle 4.02487 / 2.97 ( 2777) metal coordination : bond 0.00331 / 0.20 ( 16) metal coordination : angle 3.00835 / 2.21 ( 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 386 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.593 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 21 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7281 (tpm170) REVERT: A 24 GLU cc_start: 0.8542 (tp30) cc_final: 0.8019 (tp30) REVERT: A 30 CYS cc_start: 0.7801 (m) cc_final: 0.7401 (t) REVERT: A 56 LYS cc_start: 0.8125 (pttp) cc_final: 0.7679 (pttp) REVERT: A 58 ARG cc_start: 0.7748 (ttt180) cc_final: 0.7378 (ttm110) REVERT: A 59 PRO cc_start: 0.7952 (Cg_endo) cc_final: 0.7658 (Cg_exo) REVERT: A 60 ASN cc_start: 0.7711 (t160) cc_final: 0.7240 (t0) REVERT: A 61 LEU cc_start: 0.7750 (tp) cc_final: 0.7289 (tp) REVERT: A 126 MET cc_start: 0.6968 (mpp) cc_final: 0.6745 (mpp) REVERT: A 132 MET cc_start: 0.8083 (mtm) cc_final: 0.7507 (mtm) REVERT: A 135 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8103 (mt-10) REVERT: A 138 LYS cc_start: 0.8554 (mttm) cc_final: 0.8080 (mmmt) REVERT: A 185 LEU cc_start: 0.8936 (mp) cc_final: 0.8665 (pp) REVERT: A 237 ARG cc_start: 0.3210 (ttp-110) cc_final: 0.1448 (ptm160) REVERT: A 239 MET cc_start: 0.4566 (mmm) cc_final: 0.4192 (ptp) REVERT: A 329 MET cc_start: -0.0184 (mtp) cc_final: -0.1000 (mmm) REVERT: A 337 ASN cc_start: -0.0829 (p0) cc_final: -0.1615 (p0) REVERT: B 8 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7249 (ttp80) REVERT: B 27 GLN cc_start: 0.7838 (tp40) cc_final: 0.7586 (tp40) REVERT: B 28 GLN cc_start: 0.7659 (tp-100) cc_final: 0.7079 (tp-100) REVERT: B 56 LYS cc_start: 0.7903 (mtmm) cc_final: 0.7390 (mtmm) REVERT: B 61 LEU cc_start: 0.8278 (tp) cc_final: 0.8010 (tp) REVERT: B 67 PHE cc_start: 0.8024 (m-80) cc_final: 0.7779 (m-10) REVERT: B 95 HIS cc_start: 0.6963 (m90) cc_final: 0.6379 (m90) REVERT: B 98 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6741 (mt-10) REVERT: B 101 LYS cc_start: 0.8756 (mptt) cc_final: 0.8311 (mptt) REVERT: B 102 LYS cc_start: 0.8234 (mptt) cc_final: 0.7821 (mptt) REVERT: B 138 LYS cc_start: 0.7946 (mttt) cc_final: 0.7409 (ttmm) REVERT: B 148 ASN cc_start: 0.8168 (m-40) cc_final: 0.7763 (t0) REVERT: B 149 ILE cc_start: 0.8581 (mt) cc_final: 0.8267 (mm) REVERT: B 201 VAL cc_start: 0.7731 (t) cc_final: 0.7302 (p) REVERT: B 204 ASP cc_start: 0.7409 (t70) cc_final: 0.7102 (m-30) REVERT: B 214 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7542 (ttpp) REVERT: B 245 LEU cc_start: 0.8040 (mt) cc_final: 0.7829 (tp) REVERT: B 297 LEU cc_start: 0.8100 (tp) cc_final: 0.7853 (tp) REVERT: B 302 LEU cc_start: 0.7768 (tp) cc_final: 0.7212 (tp) REVERT: B 329 MET cc_start: 0.7321 (mmt) cc_final: 0.6788 (mmt) REVERT: B 334 HIS cc_start: 0.7135 (p90) cc_final: 0.6530 (p90) REVERT: B 345 TRP cc_start: 0.6893 (m100) cc_final: 0.6622 (m100) REVERT: B 367 TRP cc_start: 0.8164 (t-100) cc_final: 0.7698 (t-100) REVERT: B 376 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7629 (mm-30) REVERT: B 386 ASP cc_start: 0.7557 (t70) cc_final: 0.7096 (t70) REVERT: B 409 ARG cc_start: 0.8159 (mtm180) cc_final: 0.7873 (mmp80) REVERT: B 454 TRP cc_start: 0.8059 (t60) cc_final: 0.7672 (t60) REVERT: B 456 ARG cc_start: 0.7799 (mtp180) cc_final: 0.7231 (ttm110) REVERT: B 458 MET cc_start: 0.7314 (mpp) cc_final: 0.7083 (mpp) REVERT: C 22 GLN cc_start: 0.8131 (mt0) cc_final: 0.7646 (mt0) REVERT: C 24 GLU cc_start: 0.7302 (tm-30) cc_final: 0.7035 (tm-30) REVERT: C 28 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 42 GLU cc_start: 0.6954 (tp30) cc_final: 0.6676 (tp30) REVERT: C 54 ASP cc_start: 0.5055 (t70) cc_final: 0.4751 (t0) REVERT: C 90 LEU cc_start: 0.8001 (tp) cc_final: 0.7721 (tp) REVERT: C 98 GLU cc_start: 0.8357 (pt0) cc_final: 0.7926 (pp20) REVERT: C 100 HIS cc_start: 0.7453 (m90) cc_final: 0.7218 (m90) REVERT: C 229 GLU cc_start: 0.7817 (pt0) cc_final: 0.7286 (tt0) REVERT: C 273 GLU cc_start: 0.8818 (pt0) cc_final: 0.8426 (tm-30) REVERT: C 274 GLN cc_start: 0.6141 (pt0) cc_final: 0.5868 (pt0) REVERT: D 9 LEU cc_start: 0.8230 (tt) cc_final: 0.7841 (mt) REVERT: D 24 GLU cc_start: 0.8122 (tp30) cc_final: 0.7839 (tp30) REVERT: D 26 CYS cc_start: 0.7927 (m) cc_final: 0.7194 (m) REVERT: D 27 GLN cc_start: 0.7350 (mt0) cc_final: 0.6819 (mt0) REVERT: D 28 GLN cc_start: 0.7477 (tm-30) cc_final: 0.7012 (tm-30) REVERT: D 30 CYS cc_start: 0.7375 (p) cc_final: 0.7145 (p) REVERT: D 45 ASP cc_start: 0.7860 (m-30) cc_final: 0.7650 (m-30) REVERT: D 55 ARG cc_start: 0.7107 (tpt170) cc_final: 0.6873 (tpt170) REVERT: D 56 LYS cc_start: 0.8187 (tttt) cc_final: 0.7812 (ttpp) REVERT: D 57 ARG cc_start: 0.7043 (mtt90) cc_final: 0.6367 (ttm110) REVERT: D 64 TRP cc_start: 0.8132 (m100) cc_final: 0.7683 (m100) REVERT: D 92 GLN cc_start: 0.7683 (tt0) cc_final: 0.7462 (mt0) REVERT: D 102 LYS cc_start: 0.7529 (mmtt) cc_final: 0.7097 (mmtt) REVERT: D 109 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6771 (mm-30) REVERT: D 129 VAL cc_start: 0.8441 (m) cc_final: 