Starting phenix.real_space_refine on Fri Aug 7 06:56:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu7_60892/08_2026/9iu7_60892.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu7_60892/08_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_60892/08_2026/9iu7_60892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu7_60892/08_2026/9iu7_60892.map" model { file = "/net/cci-nas-00/data/ceres_data/9iu7_60892/08_2026/9iu7_60892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu7_60892/08_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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19472 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "C" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "D" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "E1" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "E2" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F1" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F2" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "G1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G2" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H2" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2429 SG CYS A 304 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: 4.49, per 1000 atoms: 0.23 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: 1.75 Conformation dependent library (CDL) restraints added in 568.3 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: 2.56 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: 4.29 Time building geometry restraints manager: 2.27 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: 26437 3.44 - 6.89: 1773 6.89 - 10.33: 113 10.33 - 13.78: 11 13.78 - 17.22: 4 Bond angle restraints: 28338 Sorted by residual: 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 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 1.90e+00 2.77e-01 8.21e+01 angle pdb=" O4' DGG2 36 " pdb=" C1' DGG2 36 " pdb=" N9 DGG2 36 " ideal model delta sigma weight residual 108.00 114.26 -6.26 7.00e-01 2.04e+00 7.99e+01 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 1.90e+00 2.77e-01 6.18e+01 angle pdb=" N VAL D 255 " pdb=" CA VAL D 255 " pdb=" CB VAL D 255 " ideal model delta sigma weight residual 110.53 119.05 -8.52 1.09e+00 8.42e-01 6.10e+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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.660 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- 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 : 1.834 19.798 28362 Z= 1.261 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 1.81421 / 1.26 (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 : 0.632 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: symmetry clash REVERT: A 6 VAL cc_start: 0.7591 (t) cc_final: 0.7266 (m) REVERT: A 21 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6855 (tpm170) REVERT: A 24 GLU cc_start: 0.8754 (tp30) cc_final: 0.7524 (tp30) REVERT: A 30 CYS cc_start: 0.7694 (m) cc_final: 0.7301 (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: 0.7112 (tp) REVERT: A 85 ARG cc_start: 0.5246 (OUTLIER) cc_final: 0.4886 (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: 0.7594 (tt) REVERT: A 126 MET cc_start: 0.6698 (mmm) cc_final: 0.6435 (mmp) REVERT: A 131 GLN cc_start: 0.7522 (tp40) cc_final: 0.7153 (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: 0.8239 (mmmt) 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: 0.4412 (ptp) REVERT: A 302 LEU cc_start: 0.2851 (tp) cc_final: 0.1956 (tp) REVERT: A 312 TYR cc_start: 0.2977 (m-10) cc_final: 0.2321 (m-10) REVERT: A 329 MET cc_start: 0.0091 (mtp) cc_final: -0.1062 (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: 0.7568 (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: 0.5226 (m-30) REVERT: B 50 VAL cc_start: 0.8410 (t) cc_final: 0.8157 (m) REVERT: B 51 ASP cc_start: 0.8393 (t0) cc_final: 0.8184 (t0) REVERT: B 54 ASP cc_start: 0.5786 (t0) cc_final: 0.5416 (t0) REVERT: B 56 LYS cc_start: 0.7842 (mtmm) cc_final: 0.7575 (mtmm) REVERT: B 60 ASN cc_start: 0.7405 (m-40) cc_final: 0.6981 (m110) REVERT: B 69 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7046 (mm-30) REVERT: B 88 ARG cc_start: 0.7991 (ttt180) cc_final: 0.7644 (tpp80) REVERT: B 94 VAL cc_start: 0.7842 (t) cc_final: 0.7583 (m) REVERT: B 95 HIS cc_start: 0.7336 (m90) cc_final: 0.6458 (m90) REVERT: B 98 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7212 (mt-10) REVERT: B 99 ASP cc_start: 0.7928 (m-30) cc_final: 0.7585 (m-30) REVERT: B 100 HIS cc_start: 0.8003 (m90) cc_final: 0.7707 (m-70) REVERT: B 101 LYS cc_start: 0.8705 (mptt) cc_final: 0.8497 (mptt) REVERT: B 125 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8329 (tt) REVERT: B 133 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7421 (tp30) REVERT: B 134 LEU cc_start: 0.7640 (tp) cc_final: 0.7076 (tt) REVERT: B 138 LYS cc_start: 0.7586 (mttt) cc_final: 0.7228 (mttt) REVERT: B 148 ASN cc_start: 0.8272 (m-40) cc_final: 0.7393 (t0) REVERT: B 149 ILE cc_start: 0.8457 (mt) cc_final: 0.8137 (mm) REVERT: B 153 LYS cc_start: 0.7802 (mtmp) cc_final: 0.7132 (mtmp) REVERT: B 174 LEU cc_start: 0.7745 (mt) cc_final: 0.7350 (mt) REVERT: B 175 VAL cc_start: 0.7686 (OUTLIER) cc_final: 0.7315 (p) REVERT: B 177 ASP cc_start: 0.5827 (t0) cc_final: 0.5284 (t0) REVERT: B 187 VAL cc_start: 0.7941 (t) cc_final: 0.7736 (p) REVERT: B 188 TYR cc_start: 0.6974 (t80) cc_final: 0.6616 (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: 0.7248 (mtm-85) REVERT: B 211 LEU cc_start: 0.7658 (mt) cc_final: 0.7335 (tp) REVERT: B 214 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7870 (ttmt) REVERT: B 220 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7422 (mt) REVERT: B 223 ARG cc_start: 0.7116 (mtm-85) cc_final: 0.6369 (mtm110) REVERT: B 236 LYS cc_start: 0.7831 (tttt) cc_final: 0.7601 (tptm) REVERT: B 257 ASP cc_start: 0.7813 (t70) cc_final: 0.6812 (p0) REVERT: B 274 GLN cc_start: 0.7257 (mt0) cc_final: 0.6833 (mt0) REVERT: B 299 LEU cc_start: 0.7297 (tp) cc_final: 0.7078 (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: 0.6960 (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: 0.8272 (tt0) REVERT: B 386 ASP cc_start: 0.7591 (t70) cc_final: 0.7263 (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: 0.7987 (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: 0.7456 (m) REVERT: C 44 LEU cc_start: 0.6765 (mp) cc_final: 0.5922 (mp) REVERT: C 90 LEU cc_start: 0.7437 (tp) cc_final: 0.7130 (tp) REVERT: C 164 LEU cc_start: 0.1281 (OUTLIER) cc_final: 0.0463 (tp) REVERT: C 199 HIS cc_start: 0.1949 (OUTLIER) cc_final: 0.1236 (m90) REVERT: C 229 GLU cc_start: 0.7621 (pt0) cc_final: 0.7055 (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: 0.6987 (mp) REVERT: D 11 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7219 (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: 0.8168 (tm-30) REVERT: D 26 CYS cc_start: 0.7905 (m) cc_final: 0.6850 (p) REVERT: D 27 GLN cc_start: 0.7471 (mt0) cc_final: 0.6620 (pt0) REVERT: D 28 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7121 (tm-30) REVERT: D 33 ARG cc_start: 0.8014 (mtp180) cc_final: 0.6858 (ttm-80) REVERT: D 42 GLU cc_start: 0.6878 (tt0) cc_final: 0.6456 (tt0) REVERT: D 60 ASN cc_start: 0.8097 (m-40) cc_final: 0.7669 (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: 0.6687 (mtm110) REVERT: D 81 ASP cc_start: 0.7910 (p0) cc_final: 0.7436 (p0) REVERT: D 82 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8167 (mmp80) REVERT: D 93 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7828 (mm) REVERT: D 98 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6077 (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: 0.7607 (tt0) REVERT: D 135 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7809 (mm-30) REVERT: D 138 LYS cc_start: 0.8626 (mttt) cc_final: 0.8140 (mtpp) REVERT: D 142 ARG cc_start: 0.7596 (ttm110) cc_final: 0.7043 (ttm-80) REVERT: D 146 HIS cc_start: 0.8195 (m170) cc_final: 0.7694 (m-70) REVERT: D 153 LYS cc_start: 0.7959 (mttt) cc_final: 0.7450 (mttt) REVERT: D 182 GLU cc_start: 0.8309 (tt0) cc_final: 0.8047 (tt0) REVERT: D 193 ASP cc_start: 0.7275 (m-30) cc_final: 0.6687 (m-30) REVERT: D 220 LEU cc_start: 0.7889 (tt) cc_final: 0.7435 (mm) REVERT: D 225 PRO cc_start: 0.8019 (Cg_exo) cc_final: 0.7643 (Cg_endo) REVERT: D 228 ARG cc_start: 0.7275 (mtt-85) cc_final: 0.6801 (mtt-85) REVERT: D 236 LYS cc_start: 0.8556 (tttt) cc_final: 0.8128 (ttmm) REVERT: D 242 GLU cc_start: 0.8674 (mt-10) cc_final: 0.7687 (mt-10) REVERT: D 244 MET cc_start: 0.7940 (mmt) cc_final: 0.7510 (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: 0.5851 (m-10) REVERT: D 269 ILE cc_start: 0.8204 (mm) cc_final: 0.7792 (mm) REVERT: D 270 LEU cc_start: 0.8260 (mt) cc_final: 0.8049 (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: 0.8412 (mt) REVERT: D 328 SER cc_start: 0.7251 (t) cc_final: 0.6937 (p) REVERT: D 345 TRP cc_start: 0.6805 (m100) cc_final: 0.5125 (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: 0.6698 (t60) REVERT: D 452 ASN cc_start: 0.6698 (t0) cc_final: 0.6085 (t0) REVERT: D 456 ARG cc_start: 0.8306 (mtp180) cc_final: 0.7727 (tpp80) REVERT: D 461 ARG cc_start: 0.6596 (ttm-80) cc_final: 0.6372 (ttp80) outliers start: 67 outliers final: 15 residues processed: 511 average time/residue: 0.1879 time to fit residues: 135.7598 Evaluate side-chains 431 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 398 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 C 219 GLN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.231270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.171118 restraints weight = 46100.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.176529 restraints weight = 21124.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.179811 restraints weight = 12514.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.181649 restraints weight = 8896.