0.8178 (p) REVERT: D 135 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7643 (mm-30) REVERT: D 138 LYS cc_start: 0.8935 (mttt) cc_final: 0.8291 (mtpp) REVERT: D 140 ARG cc_start: 0.7591 (ttp-110) cc_final: 0.7181 (ttt90) REVERT: D 153 LYS cc_start: 0.8384 (mttt) cc_final: 0.7785 (mttt) REVERT: D 182 GLU cc_start: 0.8042 (tt0) cc_final: 0.7772 (tt0) REVERT: D 186 GLU cc_start: 0.7432 (tt0) cc_final: 0.7103 (tp30) REVERT: D 189 HIS cc_start: 0.6393 (t-90) cc_final: 0.6080 (t-90) REVERT: D 226 GLN cc_start: 0.7830 (mp10) cc_final: 0.7309 (mp10) REVERT: D 242 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7498 (mt-10) REVERT: D 245 LEU cc_start: 0.8530 (mt) cc_final: 0.7664 (mt) REVERT: D 247 TYR cc_start: 0.6787 (m-10) cc_final: 0.6092 (m-10) REVERT: D 272 ARG cc_start: 0.7520 (mmm160) cc_final: 0.7099 (mmm160) REVERT: D 328 SER cc_start: 0.7609 (t) cc_final: 0.7060 (p) REVERT: D 345 TRP cc_start: 0.6324 (m100) cc_final: 0.5111 (m-10) REVERT: D 404 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7925 (mm-30) REVERT: D 406 LEU cc_start: 0.8871 (tp) cc_final: 0.8658 (mp) REVERT: D 416 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7892 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.1809 time to fit residues: 99.4576 Evaluate side-chains 360 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 146 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 126 optimal weight: 40.0000 chunk 158 optimal weight: 3.9990 chunk 200 optimal weight: 50.0000 chunk 100 optimal weight: 0.0470 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS A 148 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 131 GLN C 60 ASN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN ** D 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.226806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.168784 restraints weight = 44440.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.173911 restraints weight = 20301.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.177022 restraints weight = 12144.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 72)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.179001 restraints weight = 8655.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.180147 restraints weight = 6947.390| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20302 Z= 0.175 Angle : 0.628 9.859 28362 Z= 0.359 Chirality : 0.043 0.319 3108 Planarity : 0.006 0.124 3020 Dihedral : 23.429 86.039 4268 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.06 % Allowed : 1.00 % Favored : 98.94 % 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: 1.62 (0.20), residues: 1936 helix: 1.84 (0.17), residues: 918 sheet: -0.48 (0.28), residues: 289 loop : 0.96 (0.26), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 265 TYR 0.025 0.002 TYR D 312 PHE 0.020 0.002 PHE C 118 TRP 0.055 0.002 TRP D 35 HIS 0.010 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.18 (20286) covalent geometry : angle 0.62320 / 0.36 (28338) hydrogen bonds : bond 0.04839 / 3.32 ( 1052) hydrogen bonds : angle 4.11366 / 3.02 ( 2777) metal coordination : bond 0.00471 / 0.26 ( 16) metal coordination : angle 2.74196 / 2.00 ( 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 376 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 0.537 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 21 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7339 (tpm170) REVERT: A 24 GLU cc_start: 0.8550 (tp30) cc_final: 0.7637 (tp30) REVERT: A 58 ARG cc_start: 0.7925 (ttt180) cc_final: 0.7521 (ttm110) REVERT: A 60 ASN cc_start: 0.7883 (t0) cc_final: 0.7640 (t0) REVERT: A 61 LEU cc_start: 0.7996 (tp) cc_final: 0.7544 (tp) REVERT: A 132 MET cc_start: 0.8224 (mtm) cc_final: 0.7551 (mtm) REVERT: A 185 LEU cc_start: 0.8936 (mp) cc_final: 0.8672 (pp) REVERT: A 237 ARG cc_start: 0.3386 (ttp-110) cc_final: 0.1349 (ptm160) REVERT: A 239 MET cc_start: 0.4729 (mmm) cc_final: 0.4303 (ptp) REVERT: A 329 MET cc_start: -0.0219 (mtp) cc_final: -0.1042 (tpt) REVERT: A 337 ASN cc_start: -0.0756 (p0) cc_final: -0.1461 (p0) REVERT: B 8 ARG cc_start: 0.7389 (ttp80) cc_final: 0.6919 (ttp80) REVERT: B 21 ARG cc_start: 0.7759 (ttt-90) cc_final: 0.7334 (mmm160) REVERT: B 27 GLN cc_start: 0.7914 (tp40) cc_final: 0.7660 (tp40) REVERT: B 28 GLN cc_start: 0.7670 (tp-100) cc_final: 0.7078 (tp-100) REVERT: B 56 LYS cc_start: 0.7936 (mtmm) cc_final: 0.7406 (mtmm) REVERT: B 67 PHE cc_start: 0.8103 (m-80) cc_final: 0.7824 (m-10) REVERT: B 71 PRO cc_start: 0.7722 (Cg_exo) cc_final: 0.7481 (Cg_endo) REVERT: B 95 HIS cc_start: 0.7012 (m90) cc_final: 0.6446 (m90) REVERT: B 98 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6805 (mt-10) REVERT: B 101 LYS cc_start: 0.8768 (mptt) cc_final: 0.8321 (mptt) REVERT: B 102 LYS cc_start: 0.8296 (mptt) cc_final: 0.7824 (mptt) REVERT: B 138 LYS cc_start: 0.8005 (mttt) cc_final: 0.7370 (mtpp) REVERT: B 142 ARG cc_start: 0.7808 (tmm-80) cc_final: 0.7231 (tmm-80) REVERT: B 143 SER cc_start: 0.8273 (p) cc_final: 0.7942 (p) REVERT: B 148 ASN cc_start: 0.8255 (m-40) cc_final: 0.7788 (t0) REVERT: B 149 ILE cc_start: 0.8585 (mt) cc_final: 0.8262 (mm) REVERT: B 201 VAL cc_start: 0.7818 (t) cc_final: 0.7436 (p) REVERT: B 204 ASP cc_start: 0.7549 (t70) cc_final: 0.7152 (m-30) REVERT: B 240 ILE cc_start: 0.8228 (pt) cc_final: 0.7864 (mt) REVERT: B 297 LEU cc_start: 0.8144 (tp) cc_final: 0.7944 (tp) REVERT: B 302 LEU cc_start: 0.7801 (tp) cc_final: 0.7249 (tp) REVERT: B 329 MET cc_start: 0.7210 (mmt) cc_final: 0.6771 (mmt) REVERT: B 334 HIS cc_start: 0.7206 (p90) cc_final: 0.6635 (p90) REVERT: B 346 ASP cc_start: 0.7801 (m-30) cc_final: 0.7339 (m-30) REVERT: B 367 TRP cc_start: 0.8328 (t-100) cc_final: 0.7763 (t-100) REVERT: B 376 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7626 (mm-30) REVERT: B 386 ASP cc_start: 0.7684 (t70) cc_final: 0.7265 (t70) REVERT: B 409 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7915 (mmp80) REVERT: B 419 GLU cc_start: 0.8470 (pt0) cc_final: 0.8160 (pp20) REVERT: B 454 TRP cc_start: 0.8186 (t60) cc_final: 0.7669 (t60) REVERT: B 456 ARG cc_start: 0.7852 (mtp180) cc_final: 0.7373 (ttm110) REVERT: B 458 MET cc_start: 0.7534 (mpp) cc_final: 0.7226 (mpp) REVERT: C 22 GLN cc_start: 0.8165 (mt0) cc_final: 0.7575 (mt0) REVERT: C 28 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 42 GLU cc_start: 0.7024 (tp30) cc_final: 0.6603 (tp30) REVERT: C 89 HIS cc_start: 0.8167 (m-70) cc_final: 0.7901 (m-70) REVERT: C 90 LEU cc_start: 0.8125 (tp) cc_final: 0.7818 (tp) REVERT: C 98 GLU cc_start: 0.8371 (pt0) cc_final: 0.8002 (pp20) REVERT: C 100 HIS cc_start: 0.7489 (m90) cc_final: 0.7229 (m90) REVERT: C 229 GLU cc_start: 0.7789 (pt0) cc_final: 0.7406 (tp30) REVERT: C 273 GLU cc_start: 0.8648 (pt0) cc_final: 0.8300 (pm20) REVERT: D 9 LEU cc_start: 0.8283 (tt) cc_final: 0.7877 (mt) REVERT: D 26 CYS cc_start: 0.7957 (m) cc_final: 0.7291 (m) REVERT: D 28 GLN cc_start: 0.7388 (tm-30) cc_final: 0.6978 (tm-30) REVERT: D 30 CYS cc_start: 0.7492 (p) cc_final: 0.7256 (p) REVERT: D 33 ARG cc_start: 0.7921 (tpp80) cc_final: 0.7594 (mtm-85) REVERT: D 56 LYS cc_start: 0.8199 (tttt) cc_final: 0.7822 (ttpp) REVERT: D 57 ARG cc_start: 0.7064 (mtt90) cc_final: 0.6702 (ttm110) REVERT: D 64 TRP cc_start: 0.8021 (m100) cc_final: 0.7622 (m100) REVERT: D 79 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.6819 (mtm110) REVERT: D 92 GLN cc_start: 0.7751 (tt0) cc_final: 0.7521 (mt0) REVERT: D 102 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7219 (mmtt) REVERT: D 109 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6788 (mp0) REVERT: D 129 VAL cc_start: 0.8548 (m) cc_final: 0.8234 (p) REVERT: D 133 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7284 (mt-10) REVERT: D 135 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7626 (mm-30) REVERT: D 138 LYS cc_start: 0.8957 (mttt) cc_final: 0.8329 (mtpp) REVERT: D 153 LYS cc_start: 0.8480 (mttt) cc_final: 0.7835 (mttt) REVERT: D 182 GLU cc_start: 0.8060 (tt0) cc_final: 0.7805 (tt0) REVERT: D 186 GLU cc_start: 0.7585 (tt0) cc_final: 0.7321 (tp30) REVERT: D 189 HIS cc_start: 0.6324 (t-90) cc_final: 0.6079 (t-90) REVERT: D 214 LYS cc_start: 0.7096 (ttmm) cc_final: 0.6812 (tttp) REVERT: D 220 LEU cc_start: 0.8052 (tt) cc_final: 0.7591 (mm) REVERT: D 226 GLN cc_start: 0.7915 (mp10) cc_final: 0.7366 (mp10) REVERT: D 242 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7582 (mt-10) REVERT: D 245 LEU cc_start: 0.8550 (mt) cc_final: 0.7668 (mt) REVERT: D 247 TYR cc_start: 0.6780 (m-10) cc_final: 0.5968 (m-10) REVERT: D 272 ARG cc_start: 0.7532 (mmm160) cc_final: 0.7138 (mmm160) REVERT: D 328 SER cc_start: 0.7465 (t) cc_final: 0.7051 (p) REVERT: D 345 TRP cc_start: 0.6686 (m100) cc_final: 0.5420 (m100) REVERT: D 404 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8021 (mm-30) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.1778 time to fit residues: 95.1534 Evaluate side-chains 352 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 25 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 172 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 0.0270 chunk 93 optimal weight: 0.8980 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 GLN ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 131 GLN C 60 ASN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN ** D 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.227054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.169445 restraints weight = 44480.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.174564 restraints weight = 20376.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.177705 restraints weight = 12122.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.179636 restraints weight = 8603.