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.182964 restraints weight = 7234.484| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.2492 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= 0.209 Angle : 0.820 15.116 28362 Z= 0.452 Chirality : 0.057 0.306 3108 Planarity : 0.006 0.069 3020 Dihedral : 23.349 87.995 4268 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.26 % 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: 1.72 (0.18), residues: 1936 helix: 1.94 (0.16), residues: 919 sheet: -0.30 (0.29), residues: 250 loop : 0.83 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 33 TYR 0.024 0.002 TYR D 312 PHE 0.032 0.003 PHE B 476 TRP 0.028 0.002 TRP C 35 HIS 0.007 0.001 HIS D 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.21 (20286) covalent geometry : angle 0.79824 / 0.45 (28338) hydrogen bonds : bond 0.06113 / 4.21 ( 1052) hydrogen bonds : angle 4.22668 / 3.09 ( 2777) metal coordination : bond 0.00721 / 0.37 ( 16) metal coordination : angle 6.55002 / 4.67 ( 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 415 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7734 (t) cc_final: 0.7423 (m) REVERT: A 21 ARG cc_start: 0.7852 (mtp180) cc_final: 0.7280 (tpm170) REVERT: A 24 GLU cc_start: 0.8553 (tp30) cc_final: 0.7898 (tp30) REVERT: A 30 CYS cc_start: 0.7742 (m) cc_final: 0.7371 (t) REVERT: A 58 ARG cc_start: 0.7921 (ttt180) cc_final: 0.7406 (ttm170) REVERT: A 59 PRO cc_start: 0.8095 (Cg_endo) cc_final: 0.7793 (Cg_exo) REVERT: A 60 ASN cc_start: 0.7707 (t160) cc_final: 0.7265 (t0) REVERT: A 61 LEU cc_start: 0.7572 (tp) cc_final: 0.7122 (tp) REVERT: A 131 GLN cc_start: 0.7733 (tp40) cc_final: 0.7335 (tp40) REVERT: A 132 MET cc_start: 0.8102 (mtm) cc_final: 0.7780 (mtm) REVERT: A 138 LYS cc_start: 0.8662 (mttm) cc_final: 0.8140 (mmmt) REVERT: A 185 LEU cc_start: 0.8945 (mp) cc_final: 0.8596 (pp) REVERT: A 228 ARG cc_start: 0.7123 (mtt90) cc_final: 0.6810 (mtm180) REVERT: A 237 ARG cc_start: 0.4138 (ttp-170) cc_final: 0.2570 (ptm160) REVERT: A 239 MET cc_start: 0.4905 (mmm) cc_final: 0.4309 (ptp) REVERT: A 329 MET cc_start: 0.0413 (mtp) cc_final: -0.0096 (mmm) REVERT: B 11 ARG cc_start: 0.6981 (mtt-85) cc_final: 0.6537 (tpp80) REVERT: B 21 ARG cc_start: 0.7930 (ttt-90) cc_final: 0.7400 (ptm-80) REVERT: B 24 GLU cc_start: 0.7583 (pt0) cc_final: 0.7344 (pp20) REVERT: B 28 GLN cc_start: 0.7486 (tp-100) cc_final: 0.7080 (tp-100) REVERT: B 43 ASP cc_start: 0.6391 (m-30) cc_final: 0.5900 (m-30) REVERT: B 50 VAL cc_start: 0.8469 (t) cc_final: 0.8257 (m) REVERT: B 56 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7365 (mtmm) REVERT: B 60 ASN cc_start: 0.7504 (m-40) cc_final: 0.7241 (m-40) REVERT: B 68 GLU cc_start: 0.6640 (pt0) cc_final: 0.5806 (pt0) REVERT: B 88 ARG cc_start: 0.7958 (ttt180) cc_final: 0.7735 (tpp80) REVERT: B 94 VAL cc_start: 0.8105 (t) cc_final: 0.7774 (m) REVERT: B 101 LYS cc_start: 0.8688 (mptt) cc_final: 0.8288 (mptt) REVERT: B 102 LYS cc_start: 0.8041 (mptt) cc_final: 0.7768 (mptt) REVERT: B 109 GLU cc_start: 0.6211 (mt-10) cc_final: 0.5959 (mp0) REVERT: B 133 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7523 (mm-30) REVERT: B 134 LEU cc_start: 0.7672 (tp) cc_final: 0.7333 (tt) REVERT: B 142 ARG cc_start: 0.7856 (ttp-110) cc_final: 0.7269 (tmm-80) REVERT: B 148 ASN cc_start: 0.8392 (m-40) cc_final: 0.7541 (t0) REVERT: B 149 ILE cc_start: 0.8496 (mt) cc_final: 0.8100 (mm) REVERT: B 153 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7270 (mtmt) REVERT: B 174 LEU cc_start: 0.7647 (mt) cc_final: 0.7313 (mt) REVERT: B 182 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: B 187 VAL cc_start: 0.8261 (t) cc_final: 0.8041 (p) REVERT: B 204 ASP cc_start: 0.7650 (t70) cc_final: 0.7010 (m-30) REVERT: B 242 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7455 (mt-10) REVERT: B 282 LEU cc_start: 0.7889 (mt) cc_final: 0.7611 (mm) REVERT: B 289 LYS cc_start: 0.8696 (mppt) cc_final: 0.8438 (mppt) REVERT: B 298 LEU cc_start: 0.8047 (mt) cc_final: 0.7727 (mm) REVERT: B 299 LEU cc_start: 0.7439 (tp) cc_final: 0.7223 (tp) REVERT: B 302 LEU cc_start: 0.8284 (tp) cc_final: 0.7520 (tp) REVERT: B 329 MET cc_start: 0.7479 (mmt) cc_final: 0.6936 (mmt) REVERT: B 334 HIS cc_start: 0.6636 (p90) cc_final: 0.5994 (p90) REVERT: B 342 MET cc_start: 0.6471 (ttp) cc_final: 0.5939 (mmt) REVERT: B 344 GLU cc_start: 0.7925 (tt0) cc_final: 0.7363 (tm-30) REVERT: B 367 TRP cc_start: 0.7699 (t-100) cc_final: 0.7365 (t-100) REVERT: B 386 ASP cc_start: 0.7650 (t70) cc_final: 0.7201 (t70) REVERT: B 413 LEU cc_start: 0.8572 (mm) cc_final: 0.8086 (mm) REVERT: B 451 LYS cc_start: 0.7600 (mtmt) cc_final: 0.7344 (mttp) REVERT: B 454 TRP cc_start: 0.8085 (t60) cc_final: 0.7699 (t60) REVERT: B 456 ARG cc_start: 0.8058 (mtp180) cc_final: 0.7535 (ttm110) REVERT: B 458 MET cc_start: 0.7415 (mpp) cc_final: 0.7170 (mpp) REVERT: B 459 ASN cc_start: 0.8554 (m-40) cc_final: 0.8216 (m-40) REVERT: B 475 ASP cc_start: 0.6846 (t0) cc_final: 0.6537 (p0) REVERT: C 28 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7587 (tm-30) REVERT: C 42 GLU cc_start: 0.7538 (tp30) cc_final: 0.7176 (tp30) REVERT: C 91 GLN cc_start: 0.8168 (mt0) cc_final: 0.7749 (pt0) REVERT: C 98 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7748 (tm-30) REVERT: C 173 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6891 (mmm-85) REVERT: C 174 LEU cc_start: 0.8603 (tp) cc_final: 0.7695 (tp) REVERT: C 229 GLU cc_start: 0.7595 (pt0) cc_final: 0.7135 (tt0) REVERT: C 273 GLU cc_start: 0.8627 (pt0) cc_final: 0.8255 (tp30) REVERT: D 24 GLU cc_start: 0.8337 (tt0) cc_final: 0.8007 (tm-30) REVERT: D 26 CYS cc_start: 0.7917 (m) cc_final: 0.7193 (p) REVERT: D 27 GLN cc_start: 0.7377 (mt0) cc_final: 0.6828 (pt0) REVERT: D 28 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7103 (tm-30) REVERT: D 60 ASN cc_start: 0.8252 (m-40) cc_final: 0.7884 (m110) REVERT: D 92 GLN cc_start: 0.7779 (tt0) cc_final: 0.7536 (mt0) REVERT: D 102 LYS cc_start: 0.7530 (mmtt) cc_final: 0.7034 (mmtt) REVERT: D 131 GLN cc_start: 0.8127 (tt0) cc_final: 0.7796 (tt0) REVERT: D 135 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7623 (mm-30) REVERT: D 138 LYS cc_start: 0.8801 (mttt) cc_final: 0.8221 (mtpp) REVERT: D 139 GLU cc_start: 0.7430 (tp30) cc_final: 0.6909 (tp30) REVERT: D 142 ARG cc_start: 0.7516 (ttm110) cc_final: 0.6969 (ttm-80) REVERT: D 146 HIS cc_start: 0.8187 (m170) cc_final: 0.7824 (m-70) REVERT: D 153 LYS cc_start: 0.8295 (mttt) cc_final: 0.7694 (mttt) REVERT: D 182 GLU cc_start: 0.8039 (tt0) cc_final: 0.7747 (tt0) REVERT: D 186 GLU cc_start: 0.7338 (tt0) cc_final: 0.7106 (tp30) REVERT: D 214 LYS cc_start: 0.7489 (ttmt) cc_final: 0.7094 (ttmt) REVERT: D 220 LEU cc_start: 0.7986 (tt) cc_final: 0.7603 (mm) REVERT: D 226 GLN cc_start: 0.7682 (mp10) cc_final: 0.6921 (mp10) REVERT: D 242 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7641 (mt-10) REVERT: D 244 MET cc_start: 0.7629 (mmt) cc_final: 0.7230 (mmm) REVERT: D 245 LEU cc_start: 0.8422 (mt) cc_final: 0.7932 (mt) REVERT: D 247 TYR cc_start: 0.6689 (m-10) cc_final: 0.6252 (m-10) REVERT: D 269 ILE cc_start: 0.8008 (mm) cc_final: 0.7634 (mm) REVERT: D 278 LEU cc_start: 0.8423 (mt) cc_final: 0.8124 (mt) REVERT: D 328 SER cc_start: 0.7762 (t) cc_final: 0.7230 (p) REVERT: D 345 TRP cc_start: 0.6555 (m100) cc_final: 0.4969 (m100) REVERT: D 410 ILE cc_start: 0.8696 (mt) cc_final: 0.8432 (pt) REVERT: D 416 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.8024 (ptp-110) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.1930 time to fit residues: 112.6003 Evaluate side-chains 375 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 0.0370 chunk 207 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 132 optimal weight: 40.0000 chunk 107 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- 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** C 60 ASN C 226 GLN C 274 GLN C 485 HIS D 141 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.229373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.170372 restraints weight = 45657.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.175642 restraints weight = 20857.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.178858 restraints weight = 12302.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.180782 restraints weight = 8708.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.182002 restraints weight = 7021.423| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20302 Z= 0.177 Angle : 0.700 13.315 28362 Z= 0.394 Chirality : 0.048 0.406 3108 Planarity : 0.005 0.063 3020 Dihedral : 23.261 88.996 4268 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % 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: 1.79 (0.19), residues: 1936 helix: 2.02 (0.16), residues: 914 sheet: -0.36 (0.30), residues: 250 loop : 0.88 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 181 TYR 0.013 0.002 TYR C 188 PHE 0.024 0.002 PHE B 348 TRP 0.027 0.002 TRP B 443 HIS 0.013 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.18 (20286) covalent geometry : angle 0.68558 / 0.39 (28338) hydrogen bonds : bond 0.05365 / 3.69 ( 1052) hydrogen bonds : angle 4.09981 / 3.00 ( 2777) metal coordination : bond 0.00691 / 0.36 ( 16) metal coordination : angle 4.88968 / 3.57 ( 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 408 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 0.567 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: 0.7298 (tpm170) REVERT: A 24 GLU cc_start: 0.8550 (tp30) cc_final: 0.7506 (tp30) REVERT: A 30 CYS cc_start: 0.7717 (m) cc_final: 0.7290 (t) REVERT: A 56 LYS cc_start: 0.8013 (pttp) cc_final: 0.7683 (pttm) REVERT: A 58 ARG cc_start: 0.7797 (ttt180) cc_final: 0.7328 (ttm170) REVERT: A 59 PRO cc_start: 0.8086 (Cg_endo) cc_final: 0.7824 (Cg_exo) REVERT: A 60 ASN cc_start: 0.7688 (t160) cc_final: 0.7205 (t0) REVERT: A 61 LEU cc_start: 0.7536 (tp) cc_final: 0.7107 (tp) REVERT: A 79 ARG cc_start: 0.6846 (tpp-160) cc_final: 0.6557 (tpp80) REVERT: A 132 MET cc_start: 0.8290 (mtm) cc_final: 0.7877 (mtm) REVERT: A 185 LEU cc_start: 0.8919 (mp) cc_final: 0.8646 (pp) REVERT: A 237 ARG cc_start: 0.3698 (ttp-170) cc_final: 0.2220 (ptm160) REVERT: A 239 MET cc_start: 0.4834 (mmm) cc_final: 0.4249 (ptm) REVERT: A 329 MET cc_start: 0.0012 (mtp) cc_final: -0.0516 (mmm) REVERT: B 11 ARG cc_start: 0.7215 (mtt-85) cc_final: 0.6733 (tpp80) REVERT: B 21 ARG cc_start: 0.7911 (ttt-90) cc_final: 0.7237 (ptm-80) REVERT: B 24 GLU cc_start: 0.7646 (pt0) cc_final: 0.7275 (pp20) REVERT: B 50 VAL cc_start: 0.8462 (t) cc_final: 0.8246 (m) REVERT: B 56 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7376 (mtmm) REVERT: B 88 ARG cc_start: 0.7883 (ttt180) cc_final: 0.7528 (tpp80) REVERT: B 95 HIS cc_start: 0.7138 (m90) cc_final: 0.6521 (m90) REVERT: B 96 TRP cc_start: 0.7846 (t60) cc_final: 0.7187 (t60) REVERT: B 98 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6870 (mt-10) REVERT: B 101 LYS cc_start: 0.8745 (mptt) cc_final: 0.8272 (mptt) REVERT: B 102 LYS cc_start: 0.7978 (mptt) cc_final: 0.7722 (mptt) REVERT: B 134 LEU cc_start: 0.7606 (tp) cc_final: 0.7378 (tp) REVERT: B 138 LYS cc_start: 0.7778 (mttt) cc_final: 0.7491 (mtmm) REVERT: B 142 ARG cc_start: 0.7850 (ttp-110) cc_final: 0.7545 (tmm-80) REVERT: B 148 ASN cc_start: 0.8183 (m-40) cc_final: 0.7745 (t0) REVERT: B 149 ILE cc_start: 0.8464 (mt) cc_final: 0.8056 (mm) REVERT: B 174 LEU cc_start: 0.7668 (mt) cc_final: 0.7364 (mt) REVERT: B 187 VAL cc_start: 0.8351 (t) cc_final: 0.8100 (p) REVERT: B 189 HIS cc_start: 0.7029 (t-90) cc_final: 0.6819 (t-90) REVERT: B 204 ASP cc_start: 0.7453 (t70) cc_final: 0.7091 (m-30) REVERT: B 214 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7931 (ttmt) REVERT: B 242 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7621 (mt-10) REVERT: B 289 LYS cc_start: 0.8650 (mppt) cc_final: 0.8417 (mppt) REVERT: B 298 LEU cc_start: 0.8070 (mt) cc_final: 0.7802 (mm) REVERT: B 302 LEU cc_start: 0.7962 (tp) cc_final: 0.7339 (tp) REVERT: B 329 MET cc_start: 0.7436 (mmt) cc_final: 0.6906 (mmt) REVERT: B 334 HIS cc_start: 0.6815 (p90) cc_final: 0.6195 (p90) REVERT: B 342 MET cc_start: 0.6924 (ttp) cc_final: 0.6242 (mmt) REVERT: B 351 GLU cc_start: 0.8229 (tt0) cc_final: 0.7756 (tt0) REVERT: B 367 TRP cc_start: 0.7877 (t-100) cc_final: 0.7476 (t-100) REVERT: B 376 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7904 (pt0) REVERT: B 383 GLU cc_start: 0.8301 (pt0) cc_final: 0.7708 (pp20) REVERT: B 384 LEU cc_start: 0.8893 (mt) cc_final: 0.8641 (mt) REVERT: B 386 ASP cc_start: 0.7582 (t70) cc_final: 0.7169 (t70) REVERT: B 413 LEU cc_start: 0.8509 (mm) cc_final: 0.8226 (mm) REVERT: B 442 TRP cc_start: 0.8005 (t60) cc_final: 0.7743 (t60) REVERT: B 454 TRP cc_start: 0.8079 (t60) cc_final: 0.7723 (t60) REVERT: B 456 ARG cc_start: 0.8009 (mtp180) cc_final: 0.7663 (ttm110) REVERT: B 459 ASN cc_start: 0.8524 (m-40) cc_final: 0.8295 (m-40) REVERT: B 475 ASP cc_start: 0.6830 (t0) cc_final: 0.6494 (p0) REVERT: C 28 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7685 (tm-30) REVERT: C 67 PHE cc_start: 0.7638 (m-80) cc_final: 0.7096 (m-80) REVERT: C 90 LEU cc_start: 0.7904 (tp) cc_final: 0.7612 (tp) REVERT: C 98 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7713 (tm-30) REVERT: C 223 ARG cc_start: 0.6864 (tpt90) cc_final: 0.6486 (tpt170) REVERT: C 229 GLU cc_start: 0.7713 (pt0) cc_final: 0.7231 (tt0) REVERT: C 273 GLU cc_start: 0.8780 (pt0) cc_final: 0.8428 (tm-30) REVERT: C 364 GLU cc_start: 0.7690 (pm20) cc_final: 0.7362 (pm20) REVERT: D 26 CYS cc_start: 0.7887 (m) cc_final: 0.7090 (p) REVERT: D 27 GLN cc_start: 0.7485 (mt0) cc_final: 0.6612 (mt0) REVERT: D 28 GLN cc_start: 0.7447 (tm-30) cc_final: 0.7011 (tm-30) REVERT: D 33 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7406 (tpp80) REVERT: D 35 TRP cc_start: 0.6380 (p90) cc_final: 0.5349 (p90) REVERT: D 60 ASN cc_start: 0.8231 (m-40) cc_final: 0.7820 (m110) REVERT: D 64 TRP cc_start: 0.8048 (m100) cc_final: 0.7636 (m100) REVERT: D 69 GLU cc_start: 0.6567 (mt-10) cc_final: 0.5542 (mt-10) REVERT: D 92 GLN cc_start: 0.7699 (tt0) cc_final: 0.7451 (mt0) REVERT: D 101 LYS cc_start: 0.7853 (mmpt) cc_final: 0.7349 (mmpt) REVERT: D 102 LYS cc_start: 0.7544 (mmtt) cc_final: 0.7142 (mmtt) REVERT: D 131 GLN cc_start: 0.8085 (tt0) cc_final: 0.7801 (tt0) REVERT: D 132 MET cc_start: 0.7209 (mmm) cc_final: 0.6884 (mmt) REVERT: D 133 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7196 (mt-10) REVERT: D 135 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7612 (mm-30) REVERT: D 138 LYS cc_start: 0.8842 (mttt) cc_final: 0.8246 (mtpp) REVERT: D 139 GLU cc_start: 0.7368 (tp30) cc_final: 0.6763 (tp30) REVERT: D 140 ARG cc_start: 0.7485 (ttp-110) cc_final: 0.7169 (ttt90) REVERT: D 142 ARG cc_start: 0.7486 (ttm110) cc_final: 0.7023 (ttm110) REVERT: D 146 HIS cc_start: 0.8237 (m170) cc_final: 0.7874 (m-70) REVERT: D 153 LYS cc_start: 0.8265 (mttt) cc_final: 0.7899 (mttt) REVERT: D 182 GLU cc_start: 0.7985 (tt0) cc_final: 0.7718 (tt0) REVERT: D 186 GLU cc_start: 0.7391 (tt0) cc_final: 0.7109 (tp30) REVERT: D 220 LEU cc_start: 0.7967 (tt) cc_final: 0.7595 (mm) REVERT: D 242 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7635 (mt-10) REVERT: D 245 LEU cc_start: 0.8461 (mt) cc_final: 0.7678 (mt) REVERT: D 247 TYR cc_start: 0.6734 (m-10) cc_final: 0.6265 (m-10) REVERT: D 278 LEU cc_start: 0.8325 (mt) cc_final: 0.8096 (mt) REVERT: D 328 SER cc_start: 0.7636 (t) cc_final: 0.7135 (p) REVERT: D 345 TRP cc_start: 0.6429 (m100) cc_final: 0.4851 (m100) REVERT: D 381 ASN cc_start: 0.7586 (m110) cc_final: 0.7303 (m-40) REVERT: D 404 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8050 (mm-30) REVERT: D 416 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.8035 (mtm-85) REVERT: D 461 ARG cc_start: 0.6636 (ttm-80) cc_final: 0.6112 (tpt170) outliers start: 1 outliers final: 0 residues processed: 408 average time/residue: 0.1817 time to fit residues: 106.0070 Evaluate side-chains 376 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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: 2.9990 chunk 186 optimal weight: 7.9990 chunk 197 optimal weight: 30.0000 chunk 169 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN B 32 GLN B 60 ASN B 131 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 226 GLN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.225027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.164146 restraints weight = 44801.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169337 restraints weight = 20768.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.172503 restraints weight = 12484.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.174488 restraints weight = 8929.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.175654 restraints weight = 7221.499| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20302 Z= 0.262 Angle : 0.716 9.952 28362 Z= 0.407 Chirality : 0.048 0.418 3108 Planarity : 0.006 0.076 3020 Dihedral : 23.237 89.890 4268 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.76 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.38 (0.19), residues: 1936 helix: 1.59 (0.16), residues: 920 sheet: -0.53 (0.28), residues: 268 loop : 0.84 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 416 TYR 0.020 0.002 TYR D 312 PHE 0.021 0.002 PHE B 476 TRP 0.042 0.002 TRP D 35 HIS 0.013 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.26 (20286) covalent geometry : angle 0.70749 / 0.41 (28338) hydrogen bonds : bond 0.06054 / 4.14 ( 1052) hydrogen bonds : angle 4.28658 / 3.14 ( 2777) metal coordination : bond 0.00969 / 0.55 ( 16) metal coordination : angle 3.82025 / 2.60 ( 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 381 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 0.648 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: 0.7281 (tpm170) REVERT: A 24 GLU cc_start: 0.8613 (tp30) cc_final: 0.7629 (tp30) REVERT: A 30 CYS cc_start: 0.7802 (m) cc_final: 0.7341 (t) REVERT: A 56 LYS cc_start: 0.8243 (pttp) cc_final: 0.8009 (pttp) REVERT: A 58 ARG cc_start: 0.7908 (ttt180) cc_final: 0.7485 (ttm110) REVERT: A 59 PRO cc_start: 0.8107 (Cg_endo) cc_final: 0.7835 (Cg_exo) REVERT: A 60 ASN cc_start: 0.8002 (t0) cc_final: 0.7541 (t0) REVERT: A 61 LEU cc_start: 0.7808 (tp) cc_final: 0.7345 (tp) REVERT: A 79 ARG cc_start: 0.6993 (tpp-160) cc_final: 0.6657 (tpp-160) REVERT: A 132 MET cc_start: 0.8294 (mtm) cc_final: 0.7731 (mtm) REVERT: A 185 LEU cc_start: 0.8903 (mp) cc_final: 0.8603 (pp) REVERT: A 237 ARG cc_start: 0.3398 (ttp-110) cc_final: 0.1669 (ptm160) REVERT: A 239 MET cc_start: 0.4773 (mmm) cc_final: 0.4231 (ptm) REVERT: A 329 MET cc_start: -0.0244 (mtp) cc_final: -0.0992 (mmm) REVERT: B 8 ARG cc_start: 0.7419 (ttp80) cc_final: 0.7092 (ttp80) REVERT: B 11 ARG cc_start: 0.6931 (mtt-85) cc_final: 0.6637 (tpp80) REVERT: B 21 ARG cc_start: 0.8044 (ttt-90) cc_final: 0.7342 (tmt-80) REVERT: B 24 GLU cc_start: 0.7833 (pt0) cc_final: 0.7595 (pt0) REVERT: B 28 GLN cc_start: 0.7660 (tp-100) cc_final: 0.7108 (tp-100) REVERT: B 50 VAL cc_start: 0.8589 (t) cc_final: 0.8357 (m) REVERT: B 56 LYS cc_start: 0.7941 (mtmm) cc_final: 0.7431 (mtmm) REVERT: B 60 ASN cc_start: 0.7588 (m-40) cc_final: 0.7365 (m110) REVERT: B 67 PHE cc_start: 0.7975 (m-80) cc_final: 0.7607 (m-10) REVERT: B 71 PRO cc_start: 0.7768 (Cg_exo) cc_final: 0.7538 (Cg_endo) REVERT: B 95 HIS cc_start: 0.7147 (m90) cc_final: 0.6534 (m90) REVERT: B 96 TRP cc_start: 0.7888 (t60) cc_final: 0.7336 (t60) REVERT: B 98 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6916 (mt-10) REVERT: B 101 LYS cc_start: 0.8792 (mptt) cc_final: 0.8301 (mptt) REVERT: B 102 LYS cc_start: 0.8154 (mptt) cc_final: 0.7770 (mptt) REVERT: B 134 LEU cc_start: 0.7653 (tp) cc_final: 0.7206 (tt) REVERT: B 138 LYS cc_start: 0.7896 (mttt) cc_final: 0.7579 (mttt) REVERT: B 142 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7669 (tmm-80) REVERT: B 143 SER cc_start: 0.8503 (t) cc_final: 0.7664 (p) REVERT: B 148 ASN cc_start: 0.8281 (m-40) cc_final: 0.7813 (t0) REVERT: B 174 LEU cc_start: 0.7404 (mt) cc_final: 0.7194 (mt) REVERT: B 187 VAL cc_start: 0.8453 (t) cc_final: 0.8243 (p) REVERT: B 204 ASP cc_start: 0.7549 (t70) cc_final: 0.7067 (m-30) REVERT: B 214 LYS cc_start: 0.8172 (ttmm) cc_final: 0.7958 (ttmt) REVERT: B 236 LYS cc_start: 0.8279 (tptm) cc_final: 0.8050 (tptm) REVERT: B 242 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7617 (mt-10) REVERT: B 282 LEU cc_start: 0.8035 (mt) cc_final: 0.7707 (mt) REVERT: B 297 LEU cc_start: 0.8077 (tp) cc_final: 0.7800 (tp) REVERT: B 298 LEU cc_start: 0.8135 (mt) cc_final: 0.7933 (mt) REVERT: B 302 LEU cc_start: 0.8062 (tp) cc_final: 0.7501 (tp) REVERT: B 329 MET cc_start: 0.7585 (mmt) cc_final: 0.7007 (mmt) REVERT: B 334 HIS cc_start: 0.7195 (p90) cc_final: 0.6520 (p90) REVERT: B 335 CYS cc_start: 0.3721 (p) cc_final: 0.3360 (p) REVERT: B 342 MET cc_start: 0.6870 (ttp) cc_final: 0.6271 (mmt) REVERT: B 351 GLU cc_start: 0.8466 (tt0) cc_final: 0.7885 (tt0) REVERT: B 367 TRP cc_start: 0.8211 (t-100) cc_final: 0.7688 (t-100) REVERT: B 376 