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.180777 restraints weight = 6942.075| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20302 Z= 0.184 Angle : 0.622 8.595 28362 Z= 0.354 Chirality : 0.043 0.276 3108 Planarity : 0.005 0.093 3020 Dihedral : 23.443 87.571 4268 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.06 % Allowed : 0.56 % Favored : 99.38 % 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: 1.55 (0.20), residues: 1936 helix: 1.80 (0.17), residues: 917 sheet: -0.55 (0.28), residues: 289 loop : 0.91 (0.26), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 416 TYR 0.013 0.002 TYR D 312 PHE 0.022 0.002 PHE C 118 TRP 0.060 0.002 TRP D 35 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.18 (20286) covalent geometry : angle 0.61698 / 0.35 (28338) hydrogen bonds : bond 0.04775 / 3.28 ( 1052) hydrogen bonds : angle 4.16527 / 3.06 ( 2777) metal coordination : bond 0.00516 / 0.30 ( 16) metal coordination : angle 2.68615 / 1.96 ( 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 366 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.493 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 21 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7362 (tpm170) REVERT: A 27 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8109 (mm-40) REVERT: A 28 GLN cc_start: 0.8589 (mp10) cc_final: 0.8253 (mp10) REVERT: A 58 ARG cc_start: 0.7903 (ttt180) cc_final: 0.7528 (ttm110) REVERT: A 60 ASN cc_start: 0.7834 (t0) cc_final: 0.7630 (t0) REVERT: A 61 LEU cc_start: 0.7995 (tp) cc_final: 0.7526 (tp) REVERT: A 88 ARG cc_start: 0.7289 (tpt90) cc_final: 0.6766 (ttp80) REVERT: A 92 GLN cc_start: 0.8008 (tt0) cc_final: 0.7580 (tt0) REVERT: A 132 MET cc_start: 0.8189 (mtm) cc_final: 0.7562 (mtm) REVERT: A 185 LEU cc_start: 0.8935 (mp) cc_final: 0.8672 (pp) REVERT: A 237 ARG cc_start: 0.3466 (ttp-110) cc_final: 0.1474 (ptm160) REVERT: A 239 MET cc_start: 0.4799 (mmm) cc_final: 0.4352 (ptp) REVERT: A 329 MET cc_start: -0.0268 (mtp) cc_final: -0.1025 (mmm) REVERT: A 337 ASN cc_start: -0.1155 (p0) cc_final: -0.1596 (p0) REVERT: B 21 ARG cc_start: 0.7778 (ttt-90) cc_final: 0.7359 (mmm160) REVERT: B 27 GLN cc_start: 0.7897 (tp40) cc_final: 0.7689 (tp40) REVERT: B 28 GLN cc_start: 0.7669 (tp-100) cc_final: 0.7093 (tp-100) REVERT: B 56 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7405 (mtmm) REVERT: B 67 PHE cc_start: 0.8084 (m-80) cc_final: 0.7836 (m-10) REVERT: B 71 PRO cc_start: 0.7715 (Cg_exo) cc_final: 0.7472 (Cg_endo) REVERT: B 95 HIS cc_start: 0.7005 (m90) cc_final: 0.6432 (m90) REVERT: B 98 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6795 (mt-10) REVERT: B 101 LYS cc_start: 0.8765 (mptt) cc_final: 0.8317 (mptt) REVERT: B 102 LYS cc_start: 0.8387 (mptt) cc_final: 0.7744 (mptt) REVERT: B 138 LYS cc_start: 0.8039 (mttt) cc_final: 0.7487 (ttmm) REVERT: B 142 ARG cc_start: 0.7778 (tmm-80) cc_final: 0.7238 (tmm-80) REVERT: B 143 SER cc_start: 0.8274 (p) cc_final: 0.7922 (p) REVERT: B 148 ASN cc_start: 0.8223 (m-40) cc_final: 0.7772 (t0) REVERT: B 149 ILE cc_start: 0.8661 (mt) cc_final: 0.8240 (mm) REVERT: B 201 VAL cc_start: 0.7823 (t) cc_final: 0.7388 (p) REVERT: B 204 ASP cc_start: 0.7585 (t70) cc_final: 0.7151 (m-30) REVERT: B 214 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7557 (ttpp) REVERT: B 240 ILE cc_start: 0.8229 (pt) cc_final: 0.7911 (mt) REVERT: B 247 TYR cc_start: 0.6549 (m-10) cc_final: 0.6290 (m-80) REVERT: B 289 LYS cc_start: 0.8651 (mppt) cc_final: 0.8043 (mmtt) REVERT: B 302 LEU cc_start: 0.7719 (tp) cc_final: 0.7206 (tp) REVERT: B 329 MET cc_start: 0.7154 (mmt) cc_final: 0.6770 (mmt) REVERT: B 334 HIS cc_start: 0.7243 (p90) cc_final: 0.6639 (p90) REVERT: B 345 TRP cc_start: 0.7296 (m100) cc_final: 0.6982 (m100) REVERT: B 346 ASP cc_start: 0.7772 (m-30) cc_final: 0.7371 (m-30) REVERT: B 367 TRP cc_start: 0.8362 (t-100) cc_final: 0.7781 (t-100) REVERT: B 376 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7668 (mm-30) REVERT: B 386 ASP cc_start: 0.7674 (t70) cc_final: 0.7134 (t0) REVERT: B 409 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7891 (mmp80) REVERT: B 419 GLU cc_start: 0.8386 (pt0) cc_final: 0.8163 (pp20) REVERT: B 443 TRP cc_start: 0.7608 (t-100) cc_final: 0.7334 (t-100) REVERT: B 454 TRP cc_start: 0.8148 (t60) cc_final: 0.7564 (t60) REVERT: B 456 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7378 (ttm110) REVERT: B 458 MET cc_start: 0.7512 (mpp) cc_final: 0.7162 (mpp) REVERT: C 22 GLN cc_start: 0.8071 (mt0) cc_final: 0.7520 (mt0) REVERT: C 28 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 89 HIS cc_start: 0.8198 (m-70) cc_final: 0.7958 (m-70) REVERT: C 90 LEU cc_start: 0.8165 (tp) cc_final: 0.7860 (tp) REVERT: C 98 GLU cc_start: 0.8191 (pt0) cc_final: 0.7713 (pp20) REVERT: C 100 HIS cc_start: 0.7488 (m90) cc_final: 0.7235 (m90) REVERT: C 229 GLU cc_start: 0.7675 (pt0) cc_final: 0.7401 (tp30) REVERT: C 271 THR cc_start: 0.7624 (p) cc_final: 0.6610 (p) REVERT: C 273 GLU cc_start: 0.8702 (pt0) cc_final: 0.8251 (pm20) REVERT: D 9 LEU cc_start: 0.8292 (tt) cc_final: 0.7954 (mt) REVERT: D 26 CYS cc_start: 0.7965 (m) cc_final: 0.7254 (m) REVERT: D 28 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7092 (tm-30) REVERT: D 30 CYS cc_start: 0.7475 (p) cc_final: 0.7274 (p) REVERT: D 36 ASP