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7713 (mm-30) REVERT: B 386 ASP cc_start: 0.7673 (t70) cc_final: 0.7276 (t70) REVERT: B 391 ILE cc_start: 0.7816 (mt) cc_final: 0.7169 (mt) REVERT: B 416 ARG cc_start: 0.7900 (mpp-170) cc_final: 0.7411 (mtm-85) REVERT: B 419 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8324 (mt-10) REVERT: B 442 TRP cc_start: 0.8046 (t60) cc_final: 0.7815 (t60) REVERT: B 443 TRP cc_start: 0.7972 (t-100) cc_final: 0.7538 (t-100) REVERT: B 454 TRP cc_start: 0.8122 (t60) cc_final: 0.7763 (t60) REVERT: B 456 ARG cc_start: 0.7996 (mtp180) cc_final: 0.7674 (ttm110) REVERT: C 28 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7635 (tm-30) REVERT: C 90 LEU cc_start: 0.8112 (tp) cc_final: 0.7820 (tp) REVERT: C 95 HIS cc_start: 0.7620 (t70) cc_final: 0.7350 (t70) REVERT: C 98 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7721 (tm-30) REVERT: C 229 GLU cc_start: 0.7833 (pt0) cc_final: 0.7291 (tt0) REVERT: C 273 GLU cc_start: 0.8721 (pt0) cc_final: 0.8230 (pm20) REVERT: D 7 ILE cc_start: 0.8437 (mt) cc_final: 0.8226 (mm) REVERT: D 9 LEU cc_start: 0.8058 (tt) cc_final: 0.7784 (mt) REVERT: D 21 ARG cc_start: 0.7520 (tpp80) cc_final: 0.7062 (tpp80) REVERT: D 24 GLU cc_start: 0.8209 (tp30) cc_final: 0.7901 (tm-30) REVERT: D 26 CYS cc_start: 0.7988 (m) cc_final: 0.7258 (m) REVERT: D 27 GLN cc_start: 0.7502 (mt0) cc_final: 0.6765 (mt0) REVERT: D 28 GLN cc_start: 0.7483 (tm-30) cc_final: 0.7006 (tm-30) REVERT: D 60 ASN cc_start: 0.8314 (m-40) cc_final: 0.7917 (m110) REVERT: D 64 TRP cc_start: 0.8005 (m100) cc_final: 0.6939 (m100) REVERT: D 69 GLU cc_start: 0.6369 (mt-10) cc_final: 0.6018 (mp0) REVERT: D 73 ASP cc_start: 0.6669 (t0) cc_final: 0.6029 (t0) REVERT: D 92 GLN cc_start: 0.7766 (tt0) cc_final: 0.7518 (mt0) REVERT: D 101 LYS cc_start: 0.7980 (mmpt) cc_final: 0.7549 (mmpt) REVERT: D 109 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7002 (mm-30) REVERT: D 131 GLN cc_start: 0.8094 (tt0) cc_final: 0.7872 (tt0) REVERT: D 133 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7293 (mt-10) REVERT: D 135 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7398 (mm-30) REVERT: D 138 LYS cc_start: 0.8956 (mttt) cc_final: 0.8359 (mttt) REVERT: D 142 ARG cc_start: 0.7577 (ttm110) cc_final: 0.7152 (ttm110) REVERT: D 146 HIS cc_start: 0.8327 (m170) cc_final: 0.7952 (m-70) REVERT: D 153 LYS cc_start: 0.8335 (mttt) cc_final: 0.7779 (mttt) REVERT: D 163 TYR cc_start: 0.6135 (m-10) cc_final: 0.5830 (m-10) REVERT: D 182 GLU cc_start: 0.8071 (tt0) cc_final: 0.7795 (tt0) REVERT: D 186 GLU cc_start: 0.7482 (tt0) cc_final: 0.7167 (tp30) REVERT: D 195 HIS cc_start: 0.7081 (m90) cc_final: 0.6871 (m90) REVERT: D 214 LYS cc_start: 0.7620 (ttmt) cc_final: 0.7180 (ttmt) REVERT: D 242 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7534 (mt-10) REVERT: D 245 LEU cc_start: 0.8550 (mt) cc_final: 0.7717 (mt) REVERT: D 247 TYR cc_start: 0.6819 (m-10) cc_final: 0.6247 (m-10) REVERT: D 278 LEU cc_start: 0.8296 (mt) cc_final: 0.8064 (mt) REVERT: D 328 SER cc_start: 0.7857 (t) cc_final: 0.7326 (p) REVERT: D 342 MET cc_start: 0.7000 (ptm) cc_final: 0.6772 (ptt) REVERT: D 345 TRP cc_start: 0.6682 (m100) cc_final: 0.5168 (m100) REVERT: D 381 ASN cc_start: 0.7598 (m110) cc_final: 0.7372 (m-40) REVERT: D 404 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8102 (mm-30) REVERT: D 409 ARG cc_start: 0.8278 (tpt-90) cc_final: 0.7619 (mtp85) REVERT: D 443 TRP cc_start: 0.8375 (t60) cc_final: 0.7074 (t60) outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.1884 time to fit residues: 102.5799 Evaluate side-chains 358 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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: 0.6980 chunk 107 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 ASN ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 HIS ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN C 484 GLN D 95 HIS ** 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 = 0.4719 r_free = 0.4719 target = 0.225998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.166407 restraints weight = 44379.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.171609 restraints weight = 20185.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.174798 restraints weight = 12061.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.176794 restraints weight = 8603.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.177950 restraints weight = 6942.756| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20302 Z= 0.203 Angle : 0.652 9.835 28362 Z= 0.374 Chirality : 0.044 0.309 3108 Planarity : 0.006 0.083 3020 Dihedral : 23.300 89.810 4268 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.43 (0.19), residues: 1936 helix: 1.66 (0.17), residues: 922 sheet: -0.53 (0.28), residues: 269 loop : 0.82 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 416 TYR 0.019 0.002 TYR D 154 PHE 0.016 0.002 PHE B 476 TRP 0.046 0.002 TRP D 35 HIS 0.014 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.20 (20286) covalent geometry : angle 0.64231 / 0.37 (28338) hydrogen bonds : bond 0.05169 / 3.54 ( 1052) hydrogen bonds : angle 4.22814 / 3.10 ( 2777) metal coordination : bond 0.00808 / 0.44 ( 16) metal coordination : angle 3.90086 / 2.71 ( 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 384 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7897 (mtp180) cc_final: 0.7270 (tpm170) REVERT: A 24 GLU cc_start: 0.8530 (tp30) cc_final: 0.7656 (tp30) REVERT: A 30 CYS cc_start: 0.7809 (m) cc_final: 0.7395 (t) REVERT: A 56 LYS cc_start: 0.8159 (pttp) cc_final: 0.7923 (pttm) REVERT: A 58 ARG cc_start: 0.7853 (ttt180) cc_final: 0.7428 (ttm110) REVERT: A 59 PRO cc_start: 0.8081 (Cg_endo) cc_final: 0.7809 (Cg_exo) REVERT: A 60 ASN cc_start: 0.7948 (t160) cc_final: 0.7531 (t0) REVERT: A 61 LEU cc_start: 0.7776 (tp) cc_final: 0.7309 (tp) REVERT: A 132 MET cc_start: 0.8269 (mtm) cc_final: 0.7644 (mtm) REVERT: A 135 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8210 (mt-10) REVERT: A 185 LEU cc_start: 0.8961 (mp) cc_final: 0.8672 (pp) REVERT: A 237 ARG cc_start: 0.3348 (ttp-110) cc_final: 0.1622 (ptm160) REVERT: A 239 MET cc_start: 0.4721 (mmm) cc_final: 0.4204 (ptp) REVERT: A 329 MET cc_start: -0.0189 (mtp) cc_final: -0.0912 (mmm) REVERT: A 337 ASN cc_start: -0.0307 (p0) cc_final: -0.1139 (p0) REVERT: B 8 ARG cc_start: 0.7644 (ttp80) cc_final: 0.7162 (ttp80) REVERT: B 11 ARG cc_start: 0.7120 (mtt-85) cc_final: 0.6782 (tpp80) REVERT: B 21 ARG cc_start: 0.8005 (ttt-90) cc_final: 0.7183 (tmt-80) REVERT: B 24 GLU cc_start: 0.7815 (pt0) cc_final: 0.7581 (pt0) REVERT: B 27 GLN cc_start: 0.7773 (tp40) cc_final: 0.7523 (tp40) REVERT: B 28 GLN cc_start: 0.7703 (tp-100) cc_final: 0.7123 (tp-100) REVERT: B 50 VAL cc_start: 0.8605 (t) cc_final: 0.8367 (m) REVERT: B 51 ASP cc_start: 0.8328 (t0) cc_final: 0.8119 (t0) REVERT: B 56 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7384 (mtmm) REVERT: B 67 PHE cc_start: 0.7878 (m-80) cc_final: 0.7629 (m-10) REVERT: B 71 PRO cc_start: 0.7731 (Cg_exo) cc_final: 0.7521 (Cg_endo) REVERT: B 88 ARG cc_start: 0.8056 (tpp80) cc_final: 0.7726 (tpp80) REVERT: B 95 HIS cc_start: 0.7073 (m90) cc_final: 0.6173 (m90) REVERT: B 98 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6755 (mt-10) REVERT: B 99 ASP cc_start: 0.7875 (m-30) cc_final: 0.7630 (m-30) REVERT: B 101 LYS cc_start: 0.8790 (mptt) cc_final: 0.8355 (mptt) REVERT: B 102 LYS cc_start: 0.8210 (mptt) cc_final: 0.7829 (mptt) REVERT: B 108 THR cc_start: 0.7930 (m) cc_final: 0.7388 (t) REVERT: B 134 LEU cc_start: 0.7672 (tp) cc_final: 0.7373 (tt) REVERT: B 138 LYS cc_start: 0.7869 (mttt) cc_final: 0.7619 (mttt) REVERT: B 142 ARG cc_start: 0.7868 (ttp-110) cc_final: 0.7664 (tmm-80) REVERT: B 143 SER cc_start: 0.8479 (t) cc_final: 0.7642 (p) REVERT: B 148 ASN cc_start: 0.8247 (m-40) cc_final: 0.7796 (t0) REVERT: B 149 ILE cc_start: 0.8541 (mt) cc_final: 0.8142 (mm) REVERT: B 187 VAL cc_start: 0.8390 (t) cc_final: 0.8172 (p) REVERT: B 189 HIS cc_start: 0.6962 (t-90) cc_final: 0.6711 (t-90) REVERT: B 199 HIS cc_start: 0.7694 (p-80) cc_final: 0.7476 (p-80) REVERT: B 214 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7991 (ttmt) REVERT: B 247 TYR cc_start: 0.7225 (m-10) cc_final: 0.6371 (m-80) REVERT: B 263 LEU cc_start: 0.8500 (mm) cc_final: 0.8298 (mm) REVERT: B 297 LEU cc_start: 0.8019 (tp) cc_final: 0.7664 (tp) REVERT: B 298 LEU cc_start: 0.8151 (mt) cc_final: 0.7848 (mt) REVERT: B 302 LEU cc_start: 0.8147 (tp) cc_final: 0.7603 (tp) REVERT: B 324 TYR cc_start: 0.7070 (m-80) cc_final: 0.6078 (m-10) REVERT: B 329 MET cc_start: 0.7496 (mmt) cc_final: 0.6889 (mmt) REVERT: B 334 HIS cc_start: 0.7142 (p90) cc_final: 0.6466 (p90) REVERT: B 342 MET cc_start: 0.6753 (ttp) cc_final: 0.5780 (ttp) REVERT: B 348 PHE cc_start: 0.8351 (t80) cc_final: 0.7870 (t80) REVERT: B 351 GLU cc_start: 0.8449 (tt0) cc_final: 0.8061 (mt-10) REVERT: B 367 TRP cc_start: 0.8220 (t-100) cc_final: 0.7696 (t-100) REVERT: B 376 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7659 (mm-30) REVERT: B 386 ASP cc_start: 0.7614 (t70) cc_final: 0.7239 (t70) REVERT: B 404 GLU cc_start: 0.8212 (mp0) cc_final: 0.7638 (mp0) REVERT: B 409 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7879 (mmp80) REVERT: B 419 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8267 (mt-10) REVERT: B 442 TRP cc_start: 0.7967 (t60) cc_final: 0.7749 (t60) REVERT: B 443 TRP cc_start: 0.7976 (t-100) cc_final: 0.7525 (t-100) REVERT: B 454 TRP cc_start: 0.8145 (t60) cc_final: 0.7664 (t60) REVERT: B 456 ARG cc_start: 0.7954 (mtp180) cc_final: 0.7501 (ttm110) REVERT: C 28 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7547 (tm-30) REVERT: C 90 LEU cc_start: 0.8079 (tp) cc_final: 0.7777 (tp) REVERT: C 98 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7607 (tm-30) REVERT: C 229 GLU cc_start: 0.7867 (pt0) cc_final: 0.7446 (tt0) REVERT: C 273 GLU cc_start: 0.8670 (pt0) cc_final: 0.8058 (pm20) REVERT: C 364 GLU cc_start: 0.7694 (pm20) cc_final: 0.7361 (pm20) REVERT: D 7 ILE cc_start: 0.8437 (mt) cc_final: 0.8231 (mm) REVERT: D 9 LEU cc_start: 0.8315 (tt) cc_final: 0.7937 (mt) REVERT: D 21 ARG cc_start: 0.7542 (tpp80) cc_final: 0.7133 (tpp80) REVERT: D 26 CYS cc_start: 0.7983 (m) cc_final: 0.7310 (m) REVERT: D 27 GLN cc_start: 0.7420 (mt0) cc_final: 0.6850 (mt0) REVERT: D 28 GLN cc_start: 0.7524 (tm-30) cc_final: 0.7149 (tm-30) REVERT: D 30 CYS cc_start: 0.7585 (p) cc_final: 0.7380 (p) REVERT: D 36 ASP cc_start: 0.7878 (m-30) cc_final: 0.7517 (m-30) REVERT: D 45 ASP cc_start: 0.7851 (m-30) cc_final: 0.7597 (m-30) REVERT: D 64 TRP cc_start: 0.7927 (m100) cc_final: 0.7651 (m100) REVERT: D 92 GLN cc_start: 0.7729 (tt0) cc_final: 0.7479 (mt0) REVERT: D 101 LYS cc_start: 0.7990 (mmpt) cc_final: 0.7545 (mmpt) REVERT: D 109 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6867 (mm-30) REVERT: D 131 GLN cc_start: 0.8055 (tt0) cc_final: 0.7783 (tt0) REVERT: D 132 MET cc_start: 0.7350 (mmm) cc_final: 0.7020 (mmm) REVERT: D 133 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7342 (mt-10) REVERT: D 135 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7558 (mm-30) REVERT: D 138 LYS cc_start: 0.8958 (mttt) cc_final: 0.8300 (mtpp) REVERT: D 153 LYS cc_start: 0.8334 (mttt) cc_final: 0.7779 (mttt) REVERT: D 182 GLU cc_start: 0.8055 (tt0) cc_final: 0.7798 (tt0) REVERT: D 186 GLU cc_start: 0.7542 (tt0) cc_final: 0.7179 (tp30) REVERT: D 195 HIS cc_start: 0.7195 (m90) cc_final: 0.6974 (m90) REVERT: D 226 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7413 (mp10) REVERT: D 229 GLU cc_start: 0.6864 (mp0) cc_final: 0.6460 (mp0) REVERT: D 242 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7481 (mt-10) REVERT: D 245 LEU cc_start: 0.8541 (mt) cc_final: 0.7653 (mt) REVERT: D 247 TYR cc_start: 0.6779 (m-10) cc_final: 0.6031 (m-10) REVERT: D 272 ARG cc_start: 0.7538 (mmm160) cc_final: 0.7211 (mmm160) REVERT: D 273 GLU cc_start: 0.8130 (mp0) cc_final: 0.7857 (mp0) REVERT: D 278 LEU cc_start: 0.8295 (mt) cc_final: 0.8092 (mt) REVERT: D 328 SER cc_start: 0.7637 (t) cc_final: 0.7045 (p) REVERT: D 345 TRP cc_start: 0.6709 (m100) cc_final: 0.5391 (m100) REVERT: D 404 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8061 (mm-30) REVERT: D 416 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7714 (ptp-110) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.1843 time to fit residues: 101.4779 Evaluate side-chains 361 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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: 6.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 30.0000 chunk 163 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 161 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 352 GLN C 60 ASN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN 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 = 0.4732 r_free = 0.4732 target = 0.226659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.168433 restraints weight = 44373.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.173553 restraints weight = 20395.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.176677 restraints weight = 12161.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.178561 restraints weight = 8687.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.179704 restraints weight = 7038.190| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20302 Z= 0.199 Angle : 0.638 8.241 28362 Z= 0.366 Chirality : 0.044 0.313 3108 Planarity : 0.005 0.054 3020 Dihedral : 23.342 89.711 4268 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.69 % 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: 1.39 (0.19), residues: 1936 helix: 1.68 (0.17), residues: 916 sheet: -0.54 (0.29), residues: 274 loop : 0.75 (0.25), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 472 TYR 0.020 0.002 TYR B 324 PHE 0.015 0.002 PHE B 348 TRP 0.047 0.002 TRP D 35 HIS 0.005 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.20 (20286) covalent geometry : angle 0.63084 / 0.37 (28338) hydrogen bonds : bond 0.05166 / 3.51 ( 1052) hydrogen bonds : angle 4.22305 / 3.10 ( 2777) metal coordination : bond 0.00582 / 0.34 ( 16) metal coordination : angle 3.41661 / 2.45 ( 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 376 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 0.639 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: A 21 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7149 (tpp-160) REVERT: A 24 GLU cc_start: 0.8553 (tp30) cc_final: 0.7966 (tp30) REVERT: A 30 CYS cc_start: 0.7715 (m) cc_final: 0.7398 (t) REVERT: A 56 LYS cc_start: 0.8164 (pttp) cc_final: 0.7934 (pttm) REVERT: A 58 ARG cc_start: 0.7839 (ttt180) cc_final: 0.7461 (ttm110) REVERT: A 59 PRO cc_start: 0.7991 (Cg_endo) cc_final: 0.7706 (Cg_exo) REVERT: A 60 ASN cc_start: 0.8019 (t0) cc_final: 0.7647 (t0) REVERT: A 61 LEU cc_start: 0.7775 (tp) cc_final: 0.7287 (tp) REVERT: A 132 MET cc_start: 0.8204 (mtm) cc_final: 0.7556 (mtm) REVERT: A 135 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8125 (mt-10) REVERT: A 185 LEU cc_start: 0.8952 (mp) cc_final: 0.8687 (pp) REVERT: A 237 ARG cc_start: 0.3447 (ttp-110) cc_final: 0.1659 (ptm160) REVERT: A 239 MET cc_start: 0.4771 (mmm) cc_final: 0.4258 (ptp) REVERT: A 329 MET cc_start: -0.0253 (mtp) cc_final: -0.1029 (mmm) REVERT: A 337 ASN cc_start: -0.0789 (p0) cc_final: -0.1587 (p0) REVERT: B 8 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7166 (ttp80) REVERT: B 11 ARG cc_start: 0.6886 (mtt-85) cc_final: 0.6593 (tpp80) REVERT: B 21 ARG cc_start: 0.8004 (ttt-90) cc_final: 0.7442 (tpt90) REVERT: B 24 GLU cc_start: 0.7766 (pt0) cc_final: 0.7459 (pt0) REVERT: B 27 GLN cc_start: 0.7747 (tp40) cc_final: 0.7532 (tp40) REVERT: B 28 GLN cc_start: 0.7704 (tp-100) cc_final: 0.7107 (tp-100) REVERT: B 37 VAL cc_start: 0.8155 (t) cc_final: 0.7525 (m) REVERT: B 56 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7436 (mtmm) REVERT: B 67 PHE cc_start: 0.8024 (m-80) cc_final: 0.7703 (m-10) REVERT: B 71 PRO cc_start: 0.7726 (Cg_exo) cc_final: 0.7509 (Cg_endo) REVERT: B 95 HIS cc_start: 0.7024 (m90) cc_final: 0.6186 (m90) REVERT: B 98 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6752 (mt-10) REVERT: B 99 ASP cc_start: 0.7872 (m-30) cc_final: 0.7620 (m-30) REVERT: B 101 LYS cc_start: 0.8784 (mptt) cc_final: 0.8346 (mptt) REVERT: B 102 LYS cc_start: 0.8244 (mptt) cc_final: 0.7817 (mptt) REVERT: B 108 THR cc_start: 0.7968 (m) cc_final: 0.7401 (t) REVERT: B 138 LYS cc_start: 0.7891 (mttt) cc_final: 0.7501 (ttmm) REVERT: B 142 ARG cc_start: 0.7887 (ttp-110) cc_final: 0.7659 (tmm-80) REVERT: B 143 SER cc_start: 0.8357 (t) cc_final: 0.7860 (p) REVERT: B 148 ASN cc_start: 0.8240 (m-40) cc_final: 0.7798 (t0) REVERT: B 149 ILE cc_start: 0.8562 (mt) cc_final: 0.8201 (mm) REVERT: B 189 HIS cc_start: 0.7104 (t-90) cc_final: 0.6733 (t-90) REVERT: B 193 ASP cc_start: 0.7556 (m-30) cc_final: 0.7286 (m-30) REVERT: B 199 HIS cc_start: 0.7653 (p-80) cc_final: 0.7436 (p-80) REVERT: B 247 TYR cc_start: 0.7230 (m-10) cc_final: 0.6360 (m-80) REVERT: B 289 LYS cc_start: 0.8718 (mppt) cc_final: 0.8119 (mmtt) REVERT: B 297 LEU cc_start: 0.8149 (tp) cc_final: 0.7901 (tp) REVERT: B 302 LEU cc_start: 0.7852 (tp) cc_final: 0.7338 (tp) REVERT: B 325 ARG cc_start: 0.6605 (mtm110) cc_final: 0.6101 (mtp85) REVERT: B 329 MET cc_start: 0.7528 (mmt) cc_final: 0.6854 (mmt) REVERT: B 334 HIS cc_start: 0.7213 (p90) cc_final: 0.6558 (p90) REVERT: B 351 GLU cc_start: 0.8362 (tt0) cc_final: 0.7991 (tt0) REVERT: B 367 TRP cc_start: 0.8336 (t-100) cc_final: 0.7668 (t-100) REVERT: B 376 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7639 (mm-30) REVERT: B 386 ASP cc_start: 0.7668 (t70) cc_final: 0.7262 (t70) REVERT: B 409 ARG cc_start: 0.8132 (mtm180) cc_final: 0.7887 (mmp80) REVERT: B 416 ARG cc_start: 0.7845 (mpp-170) cc_final: 0.7412 (mtm-85) REVERT: B 419 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8246 (mt-10) REVERT: B 442 TRP cc_start: 0.7983 (t60) cc_final: 0.7752 (t60) REVERT: B 443 TRP cc_start: 0.8026 (t-100) cc_final: 0.7625 (t-100) REVERT: B 454 TRP cc_start: 0.8101 (t60) cc_final: 0.7701 (t60) REVERT: B 456 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7418 (ttm110) REVERT: C 24 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7027 (tm-30) REVERT: C 28 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7554 (tm-30) REVERT: C 90 LEU cc_start: 0.8093 (tp) cc_final: 0.7777 (tp) REVERT: C 229 GLU cc_start: 0.7859 (pt0) cc_final: 0.7461 (tt0) REVERT: C 271 THR cc_start: 0.7399 (p) cc_final: 0.5558 (p) REVERT: C 273 GLU cc_start: 0.8837 (pt0) cc_final: 0.8346 (pm20) REVERT: D 9 LEU cc_start: 0.8300 (tt) cc_final: 0.7944 (mt) REVERT: D 21 ARG cc_start: 0.7582 (tpp80) cc_final: 0.7106 (tpp80) REVERT: D 24 GLU cc_start: 0.8180 (tp30) cc_final: 0.7940 (tm-30) REVERT: D 26 CYS cc_start: 0.7976 (m) cc_final: 0.7260 (m) REVERT: D 27 GLN cc_start: 0.7389 (mt0) cc_final: 0.6829 (mt0) REVERT: D 28 GLN cc_start: 0.7446 (tm-30) cc_final: 0.7077 (tm-30) REVERT: D 30 CYS cc_start: 0.7581 (p) cc_final: 0.7375 (p) REVERT: D 36 ASP cc_start: 0.7919 (m-30) cc_final: 0.7410 (t0) REVERT: D 45 ASP cc_start: 0.7875 (m-30) cc_final: 0.7661 (m-30) REVERT: D 56 LYS cc_start: 0.8200 (tttt) cc_final: 0.7949 (ttpp) REVERT: D 57 ARG cc_start: 0.7174 (mtt90) cc_final: 0.6902 (ttm110) REVERT: D 64 TRP cc_start: 0.7867 (m100) cc_final: 0.7552 (m100) REVERT: D 73 ASP cc_start: 0.6975 (t0) cc_final: 0.6573 (t0) REVERT: D 92 GLN cc_start: 0.7746 (tt0) cc_final: 0.7488 (mt0) REVERT: D 101 LYS cc_start: 0.7877 (mmpt) cc_final: 0.7582 (mmpt) REVERT: D 109 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6793 (mm-30) REVERT: D 129 VAL cc_start: 0.8542 (m) cc_final: 0.8213 (p) REVERT: D 131 GLN cc_start: 0.8042 (tt0) cc_final: 0.7796 (tt0) REVERT: D 135 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7632 (mm-30) REVERT: D 138 LYS cc_start: 0.8965 (mttt) cc_final: 0.8345 (mtpp) REVERT: D 139 GLU cc_start: 0.7200 (pp20) cc_final: 0.6929 (pp20) REVERT: D 153 LYS cc_start: 0.8464 (mttt) cc_final: 0.7855 (mttt) REVERT: D 163 TYR cc_start: 0.6188 (m-10) cc_final: 0.5859 (m-10) REVERT: D 182 GLU cc_start: 0.8058 (tt0) cc_final: 0.7800 (tt0) REVERT: D 186 GLU cc_start: 0.7572 (tt0) cc_final: 0.7184 (tp30) REVERT: D 226 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7510 (mp10) REVERT: D 242 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7459 (mt-10) REVERT: D 245 LEU cc_start: 0.8385 (mt) cc_final: 0.7613 (mt) REVERT: D 247 TYR cc_start: 0.6809 (m-10) cc_final: 0.5972 (m-10) REVERT: D 272 ARG cc_start: 0.7613 (mmm160) cc_final: 0.7131 (mmm160) REVERT: D 302 LEU cc_start: 0.8068 (tp) cc_final: 0.7658 (mt) REVERT: D 328 SER cc_start: 0.7437 (t) cc_final: 0.7013 (p) REVERT: D 404 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8044 (mm-30) REVERT: D 409 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7713 (mtp85) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.1841 time to fit residues: 98.6262 Evaluate side-chains 350 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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: 0.8980 chunk 80 optimal weight: 2.9990 chunk 126 optimal weight: 40.0000 chunk 158 optimal weight: 3.9990 chunk 200 optimal weight: 50.0000 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 131 GLN B 203 HIS ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN 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 = 0.4719 r_free = 0.4719 target = 0.225261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.166526 restraints weight = 44390.