cc_start: 0.7890 (m-30) cc_final: 0.7433 (t0) REVERT: D 55 ARG cc_start: 0.7208 (tpt170) cc_final: 0.6897 (tpt-90) REVERT: D 56 LYS cc_start: 0.8177 (tttt) cc_final: 0.7798 (ttpp) REVERT: D 57 ARG cc_start: 0.7192 (mtt90) cc_final: 0.6816 (ttm110) REVERT: D 64 TRP cc_start: 0.7984 (m100) cc_final: 0.7556 (m100) REVERT: D 68 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7201 (mt-10) REVERT: D 92 GLN cc_start: 0.7795 (tt0) cc_final: 0.7549 (mt0) REVERT: D 102 LYS cc_start: 0.7576 (mmtt) cc_final: 0.7202 (mmtt) REVERT: D 109 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6726 (mm-30) REVERT: D 129 VAL cc_start: 0.8536 (m) cc_final: 0.8233 (p) REVERT: D 133 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7326 (mt-10) REVERT: D 135 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7615 (mm-30) REVERT: D 138 LYS cc_start: 0.8957 (mttt) cc_final: 0.8359 (mtpp) REVERT: D 153 LYS cc_start: 0.8492 (mttt) cc_final: 0.7857 (mttt) REVERT: D 182 GLU cc_start: 0.8013 (tt0) cc_final: 0.7752 (tt0) REVERT: D 186 GLU cc_start: 0.7599 (tt0) cc_final: 0.7309 (tp30) REVERT: D 226 GLN cc_start: 0.8021 (mp10) cc_final: 0.7382 (mp10) REVERT: D 242 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7615 (mt-10) REVERT: D 245 LEU cc_start: 0.8389 (mt) cc_final: 0.7347 (mp) REVERT: D 247 TYR cc_start: 0.6769 (m-10) cc_final: 0.5990 (m-10) REVERT: D 272 ARG cc_start: 0.7516 (mmm160) cc_final: 0.7093 (mmm160) REVERT: D 328 SER cc_start: 0.7611 (t) cc_final: 0.7090 (p) REVERT: D 345 TRP cc_start: 0.6743 (m100) cc_final: 0.5318 (m100) REVERT: D 404 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8020 (mm-30) REVERT: D 416 ARG cc_start: 0.8422 (ptp90) cc_final: 0.7957 (ptt-90) REVERT: D 443 TRP cc_start: 0.7924 (t60) cc_final: 0.7189 (t60) outliers start: 1 outliers final: 0 residues processed: 365 average time/residue: 0.1606 time to fit residues: 84.2972 Evaluate side-chains 346 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 60 optimal weight: 1.9990 chunk 121 optimal weight: 0.0570 chunk 15 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 160 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 overall best weight: 2.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 203 HIS C 60 ASN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN D 60 ASN D 100 HIS ** D 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.225054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.165961 restraints weight = 44257.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.171095 restraints weight = 20468.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.174211 restraints weight = 12282.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.176170 restraints weight = 8831.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.177348 restraints weight = 7169.810| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20302 Z= 0.225 Angle : 0.650 9.730 28362 Z= 0.372 Chirality : 0.044 0.227 3108 Planarity : 0.006 0.101 3020 Dihedral : 23.468 88.482 4268 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.06 % Allowed : 0.62 % Favored : 99.31 % 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: 1.32 (0.19), residues: 1936 helix: 1.58 (0.17), residues: 920 sheet: -0.48 (0.29), residues: 292 loop : 0.76 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 272 TYR 0.020 0.002 TYR C 188 PHE 0.025 0.002 PHE B 476 TRP 0.071 0.002 TRP D 35 HIS 0.010 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.23 (20286) covalent geometry : angle 0.64468 / 0.37 (28338) hydrogen bonds : bond 0.05309 / 3.65 ( 1052) hydrogen bonds : angle 4.32683 / 3.18 ( 2777) metal coordination : bond 0.00663 / 0.38 ( 16) metal coordination : angle 2.80353 / 1.97 ( 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 358 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.596 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: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7318 (tpm170) REVERT: A 27 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8574 (mm-40) REVERT: A 60 ASN cc_start: 0.8082 (t0) cc_final: 0.7863 (t0) REVERT: A 61 LEU cc_start: 0.8087 (tp) cc_final: 0.7768 (tp) REVERT: A 88 ARG cc_start: 0.7500 (tpt90) cc_final: 0.6857 (ttp80) REVERT: A 92 GLN cc_start: 0.8051 (tt0) cc_final: 0.7668 (tt0) REVERT: A 132 MET cc_start: 0.8211 (mtm) cc_final: 0.7592 (mtm) REVERT: A 185 LEU cc_start: 0.8957 (mp) cc_final: 0.8686 (pp) REVERT: A 237 ARG cc_start: 0.3925 (ttp-110) cc_final: 0.2795 (ptp-170) REVERT: A 239 MET cc_start: 0.4932 (mmm) cc_final: 0.4437 (ptp) REVERT: A 329 MET cc_start: -0.0514 (mtp) cc_final: -0.1190 (mmm) REVERT: A 337 ASN cc_start: -0.1024 (p0) cc_final: -0.1428 (p0) REVERT: B 21 ARG cc_start: 0.7849 (ttt-90) cc_final: 0.7436 (mmm160) REVERT: B 28 GLN cc_start: 0.8007 (tp-100) cc_final: 0.7448 (tp-100) REVERT: B 56 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7346 (mtmm) REVERT: B 67 PHE cc_start: 0.8068 (m-80) cc_final: 0.7848 (m-10) REVERT: B 71 PRO cc_start: 0.7714 (Cg_exo) cc_final: 