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.171661 restraints weight = 20643.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.174775 restraints weight = 12428.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.176694 restraints weight = 8846.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.177880 restraints weight = 7163.057| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20302 Z= 0.230 Angle : 0.666 10.008 28362 Z= 0.381 Chirality : 0.045 0.374 3108 Planarity : 0.006 0.061 3020 Dihedral : 23.439 89.355 4268 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.06 % Allowed : 1.31 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.18 (0.19), residues: 1936 helix: 1.51 (0.17), residues: 922 sheet: -0.66 (0.28), residues: 292 loop : 0.68 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 416 TYR 0.022 0.002 TYR B 188 PHE 0.025 0.002 PHE B 348 TRP 0.057 0.002 TRP D 35 HIS 0.014 0.002 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.23 (20286) covalent geometry : angle 0.66097 / 0.38 (28338) hydrogen bonds : bond 0.05464 / 3.75 ( 1052) hydrogen bonds : angle 4.31804 / 3.17 ( 2777) metal coordination : bond 0.00675 / 0.40 ( 16) metal coordination : angle 3.00558 / 2.14 ( 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 369 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 0.608 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: 0.7915 (mtp180) cc_final: 0.7222 (tpp-160) REVERT: A 24 GLU cc_start: 0.8542 (tp30) cc_final: 0.7925 (tp30) REVERT: A 30 CYS cc_start: 0.7801 (m) cc_final: 0.7476 (t) REVERT: A 58 ARG cc_start: 0.7976 (ttt180) cc_final: 0.7641 (ttm110) REVERT: A 59 PRO cc_start: 0.8034 (Cg_endo) cc_final: 0.7732 (Cg_exo) REVERT: A 60 ASN cc_start: 0.8059 (t0) cc_final: 0.7682 (t0) REVERT: A 61 LEU cc_start: 0.8047 (tp) cc_final: 0.7551 (tp) REVERT: A 132 MET cc_start: 0.8241 (mtm) cc_final: 0.7604 (mtm) REVERT: A 135 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8155 (mt-10) REVERT: A 185 LEU cc_start: 0.8945 (mp) cc_final: 0.8676 (pp) REVERT: A 237 ARG cc_start: 0.3586 (ttp-110) cc_final: 0.2544 (ptp-170) REVERT: A 239 MET cc_start: 0.4881 (mmm) cc_final: 0.4336 (ptp) REVERT: A 329 MET cc_start: -0.0544 (mtp) cc_final: -0.1244 (mmm) REVERT: A 337 ASN cc_start: -0.1350 (p0) cc_final: -0.2037 (p0) REVERT: B 8 ARG cc_start: 0.7691 (ttp80) cc_final: 0.6876 (ttp80) REVERT: B 11 ARG cc_start: 0.6936 (mtt-85) cc_final: 0.6671 (tpp80) REVERT: B 21 ARG cc_start: 0.8047 (ttt-90) cc_final: 0.7228 (mmm160) REVERT: B 24 GLU cc_start: 0.7832 (pt0) cc_final: 0.7501 (pt0) REVERT: B 28 GLN cc_start: 0.7733 (tp-100) cc_final: 0.7068 (tp-100) REVERT: B 37 VAL cc_start: 0.8338 (t) cc_final: 0.7584 (m) REVERT: B 43 ASP cc_start: 0.6548 (m-30) cc_final: 0.6000 (p0) REVERT: B 56 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7491 (mtmm) REVERT: B 67 PHE cc_start: 0.8044 (m-80) cc_final: 0.7768 (m-10) REVERT: B 71 PRO cc_start: 0.7743 (Cg_exo) cc_final: 0.7512 (Cg_endo) REVERT: B 95 HIS cc_start: 0.7017 (m90) cc_final: 0.6535 (m90) REVERT: B 98 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6827 (mt-10) REVERT: B 101 LYS cc_start: 0.8784 (mptt) cc_final: 0.8364 (mptt) REVERT: B 102 LYS cc_start: 0.8371 (mptt) cc_final: 0.7857 (mptt) REVERT: B 138 LYS cc_start: 0.8034 (mttt) cc_final: 0.7709 (mttp) REVERT: B 142 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7676 (tmm-80) REVERT: B 143 SER cc_start: 0.8461 (t) cc_final: 0.7884 (p) REVERT: B 148 ASN cc_start: 0.8303 (m-40) cc_final: 0.7817 (t0) REVERT: B 149 ILE cc_start: 0.8596 (mt) cc_final: 0.8214 (mm) REVERT: B 189 HIS cc_start: 0.7085 (t-90) cc_final: 0.6752 (t-90) REVERT: B 193 ASP cc_start: 0.7474 (m-30) cc_final: 0.7187 (m-30) REVERT: B 199 HIS cc_start: 0.7717 (p-80) cc_final: 0.7461 (p-80) REVERT: B 204 ASP cc_start: 0.7557 (t70) cc_final: 0.7195 (m-30) REVERT: B 214 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7598 (ttpp) REVERT: B 289 LYS cc_start: 0.8677 (mppt) cc_final: 0.8413 (mppt) REVERT: B 297 LEU cc_start: 0.8169 (tp) cc_final: 0.7966 (tp) REVERT: B 302 LEU cc_start: 0.7497 (tp) cc_final: 0.7015 (tp) REVERT: B 325 ARG cc_start: 0.6949 (mtm110) cc_final: 0.6392 (mtp85) REVERT: B 329 MET cc_start: 0.7321 (mmt) cc_final: 0.6891 (mmt) REVERT: B 334 HIS cc_start: 0.7432 (p90) cc_final: 0.6803 (p90) REVERT: B 346 ASP cc_start: 0.7974 (m-30) cc_final: 0.7395 (m-30) REVERT: B 367 TRP cc_start: 0.8362 (t-100) cc_final: 0.7675 (t-100) REVERT: B 376 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7647 (mm-30) REVERT: B 383 GLU cc_start: 0.8251 (pt0) cc_final: 0.7746 (pp20) REVERT: B 386 ASP cc_start: 0.7801 (t70) cc_final: 0.7278 (t70) REVERT: B 389 SER cc_start: 0.8982 (m) cc_final: 0.8663 (p) REVERT: B 391 ILE cc_start: 0.7659 (mt) cc_final: 0.7388 (mt) REVERT: B 413 LEU cc_start: 0.8648 (mm) cc_final: 0.8412 (mm) REVERT: B 416 ARG cc_start: 0.7937 (mpp-170) cc_final: 0.7350 (mtm-85) REVERT: B 419 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 454 TRP cc_start: 0.8111 (t60) cc_final: 0.7683 (t60) REVERT: B 456 ARG cc_start: 0.7897 (mtp180) cc_final: 0.7436 (ttm110) REVERT: C 22 GLN cc_start: 0.8110 (mt0) cc_final: 0.7571 (mt0) REVERT: C 28 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7593 (tm-30) REVERT: C 30 CYS cc_start: 0.8855 (m) cc_final: 0.8647 (m) REVERT: C 43 ASP cc_start: 0.6806 (m-30) cc_final: 0.6506 (m-30) REVERT: C 89 HIS cc_start: 0.8259 (m-70) cc_final: 0.8000 (m-70) REVERT: C 90 LEU cc_start: 0.8198 (tp) cc_final: 0.7890 (tp) REVERT: C 98 GLU cc_start: 0.8340 (pt0) cc_final: 0.7772 (pp20) REVERT: C 100 HIS cc_start: 0.7405 (m90) cc_final: 0.7111 (m90) REVERT: C 223 ARG cc_start: 0.7310 (tpt90) cc_final: 0.7062 (tpt170) REVERT: C 229 GLU cc_start: 0.7835 (pt0) cc_final: 0.7550 (tt0) REVERT: C 239 MET cc_start: 0.4611 (ttt) cc_final: 0.4409 (ttt) REVERT: C 273 GLU cc_start: 0.8807 (pt0) cc_final: 0.8290 (tp30) REVERT: D 9 LEU cc_start: 0.8306 (tt) cc_final: 0.7990 (mt) REVERT: D 21 ARG cc_start: 0.7599 (tpp80) cc_final: 0.7124 (tpp80) REVERT: D 24 GLU cc_start: 0.8137 (tp30) cc_final: 0.7922 (tm-30) REVERT: D 26 CYS cc_start: 0.7948 (m) cc_final: 0.7146 (m) REVERT: D 28 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7106 (tm-30) REVERT: D 36 ASP cc_start: 0.7901 (m-30) cc_final: 0.7385 (t0) REVERT: D 45 ASP cc_start: 0.7927 (m-30) cc_final: 0.7700 (m-30) REVERT: D 57 ARG cc_start: 0.7165 (mtt90) cc_final: 0.6844 (ttm110) REVERT: D 73 ASP cc_start: 0.7042 (t0) cc_final: 0.6456 (t0) REVERT: D 92 GLN cc_start: 0.7820 (tt0) cc_final: 0.7532 (mt0) REVERT: D 101 LYS cc_start: 0.7866 (mmpt) cc_final: 0.7405 (mmpt) REVERT: D 102 LYS cc_start: 0.7514 (mmtt) cc_final: 0.7215 (mmtt) REVERT: D 109 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6717 (mm-30) REVERT: D 129 VAL cc_start: 0.8598 (m) cc_final: 0.8284 (p) REVERT: D 131 GLN cc_start: 0.7992 (tt0) cc_final: 0.7750 (tt0) REVERT: D 132 MET cc_start: 0.7479 (mmm) cc_final: 0.6557 (mmm) REVERT: D 133 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7197 (mt-10) REVERT: D 138 LYS cc_start: 0.8897 (mttt) cc_final: 0.8318 (mtpp) REVERT: D 139 GLU cc_start: 0.7302 (pp20) cc_final: 0.7003 (pp20) REVERT: D 153 LYS cc_start: 0.8532 (mttt) cc_final: 0.7896 (mttt) REVERT: D 182 GLU cc_start: 0.8049 (tt0) cc_final: 0.7363 (tp30) REVERT: D 186 GLU cc_start: 0.7647 (tt0) cc_final: 0.7322 (tp30) REVERT: D 189 HIS cc_start: 0.6306 (t-90) cc_final: 0.6078 (t-90) REVERT: D 226 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7786 (mp10) REVERT: D 229 GLU cc_start: 0.6950 (mp0) cc_final: 0.6476 (mp0) REVERT: D 242 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7435 (tp30) REVERT: D 272 ARG cc_start: 0.7608 (mmm160) cc_final: 0.7100 (mmm160) REVERT: D 302 LEU cc_start: 0.8122 (tp) cc_final: 0.7538 (mp) REVERT: D 328 SER cc_start: 0.7430 (t) cc_final: 0.7082 (t) REVERT: D 345 TRP cc_start: 0.6827 (m100) cc_final: 0.5353 (m100) REVERT: D 350 GLU cc_start: 0.7928 (tp30) cc_final: 0.7597 (tp30) REVERT: D 404 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7867 (mm-30) REVERT: D 409 ARG cc_start: 0.7603 (mtp85) cc_final: 0.7217 (mtp85) REVERT: D 416 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.8069 (ptp-170) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.1842 time to fit residues: 96.9626 Evaluate side-chains 353 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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: 5.9990 chunk 97 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 172 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 127 optimal weight: 0.0170 chunk 106 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 overall best weight: 2.3424 ------------------------------------------------------------------------------- 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 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN C 484 GLN D 100 HIS D 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.224607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.164766 restraints weight = 44469.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.169928 restraints weight = 20741.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.173088 restraints weight = 12517.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.175060 restraints weight = 8966.