0.7484 (Cg_endo) REVERT: B 95 HIS cc_start: 0.7069 (m90) cc_final: 0.6468 (m90) REVERT: B 98 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6809 (mt-10) REVERT: B 101 LYS cc_start: 0.8756 (mptt) cc_final: 0.8338 (mptt) REVERT: B 102 LYS cc_start: 0.8409 (mptt) cc_final: 0.7773 (mptt) REVERT: B 138 LYS cc_start: 0.8076 (mttt) cc_final: 0.7465 (mmtt) REVERT: B 148 ASN cc_start: 0.8279 (m-40) cc_final: 0.7792 (t0) REVERT: B 149 ILE cc_start: 0.8627 (mt) cc_final: 0.8253 (mm) REVERT: B 186 GLU cc_start: 0.7619 (pt0) cc_final: 0.7284 (pp20) REVERT: B 204 ASP cc_start: 0.7646 (t70) cc_final: 0.7214 (m-30) REVERT: B 214 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7904 (ttmt) REVERT: B 247 TYR cc_start: 0.6849 (m-10) cc_final: 0.6578 (m-80) REVERT: B 279 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7431 (mtt180) REVERT: B 289 LYS cc_start: 0.8645 (mppt) cc_final: 0.8377 (mppt) REVERT: B 302 LEU cc_start: 0.7513 (tp) cc_final: 0.6971 (tp) REVERT: B 329 MET cc_start: 0.7608 (mmt) cc_final: 0.6926 (mmt) REVERT: B 334 HIS cc_start: 0.7330 (p90) cc_final: 0.6720 (p90) REVERT: B 345 TRP cc_start: 0.7273 (m100) cc_final: 0.6967 (m100) REVERT: B 346 ASP cc_start: 0.7732 (m-30) cc_final: 0.7344 (m-30) REVERT: B 367 TRP cc_start: 0.8466 (t-100) cc_final: 0.7780 (t-100) REVERT: B 376 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B 386 ASP cc_start: 0.7806 (t70) cc_final: 0.7274 (t0) REVERT: B 409 ARG cc_start: 0.8182 (mtm180) cc_final: 0.7970 (mmp80) REVERT: B 419 GLU cc_start: 0.8379 (pt0) cc_final: 0.8171 (pp20) REVERT: B 442 TRP cc_start: 0.8014 (t60) cc_final: 0.7730 (t60) REVERT: B 443 TRP cc_start: 0.7824 (t-100) cc_final: 0.7346 (t-100) REVERT: B 456 ARG cc_start: 0.7859 (mtp180) cc_final: 0.7505 (ttm110) REVERT: B 457 SER cc_start: 0.8878 (t) cc_final: 0.8605 (m) REVERT: C 22 GLN cc_start: 0.8088 (mt0) cc_final: 0.7606 (mt0) REVERT: C 28 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 89 HIS cc_start: 0.8300 (m-70) cc_final: 0.8082 (m-70) REVERT: C 90 LEU cc_start: 0.8270 (tp) cc_final: 0.7969 (tp) REVERT: C 98 GLU cc_start: 0.8254 (pt0) cc_final: 0.7711 (pp20) REVERT: C 100 HIS cc_start: 0.7515 (m90) cc_final: 0.7122 (m90) REVERT: C 219 GLN cc_start: 0.8594 (mt0) cc_final: 0.8383 (mt0) REVERT: C 271 THR cc_start: 0.7813 (p) cc_final: 0.6984 (p) REVERT: C 273 GLU cc_start: 0.8697 (pt0) cc_final: 0.8277 (pm20) REVERT: D 9 LEU cc_start: 0.8174 (tt) cc_final: 0.7963 (mt) REVERT: D 20 GLU cc_start: 0.7546 (mp0) cc_final: 0.7325 (pm20) REVERT: D 21 ARG cc_start: 0.7855 (ttt90) cc_final: 0.7130 (ptm160) REVERT: D 26 CYS cc_start: 0.7853 (m) cc_final: 0.7112 (m) REVERT: D 28 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7149 (tm-30) REVERT: D 36 ASP cc_start: 0.7849 (m-30) cc_final: 0.7418 (t0) REVERT: D 64 TRP cc_start: 0.7940 (m100) cc_final: 0.7565 (m100) REVERT: D 73 ASP cc_start: 0.7075 (t0) cc_final: 0.6846 (t0) REVERT: D 87 ILE cc_start: 0.8213 (mt) cc_final: 0.7987 (mt) REVERT: D 102 LYS cc_start: 0.7658 (mmtt) cc_final: 0.7217 (mmtt) REVERT: D 109 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6687 (mm-30) REVERT: D 129 VAL cc_start: 0.8629 (m) cc_final: 0.8233 (p) REVERT: D 133 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7355 (mt-10) REVERT: D 138 LYS cc_start: 0.8975 (mttt) cc_final: 0.8311 (mtpp) REVERT: D 153 LYS cc_start: 0.8559 (mttt) cc_final: 0.7921 (mttt) REVERT: D 182 GLU cc_start: 0.7990 (tt0) cc_final: 0.7320 (tp30) REVERT: D 186 GLU cc_start: 0.7656 (tt0) cc_final: 0.7190 (tp30) REVERT: D 189 HIS cc_start: 0.6169 (t-90) cc_final: 0.5822 (t-90) REVERT: D 226 GLN cc_start: 0.7992 (mp10) cc_final: 0.7396 (mp10) REVERT: D 242 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7858 (tp30) REVERT: D 272 ARG cc_start: 0.7661 (mmm160) cc_final: 0.7073 (mmm160) REVERT: D 302 LEU cc_start: 0.8171 (tp) cc_final: 0.7723 (mt) REVERT: D 328 SER cc_start: 0.7530 (t) cc_final: 0.7082 (p) REVERT: D 342 MET cc_start: 0.7019 (ptm) cc_final: 0.6817 (ptt) REVERT: D 345 TRP cc_start: 0.6868 (m100) cc_final: 0.5274 (m100) REVERT: D 404 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8040 (mm-30) REVERT: D 416 ARG cc_start: 0.8118 (ptp90) cc_final: 0.7843 (ptt-90) outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.1632 time to fit residues: 83.8141 Evaluate side-chains 341 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 71 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.0010 chunk 51 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 159 optimal weight: 1.9990 chunk 205 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 chunk 177 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 GLN A 60 ASN B 189 HIS C 60 ASN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN D 60 ASN ** D 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.228581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.174405 restraints weight = 44735.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.175885 restraints weight = 23781.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.177451 restraints weight = 16566.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.178631 restraints weight = 12424.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.179046 restraints weight = 10739.149| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20302 Z= 0.139 Angle : 0.603 9.416 28362 Z= 0.342 Chirality : 0.041 0.205 3108 Planarity : 0.005 0.061 3020 Dihedral : 23.505 88.482 4268 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.06 % Allowed : 0.25 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.49 (0.20), residues: 1936 helix: 1.75 (0.17), residues: 915 sheet: -0.54 (0.29), residues: 289 loop : 0.88 (0.26), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 228 TYR 0.022 0.002 TYR D 312 PHE 0.024 0.001 PHE C 118 TRP 0.067 0.002 TRP D 35 HIS 0.006 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (20286) covalent geometry : angle 0.59837 / 0.34 (28338) hydrogen bonds : bond 0.04217 / 2.89 ( 1052) hydrogen bonds : angle 4.17415 / 3.09 ( 2777) metal coordination : bond 0.00281 / 0.15 ( 16) metal coordination : angle 2.69684 / 1.75 ( 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 381 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 0.609 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 21 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7253 (tpm170) REVERT: A 27 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8570 (mm110) REVERT: A 28 GLN cc_start: 0.8769 (mp10) cc_final: 0.8247 (mp10) REVERT: A 58 ARG cc_start: 0.7938 (ttt180) cc_final: 0.7624 (ttm110) REVERT: A 60 ASN cc_start: 0.7935 (t160) cc_final: 0.7699 (t0) REVERT: A 61 LEU cc_start: 0.8013 (tp) cc_final: 0.7566 (tp) REVERT: A 132 MET cc_start: 0.8062 (mtm) cc_final: 0.7513 (mtm) REVERT: A 185 LEU cc_start: 0.8971 (mp) cc_final: 0.8681 (pp) REVERT: A 237 ARG cc_start: 0.3742 (ttp-110) cc_final: 0.2989 (ptp-170) REVERT: A 239 MET cc_start: 0.4755 (mmm) cc_final: 0.4368 (ptp) REVERT: A 329 MET cc_start: 0.0294 (mtp) cc_final: -0.0629 (mmm) REVERT: A 337 ASN cc_start: -0.0621 (p0) cc_final: -0.0957 (p0) REVERT: B 8 ARG cc_start: 0.7408 (ttp80) cc_final: 0.6879 (ttp80) REVERT: B 27 GLN cc_start: 0.7946 (tp40) cc_final: 0.7692 (tp40) REVERT: B 37 VAL cc_start: 0.8257 (t) cc_final: 0.7663 (m) REVERT: B 56 LYS cc_start: 0.7952 (mtmm) cc_final: 0.7434 (mtmm) REVERT: B 60 ASN cc_start: 0.7258 (m110) cc_final: 0.6946 (m110) REVERT: B 61 LEU cc_start: 0.8329 (tp) cc_final: 0.8022 (tp) REVERT: B 67 PHE cc_start: 0.8059 (m-80) cc_final: 0.7852 (m-10) REVERT: B 71 PRO cc_start: 0.7717 (Cg_exo) cc_final: 0.7436 (Cg_endo) REVERT: B 95 HIS cc_start: 0.7042 (m90) cc_final: 0.6358 (m90) REVERT: B 98 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6733 (mt-10) REVERT: B 101 LYS cc_start: 0.8686 (mptt) cc_final: 0.8290 (mptt) REVERT: B 102 LYS cc_start: 0.8357 (mptt) cc_final: 0.7747 (mptt) REVERT: B 138 LYS cc_start: 0.8020 (mttt) cc_final: 0.7432 (ttmm) REVERT: B 142 ARG cc_start: 0.7802 (tmm-80) cc_final: 0.7209 (tmm-80) REVERT: B 143 SER cc_start: 0.8248 (p) cc_final: 0.7856 (p) REVERT: B 148 ASN cc_start: 0.8206 (m-40) cc_final: 0.7724 (t0) REVERT: B 149 ILE cc_start: 0.8685 (mt) cc_final: 0.8272 (mm) REVERT: B 186 GLU cc_start: 0.7554 (pt0) cc_final: 0.7301 (pp20) REVERT: B 204 ASP cc_start: 0.7486 (t70) cc_final: 0.7136 (m-30) REVERT: B 214 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7443 (ttpp) REVERT: B 226 GLN cc_start: 0.7382 (tp40) cc_final: 0.6822 (tp40) REVERT: B 236 LYS cc_start: 0.8093 (tptm) cc_final: 0.7855 (tptp) REVERT: B 240 ILE cc_start: 0.8131 (pt) cc_final: 0.7903 (mt) REVERT: B 242 GLU cc_start: 0.7448 (tt0) cc_final: 0.6473 (tp30) REVERT: B 245 LEU cc_start: 0.7881 (tp) cc_final: 0.7595 (tt) REVERT: B 247 TYR cc_start: 0.6663 (m-10) cc_final: 0.6204 (m-80) REVERT: B 279 ARG cc_start: 0.7670 (mtt180) cc_final: 0.7387 (mtt180) REVERT: B 282 LEU cc_start: 0.7893 (mt) cc_final: 0.7588 (mt) REVERT: B 289 LYS cc_start: 0.8590 (mppt) cc_final: 0.8329 (mppt) REVERT: B 302 LEU cc_start: 0.7733 (tp) cc_final: 0.7212 (tp) REVERT: B 329 MET cc_start: 0.7291 (mmt) cc_final: 0.6966 (mmt) REVERT: B 334 HIS cc_start: 0.7180 (p90) cc_final: 0.6667 (p90) REVERT: B 345 TRP cc_start: 0.7283 (m100) cc_final: 0.6890 (m100) REVERT: B 346 ASP cc_start: 0.7688 (m-30) cc_final: 0.7258 (m-30) REVERT: B 367 TRP cc_start: 0.8445 (t-100) cc_final: 0.7871 (t-100) REVERT: B 376 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7997 (mt-10) REVERT: B 386 ASP cc_start: 0.7722 (t70) cc_final: 0.7151 (t0) REVERT: B 389 SER cc_start: 0.9049 (m) cc_final: 0.8847 (t) REVERT: B 419 GLU cc_start: 0.8449 (pt0) cc_final: 0.8233 (pp20) REVERT: B 443 TRP cc_start: 0.7843 (t-100) cc_final: 0.7469 (t-100) REVERT: B 456 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7428 (ttm110) REVERT: B 457 SER cc_start: 0.8843 (t) cc_final: 0.8578 (m) REVERT: B 458 MET cc_start: 0.7459 (mpp) cc_final: 0.6580 (mpp) REVERT: C 22 GLN cc_start: 0.8145 (mt0) cc_final: 0.7606 (mt0) REVERT: C 24 