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.176207 restraints weight = 7283.000| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20302 Z= 0.241 Angle : 0.668 7.173 28362 Z= 0.382 Chirality : 0.045 0.364 3108 Planarity : 0.006 0.141 3020 Dihedral : 23.528 89.414 4268 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.06 % Allowed : 0.94 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.12 (0.19), residues: 1936 helix: 1.47 (0.17), residues: 920 sheet: -0.74 (0.28), residues: 294 loop : 0.66 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 88 TYR 0.018 0.002 TYR D 312 PHE 0.026 0.002 PHE A 314 TRP 0.060 0.002 TRP D 35 HIS 0.007 0.001 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.24 (20286) covalent geometry : angle 0.66192 / 0.38 (28338) hydrogen bonds : bond 0.05547 / 3.78 ( 1052) hydrogen bonds : angle 4.43620 / 3.25 ( 2777) metal coordination : bond 0.00848 / 0.48 ( 16) metal coordination : angle 3.09289 / 1.98 ( 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 359 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 0.635 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: 0.7934 (mtp180) cc_final: 0.7231 (tpp-160) REVERT: A 24 GLU cc_start: 0.8575 (tp30) cc_final: 0.7969 (tp30) REVERT: A 30 CYS cc_start: 0.7853 (m) cc_final: 0.7512 (t) REVERT: A 60 ASN cc_start: 0.8118 (t0) cc_final: 0.7834 (t0) REVERT: A 61 LEU cc_start: 0.8152 (tp) cc_final: 0.7827 (tp) REVERT: A 132 MET cc_start: 0.8457 (mtm) cc_final: 0.7691 (mtm) REVERT: A 138 LYS cc_start: 0.8700 (mttm) cc_final: 0.8327 (mttm) REVERT: A 185 LEU cc_start: 0.8963 (mp) cc_final: 0.8692 (pp) REVERT: A 237 ARG cc_start: 0.3940 (ttp-110) cc_final: 0.2741 (ptp-170) REVERT: A 239 MET cc_start: 0.4888 (mmm) cc_final: 0.4387 (ptp) REVERT: A 329 MET cc_start: -0.0595 (mtp) cc_final: -0.1256 (mmm) REVERT: A 337 ASN cc_start: -0.1021 (p0) cc_final: -0.1718 (p0) REVERT: B 8 ARG cc_start: 0.7525 (ttp80) cc_final: 0.6862 (ttp80) REVERT: B 11 ARG cc_start: 0.6987 (mtt-85) cc_final: 0.6701 (tpp80) REVERT: B 21 ARG cc_start: 0.8078 (ttt-90) cc_final: 0.7522 (mmm160) REVERT: B 24 GLU cc_start: 0.7874 (pt0) cc_final: 0.7177 (pp20) REVERT: B 28 GLN cc_start: 0.7755 (tp-100) cc_final: 0.7320 (tp-100) REVERT: B 32 GLN cc_start: 0.8129 (mp10) cc_final: 0.7747 (mm-40) REVERT: B 56 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7472 (mtmm) REVERT: B 67 PHE cc_start: 0.8081 (m-80) cc_final: 0.7819 (m-10) REVERT: B 71 PRO cc_start: 0.7756 (Cg_exo) cc_final: 0.7523 (Cg_endo) REVERT: B 95 HIS cc_start: 0.6989 (m90) cc_final: 0.6511 (m90) REVERT: B 98 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6813 (mt-10) REVERT: B 101 LYS cc_start: 0.8798 (mptt) cc_final: 0.8363 (mptt) REVERT: B 102 LYS cc_start: 0.8389 (mptt) cc_final: 0.7773 (mptt) REVERT: B 138 LYS cc_start: 0.8136 (mttt) cc_final: 0.7897 (mtmt) REVERT: B 142 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7649 (ttp-110) REVERT: B 148 ASN cc_start: 0.8313 (m-40) cc_final: 0.7714 (t0) REVERT: B 149 ILE cc_start: 0.8619 (mt) cc_final: 0.8201 (mm) REVERT: B 204 ASP cc_start: 0.7564 (t70) cc_final: 0.7161 (m-30) REVERT: B 247 TYR cc_start: 0.6895 (m-10) cc_final: 0.6445 (m-80) REVERT: B 289 LYS cc_start: 0.8658 (mppt) cc_final: 0.8387 (mppt) REVERT: B 302 LEU cc_start: 0.7498 (tp) cc_final: 0.7000 (tp) REVERT: B 329 MET cc_start: 0.7367 (mmt) cc_final: 0.7152 (mmt) REVERT: B 334 HIS cc_start: 0.7472 (p90) cc_final: 0.6873 (p90) REVERT: B 342 MET cc_start: 0.7078 (ttp) cc_final: 0.6380 (ttp) REVERT: B 346 ASP cc_start: 0.8129 (m-30) cc_final: 0.7666 (m-30) REVERT: B 367 TRP cc_start: 0.8421 (t-100) cc_final: 0.7766 (t-100) REVERT: B 376 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7656 (mm-30) REVERT: B 383 GLU cc_start: 0.8284 (pt0) cc_final: 0.7774 (pp20) REVERT: B 386 ASP cc_start: 0.7833 (t70) cc_final: 0.7286 (t70) REVERT: B 389 SER cc_start: 0.9030 (m) cc_final: 0.8662 (p) REVERT: B 391 ILE cc_start: 0.7783 (mt) cc_final: 0.7424 (mt) REVERT: B 413 LEU cc_start: 0.8672 (mm) cc_final: 0.8208 (mm) REVERT: B 416 ARG cc_start: 0.7904 (mpp-170) cc_final: 0.7458 (mtm-85) REVERT: B 419 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8312 (mt-10) REVERT: B 454 TRP cc_start: 0.8166 (t60) cc_final: 0.7738 (t60) REVERT: B 456 ARG cc_start: 0.7901 (mtp180) cc_final: 0.7499 (ttm110) REVERT: C 22 GLN cc_start: 0.8134 (mt0) cc_final: 0.7591 (mt0) REVERT: C 28 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7628 (tm-30) REVERT: C 89 HIS cc_start: 0.8298 (m-70) cc_final: 0.8038 (m-70) REVERT: C 90 LEU cc_start: 0.8215 (tp) cc_final: 0.7878 (tp) REVERT: C 98 GLU cc_start: 0.8457 (pt0) cc_final: 0.8003 (pp20) REVERT: C 100 HIS cc_start: 0.7549 (m90) cc_final: 0.7189 (m90) REVERT: C 229 GLU cc_start: 0.7807 (pt0) cc_final: 0.7452 (tp30) REVERT: C 239 MET cc_start: 0.4942 (ttt) cc_final: 0.4726 (ttt) REVERT: C 273 GLU cc_start: 0.8811 (pt0) cc_final: 0.8277 (tp30) REVERT: D 9 LEU cc_start: 0.8113 (tt) cc_final: 0.7903 (mt) REVERT: D 21 ARG cc_start: 0.7600 (tpp80) cc_final: 0.7101 (tpp80) REVERT: D 26 CYS cc_start: 0.7907 (m) cc_final: 0.7240 (m) REVERT: D 28 GLN cc_start: 0.7481 (tm-30) cc_final: 0.7135 (tm-30) REVERT: D 30 CYS cc_start: 0.7798 (p) cc_final: 0.7558 (p) REVERT: D 36 ASP cc_start: 0.7845 (m-30) cc_final: 0.7335 (t0) REVERT: D 45 ASP cc_start: 0.7916 (m-30) cc_final: 0.7711 (m-30) REVERT: D 73 ASP cc_start: 0.7056 (t0) cc_final: 0.6456 (t0) REVERT: D 101 LYS cc_start: 0.7870 (mmpt) cc_final: 0.7400 (mmpt) REVERT: D 102 LYS cc_start: 0.7597 (mmtt) cc_final: 0.7234 (mmtt) REVERT: D 109 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6675 (mm-30) REVERT: D 129 VAL cc_start: 0.8612 (m) cc_final: 0.8385 (p) REVERT: D 132 MET cc_start: 0.7543 (mmm) cc_final: 0.7245 (mmm) REVERT: D 135 GLU cc_start: 0.7609 (pp20) cc_final: 0.6993 (pp20) REVERT: D 138 LYS cc_start: 0.8959 (mttt) cc_final: 0.8226 (mttp) REVERT: D 142 ARG cc_start: 0.7671 (ttm110) cc_final: 0.7469 (ttm110) REVERT: D 153 LYS cc_start: 0.8536 (mttt) cc_final: 0.7908 (mttt) REVERT: D 182 GLU cc_start: 0.8007 (tt0) cc_final: 0.7282 (tp30) REVERT: D 186 GLU cc_start: 0.7686 (tt0) cc_final: 0.7390 (tp30) REVERT: D 189 HIS cc_start: 0.6302 (t-90) cc_final: 0.5886 (t-90) REVERT: D 226 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7935 (mp10) REVERT: D 229 GLU cc_start: 0.6914 (mp0) cc_final: 0.6487 (mp0) REVERT: D 242 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7813 (tp30) REVERT: D 272 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7260 (mmm160) REVERT: D 302 LEU cc_start: 0.8175 (tp) cc_final: 0.7697 (mp) REVERT: D 328 SER cc_start: 0.7425 (t) cc_final: 0.7090 (p) REVERT: D 345 TRP cc_start: 0.6941 (m100) cc_final: 0.5461 (m100) REVERT: D 350 GLU cc_start: 0.7872 (tp30) cc_final: 0.7503 (tp30) REVERT: D 404 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7929 (mm-30) REVERT: D 409 ARG cc_start: 0.7603 (mtp85) cc_final: 0.7079 (mtp85) REVERT: D 416 ARG cc_start: 0.8300 (mtm-85) cc_final: 0.8078 (ptp90) REVERT: D 443 TRP cc_start: 0.8141 (t60) cc_final: 0.7648 (t60) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.1841 time to fit residues: 94.5487 Evaluate side-chains 345 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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: 0.6980 chunk 121 optimal weight: 6.9990 chunk 15 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 24 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 ASN A 111 HIS A 148 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 221 GLN ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN C 274 GLN C 484 GLN D 60 ASN D 89 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.226592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.167734 restraints weight = 44566.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.172884 restraints weight = 20542.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.176059 restraints weight = 12309.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.177971 restraints weight = 8772.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.179150 restraints weight = 7116.022| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20302 Z= 0.143 Angle : 0.606 8.968 28362 Z= 0.348 Chirality : 0.042 0.198 3108 Planarity : 0.005 0.072 3020 Dihedral : 23.563 89.451 4268 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.06 % Allowed : 0.69 % Favored : 99.25 % 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: 1.43 (0.20), residues: 1936 helix: 1.76 (0.17), residues: 915 sheet: -0.66 (0.29), residues: 294 loop : 0.81 (0.25), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 325 TYR 0.032 0.002 TYR D 154 PHE 0.034 0.002 PHE B 348 TRP 0.094 0.002 TRP A 96 HIS 0.008 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (20286) covalent geometry : angle 0.60126 / 0.35 (28338) hydrogen bonds : bond 0.04476 / 3.04 ( 1052) hydrogen bonds : angle 4.24040 / 3.12 ( 2777) metal coordination : bond 0.00283 / 0.15 ( 16) metal coordination : angle 2.66070 / 1.80 ( 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 365 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 0.615 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: 0.7916 (mtp180) cc_final: 0.7208 (tpp-160) REVERT: A 24 GLU cc_start: 0.8559 (tp30) cc_final: 0.7965 (tp30) REVERT: A 56 LYS cc_start: 0.8181 (pttp) cc_final: 0.7784 (pttp) REVERT: A 58 ARG cc_start: 0.7937 (ttt180) cc_final: 0.7649 (ttm110) REVERT: A 59 PRO cc_start: 0.8029 (Cg_endo) cc_final: 0.7753 (Cg_exo) REVERT: A 60 ASN cc_start: 0.7876 (t160) cc_final: 0.7472 (t0) REVERT: A 61 LEU cc_start: 0.7965 (tp) cc_final: 0.7521 (tp) REVERT: A 132 MET cc_start: 0.8192 (mtm) cc_final: 0.7571 (mtm) REVERT: A 138 LYS cc_start: 0.8675 (mttm) cc_final: 0.8289 (mttp) REVERT: A 185 LEU cc_start: 0.8971 (mp) cc_final: 0.8708 (pp) REVERT: A 237 ARG cc_start: 0.3861 (ttp-110) cc_final: 0.2915 (ptp-170) REVERT: A 239 MET cc_start: 0.4859 (mmm) cc_final: 0.4390 (ptp) REVERT: A 329 MET cc_start: -0.0627 (mtp) cc_final: -0.1286 (mmm) REVERT: A 337 ASN cc_start: -0.1038 (p0) cc_final: -0.1679 (p0) REVERT: A 462 LEU cc_start: 0.7162 (mp) cc_final: 0.6960 (mp) REVERT: B 11 ARG cc_start: 0.7173 (mtt-85) cc_final: 0.6813 (tpp80) REVERT: B 21 ARG cc_start: 0.7888 (ttt-90) cc_final: 0.7228 (ptm-80) REVERT: B 24 GLU cc_start: 0.7794 (pt0) cc_final: 0.7111 (pp20) REVERT: B 27 GLN cc_start: 0.7904 (tp40) cc_final: 0.7609 (tp40) REVERT: B 28 