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7278 (tm-30) REVERT: C 28 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7676 (tm-30) REVERT: C 89 HIS cc_start: 0.8232 (m-70) cc_final: 0.7967 (m-70) REVERT: C 90 LEU cc_start: 0.8226 (tp) cc_final: 0.7942 (tp) REVERT: C 95 HIS cc_start: 0.7429 (t70) cc_final: 0.7154 (t70) REVERT: C 98 GLU cc_start: 0.8203 (pt0) cc_final: 0.7689 (pp20) REVERT: C 100 HIS cc_start: 0.7563 (m90) cc_final: 0.7257 (m90) REVERT: C 271 THR cc_start: 0.7844 (p) cc_final: 0.6747 (p) REVERT: C 273 GLU cc_start: 0.8724 (pt0) cc_final: 0.8250 (pm20) REVERT: C 483 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6835 (pt0) REVERT: D 9 LEU cc_start: 0.8232 (tt) cc_final: 0.7967 (mt) REVERT: D 20 GLU cc_start: 0.7585 (mp0) cc_final: 0.7072 (pm20) REVERT: D 21 ARG cc_start: 0.7593 (ttt90) cc_final: 0.6818 (ptm160) REVERT: D 26 CYS cc_start: 0.7768 (m) cc_final: 0.7165 (m) REVERT: D 27 GLN cc_start: 0.7510 (mt0) cc_final: 0.6854 (mt0) REVERT: D 28 GLN cc_start: 0.7458 (tm-30) cc_final: 0.7086 (tm-30) REVERT: D 30 CYS cc_start: 0.7507 (p) cc_final: 0.7268 (p) REVERT: D 33 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7547 (mtm-85) REVERT: D 36 ASP cc_start: 0.7808 (m-30) cc_final: 0.7408 (t0) REVERT: D 68 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7203 (mm-30) REVERT: D 79 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.6731 (mtp85) REVERT: D 92 GLN cc_start: 0.7555 (mt0) cc_final: 0.7203 (mt0) REVERT: D 102 LYS cc_start: 0.7684 (mmtt) cc_final: 0.7271 (mmtt) REVERT: D 109 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6673 (mp0) REVERT: D 129 VAL cc_start: 0.8509 (m) cc_final: 0.8223 (p) REVERT: D 132 MET cc_start: 0.7537 (tpt) cc_final: 0.7327 (mmm) REVERT: D 135 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7640 (mm-30) REVERT: D 138 LYS cc_start: 0.8933 (mttt) cc_final: 0.8429 (ttmm) REVERT: D 153 LYS cc_start: 0.8425 (mttt) cc_final: 0.7850 (mttt) REVERT: D 182 GLU cc_start: 0.7983 (tt0) cc_final: 0.7705 (tt0) REVERT: D 186 GLU cc_start: 0.7603 (tt0) cc_final: 0.7296 (tp30) REVERT: D 189 HIS cc_start: 0.6273 (t-90) cc_final: 0.5858 (t-90) REVERT: D 220 LEU cc_start: 0.8008 (tt) cc_final: 0.7580 (mm) REVERT: D 226 GLN cc_start: 0.7989 (mp10) cc_final: 0.7456 (mp10) REVERT: D 242 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7774 (mt-10) REVERT: D 245 LEU cc_start: 0.8553 (mt) cc_final: 0.7467 (mp) REVERT: D 247 TYR cc_start: 0.6747 (m-10) cc_final: 0.5947 (m-10) REVERT: D 272 ARG cc_start: 0.7633 (mmm160) cc_final: 0.7096 (mmm160) REVERT: D 300 ARG cc_start: 0.7043 (tpp80) cc_final: 0.6814 (tpp80) REVERT: D 302 LEU cc_start: 0.8324 (tp) cc_final: 0.8102 (tp) REVERT: D 328 SER cc_start: 0.7554 (t) cc_final: 0.6952 (p) REVERT: D 345 TRP cc_start: 0.6762 (m100) cc_final: 0.5314 (m100) REVERT: D 404 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7940 (mm-30) REVERT: D 416 ARG cc_start: 0.8434 (ptp90) cc_final: 0.7796 (ptt180) REVERT: D 443 TRP cc_start: 0.7996 (t60) cc_final: 0.7570 (t60) outliers start: 1 outliers final: 0 residues processed: 380 average time/residue: 0.1682 time to fit residues: 91.5127 Evaluate side-chains 352 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 115 optimal weight: 30.0000 chunk 32 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 64 optimal weight: 0.0870 chunk 97 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN C 60 ASN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN D 60 ASN D 334 HIS ** D 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.227089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.169198 restraints weight = 44341.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.174409 restraints weight = 20457.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.177580 restraints weight = 12159.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.179512 restraints weight = 8656.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.180688 restraints weight = 6978.708| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20302 Z= 0.172 Angle : 0.614 7.919 28362 Z= 0.349 Chirality : 0.042 0.307 3108 Planarity : 0.005 0.099 3020 Dihedral : 23.473 88.462 4268 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.06 % Allowed : 0.12 % Favored : 99.81 % 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: 1.46 (0.20), residues: 1936 helix: 1.73 (0.17), residues: 915 sheet: -0.51 (0.29), residues: 282 loop : 0.81 (0.25), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 181 TYR 0.018 0.002 TYR B 324 PHE 0.040 0.002 PHE B 476 TRP 0.065 0.002 TRP D 35 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (20286) covalent geometry : angle 0.61093 / 0.35 (28338) hydrogen bonds : bond 0.04605 / 3.18 ( 1052) hydrogen bonds : angle 4.21569 / 3.11 ( 2777) metal coordination : bond 0.00385 / 0.21 ( 16) metal coordination : angle 2.26674 / 1.59 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4346.87 seconds wall clock time: 75 minutes 6.71 seconds (4506.71 seconds total)