GLN cc_start: 0.7742 (tp-100) cc_final: 0.7128 (tp-100) REVERT: B 37 VAL cc_start: 0.8407 (t) cc_final: 0.7822 (m) REVERT: B 43 ASP cc_start: 0.7267 (t70) cc_final: 0.6716 (t0) REVERT: B 56 LYS cc_start: 0.7937 (mtmm) cc_final: 0.7440 (mtmm) REVERT: B 67 PHE cc_start: 0.8016 (m-80) cc_final: 0.7752 (m-10) REVERT: B 68 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6948 (mm-30) REVERT: B 71 PRO cc_start: 0.7748 (Cg_exo) cc_final: 0.7501 (Cg_endo) REVERT: B 95 HIS cc_start: 0.7012 (m90) cc_final: 0.6459 (m90) REVERT: B 98 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6722 (mt-10) REVERT: B 101 LYS cc_start: 0.8775 (mptt) cc_final: 0.8322 (mptt) REVERT: B 102 LYS cc_start: 0.8359 (mptt) cc_final: 0.7789 (mptt) REVERT: B 138 LYS cc_start: 0.8084 (mttt) cc_final: 0.7629 (ttmm) REVERT: B 142 ARG cc_start: 0.7870 (ttp-110) cc_final: 0.7572 (tmm-80) REVERT: B 143 SER cc_start: 0.8329 (p) cc_final: 0.7516 (p) REVERT: B 148 ASN cc_start: 0.8198 (m-40) cc_final: 0.7719 (t0) REVERT: B 149 ILE cc_start: 0.8642 (mt) cc_final: 0.8220 (mm) REVERT: B 201 VAL cc_start: 0.7784 (t) cc_final: 0.7327 (p) REVERT: B 204 ASP cc_start: 0.7562 (t70) cc_final: 0.7197 (m-30) REVERT: B 214 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7472 (ttpp) REVERT: B 226 GLN cc_start: 0.7341 (tp40) cc_final: 0.6809 (tp40) REVERT: B 229 GLU cc_start: 0.6486 (pm20) cc_final: 0.6272 (pm20) REVERT: B 236 LYS cc_start: 0.8270 (tptp) cc_final: 0.7969 (tptp) REVERT: B 247 TYR cc_start: 0.6661 (m-10) cc_final: 0.6279 (m-80) REVERT: B 289 LYS cc_start: 0.8616 (mppt) cc_final: 0.8345 (mppt) REVERT: B 302 LEU cc_start: 0.7676 (tp) cc_final: 0.7204 (tp) REVERT: B 325 ARG cc_start: 0.6310 (mtp-110) cc_final: 0.5769 (mtp85) REVERT: B 329 MET cc_start: 0.7459 (mmt) cc_final: 0.6790 (mmt) REVERT: B 334 HIS cc_start: 0.7269 (p90) cc_final: 0.6647 (p90) REVERT: B 346 ASP cc_start: 0.8043 (m-30) cc_final: 0.7558 (m-30) REVERT: B 367 TRP cc_start: 0.8362 (t-100) cc_final: 0.7822 (t-100) REVERT: B 376 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7592 (mm-30) REVERT: B 383 GLU cc_start: 0.8191 (pt0) cc_final: 0.7668 (pp20) REVERT: B 386 ASP cc_start: 0.7637 (t70) cc_final: 0.7097 (t70) REVERT: B 389 SER cc_start: 0.8927 (m) cc_final: 0.8587 (p) REVERT: B 391 ILE cc_start: 0.7613 (mt) cc_final: 0.7293 (mt) REVERT: B 413 LEU cc_start: 0.8580 (mm) cc_final: 0.8097 (mm) REVERT: B 416 ARG cc_start: 0.7858 (mpp-170) cc_final: 0.7363 (mtm-85) REVERT: B 454 TRP cc_start: 0.8177 (t60) cc_final: 0.7533 (t60) REVERT: B 456 ARG cc_start: 0.7828 (mtp180) cc_final: 0.7315 (ttm110) REVERT: C 22 GLN cc_start: 0.8094 (mt0) cc_final: 0.7616 (mt0) REVERT: C 24 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7211 (tm-30) REVERT: C 28 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7648 (tm-30) REVERT: C 43 ASP cc_start: 0.6710 (m-30) cc_final: 0.6376 (m-30) REVERT: C 89 HIS cc_start: 0.8229 (m-70) cc_final: 0.7972 (m-70) REVERT: C 90 LEU cc_start: 0.8155 (tp) cc_final: 0.7864 (tp) REVERT: C 91 GLN cc_start: 0.8153 (mt0) cc_final: 0.7657 (pt0) REVERT: C 95 HIS cc_start: 0.7591 (t70) cc_final: 0.7331 (t70) REVERT: C 98 GLU cc_start: 0.8225 (pt0) cc_final: 0.7735 (pp20) REVERT: C 100 HIS cc_start: 0.7495 (m90) cc_final: 0.7212 (m90) REVERT: C 273 GLU cc_start: 0.8750 (pt0) cc_final: 0.8273 (tp30) REVERT: D 9 LEU cc_start: 0.8184 (tt) cc_final: 0.7915 (mt) REVERT: D 20 GLU cc_start: 0.7616 (mp0) cc_final: 0.7281 (pm20) REVERT: D 21 ARG cc_start: 0.7502 (tpp80) cc_final: 0.7016 (tpp80) REVERT: D 24 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7993 (tm-30) REVERT: D 26 CYS cc_start: 0.7860 (m) cc_final: 0.7206 (m) REVERT: D 28 GLN cc_start: 0.7395 (tm-30) cc_final: 0.7004 (tm-30) REVERT: D 30 CYS cc_start: 0.7635 (p) cc_final: 0.7373 (p) REVERT: D 36 ASP cc_start: 0.7858 (m-30) cc_final: 0.7374 (t0) REVERT: D 45 ASP cc_start: 0.7889 (m-30) cc_final: 0.7681 (m-30) REVERT: D 73 ASP cc_start: 0.7002 (t0) cc_final: 0.6574 (t0) REVERT: D 79 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.6853 (mtp85) REVERT: D 92 GLN cc_start: 0.7614 (mt0) cc_final: 0.7201 (mt0) REVERT: D 101 LYS cc_start: 0.7841 (mmpt) cc_final: 0.7393 (mmpt) REVERT: D 102 LYS cc_start: 0.7516 (mmtt) cc_final: 0.7202 (mmtt) REVERT: D 109 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6713 (mp0) REVERT: D 132 MET cc_start: 0.7309 (mmm) cc_final: 0.6538 (mmm) REVERT: D 135 GLU cc_start: 0.7504 (pp20) cc_final: 0.6403 (pp20) REVERT: D 138 LYS cc_start: 0.8933 (mttt) cc_final: 0.8203 (mttp) REVERT: D 139 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6867 (tm-30) REVERT: D 153 LYS cc_start: 0.8390 (mttt) cc_final: 0.7821 (mttt) REVERT: D 182 GLU cc_start: 0.7976 (tt0) cc_final: 0.7704 (tt0) REVERT: D 186 GLU cc_start: 0.7628 (tt0) cc_final: 0.7341 (tp30) REVERT: D 189 HIS cc_start: 0.6137 (t-90) cc_final: 0.5741 (t-90) REVERT: D 214 LYS cc_start: 0.7447 (ttmt) cc_final: 0.6896 (tppt) REVERT: D 220 LEU cc_start: 0.7994 (tt) cc_final: 0.7556 (mm) REVERT: D 226 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7772 (mp10) REVERT: D 242 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7711 (mt-10) REVERT: D 245 LEU cc_start: 0.8398 (mt) cc_final: 0.7339 (mp) REVERT: D 247 TYR cc_start: 0.6757 (m-10) cc_final: 0.5958 (m-10) REVERT: D 328 SER cc_start: 0.7389 (t) cc_final: 0.7032 (p) REVERT: D 342 MET cc_start: 0.7038 (ptm) cc_final: 0.6809 (ptt) REVERT: D 345 TRP cc_start: 0.6822 (m100) cc_final: 0.5313 (m100) REVERT: D 381 ASN cc_start: 0.7880 (m110) cc_final: 0.7679 (m110) REVERT: D 404 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7848 (mm-30) REVERT: D 409 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7211 (mtp85) REVERT: D 443 TRP cc_start: 0.8157 (t60) cc_final: 0.7509 (t60) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.1825 time to fit residues: 95.2425 Evaluate side-chains 343 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 205 optimal weight: 40.0000 chunk 43 optimal weight: 50.0000 chunk 177 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 131 GLN ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN C 484 GLN D 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.225072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.165839 restraints weight = 44247.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.170980 restraints weight = 20661.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.174112 restraints weight = 12500.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.176077 restraints weight = 8938.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.177270 restraints weight = 7223.560| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.5234 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= 0.220 Angle : 0.656 8.512 28362 Z= 0.374 Chirality : 0.044 0.307 3108 Planarity : 0.006 0.156 3020 Dihedral : 23.560 89.001 4268 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 1.29 (0.20), residues: 1936 helix: 1.65 (0.17), residues: 914 sheet: -0.69 (0.29), residues: 285 loop : 0.69 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 416 TYR 0.029 0.002 TYR B 188 PHE 0.031 0.002 PHE B 348 TRP 0.067 0.002 TRP D 35 HIS 0.007 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.22 (20286) covalent geometry : angle 0.65201 / 0.37 (28338) hydrogen bonds : bond 0.05277 / 3.62 ( 1052) hydrogen bonds : angle 4.38845 / 3.24 ( 2777) metal coordination : bond 0.00603 / 0.35 ( 16) metal coordination : angle 2.48742 / 1.66 ( 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 348 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 347 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7915 (mtp180) cc_final: 0.7231 (tpp-160) REVERT: A 24 GLU cc_start: 0.8472 (tp30) cc_final: 0.8206 (tp30) REVERT: A 28 GLN cc_start: 0.8997 (tp40) cc_final: 0.8581 (tp40) REVERT: A 61 LEU cc_start: 0.8154 (tp) cc_final: 0.7857 (tp) REVERT: A 100 HIS cc_start: 0.7700 (m90) cc_final: 0.7474 (m90) REVERT: A 132 MET cc_start: 0.8327 (mtm) cc_final: 0.7591 (mtm) REVERT: A 138 LYS cc_start: 0.8701 (mttm) cc_final: 0.8318 (mttp) REVERT: A 185 LEU cc_start: 0.8976 (mp) cc_final: 0.8703 (pp) REVERT: A 237 ARG cc_start: 0.4030 (ttp-110) cc_final: 0.2849 (ptp-170) REVERT: A 239 MET cc_start: 0.4982 (mmm) cc_final: 0.4491 (ptp) REVERT: A 329 MET cc_start: -0.0590 (mtp) cc_final: -0.1280 (mmm) REVERT: A 337 ASN cc_start: -0.0973 (p0) cc_final: -0.1590 (p0) REVERT: B 11 ARG cc_start: 0.6960 (mtt-85) cc_final: 0.6672 (tpp80) REVERT: B 21 ARG cc_start: 0.7977 (ttt-90) cc_final: 0.7379 (mmm160) REVERT: B 24 GLU cc_start: 0.7840 (pt0) cc_final: 0.7081 (pp20) REVERT: B 28 GLN cc_start: 0.7978 (tp-100) cc_final: 0.7364 (tp-100) REVERT: B 37 VAL cc_start: 0.8443 (t) cc_final: 0.8210 (m) REVERT: B 43 ASP cc_start: 0.7450 (t70) cc_final: 0.6792 (t0) REVERT: B 50 VAL cc_start: 0.8517 (t) cc_final: 0.8310 (m) REVERT: B 56 LYS cc_start: 0.7847 (mtmm) cc_final: 0.7315 (mtmm) REVERT: B 67 PHE cc_start: 0.8061 (m-80) cc_final: 0.7845 (m-10) REVERT: B 71 PRO cc_start: 0.7761 (Cg_exo) cc_final: 0.7516 (Cg_endo) REVERT: B 95 HIS cc_start: 0.6942 (m90) cc_final: 0.6417 (m90) REVERT: B 98 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6809 (mt-10) REVERT: B 101 LYS cc_start: 0.8734 (mptt) cc_final: 0.8378 (mptt) REVERT: B 102 LYS cc_start: 0.8382 (mptt) cc_final: 0.7802 (mptt) REVERT: B 138 LYS cc_start: 0.8129 (mttt) cc_final: 0.7894 (mtmt) REVERT: B 142 ARG cc_start: 0.7869 (ttp-110) cc_final: 0.7553 (ttp-110) REVERT: B 148 ASN cc_start: 0.8277 (m-40) cc_final: 0.7763 (t0) REVERT: B 149 ILE cc_start: 0.8620 (mt) cc_final: 0.8242 (mm) REVERT: B 201 VAL cc_start: 0.7780 (t) cc_final: 0.7360 (p) REVERT: B 204 ASP cc_start: 0.7534 (t70) cc_final: 0.7192 (m-30) REVERT: B 229 GLU cc_start: 0.6499 (pm20) cc_final: 0.6195 (pm20) REVERT: B 236 LYS cc_start: 0.8239 (tptp) cc_final: 0.8029 (tptp) REVERT: B 247 TYR cc_start: 0.6895 (m-10) cc_final: 0.6380 (m-80) REVERT: B 279 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7403 (mtt180) REVERT: B 289 LYS cc_start: 0.8636 (mppt) cc_final: 0.8353 (mppt) REVERT: B 302 LEU cc_start: 0.7447 (tp) cc_final: 0.6988 (tp) REVERT: B 325 ARG cc_start: 0.6828 (mtp-110) cc_final: 0.6229 (mtp85) REVERT: B 329 MET cc_start: 0.7545 (mmt) cc_final: 0.6811 (mmt) REVERT: B 334 HIS cc_start: 0.7328 (p90) cc_final: 0.6714 (p90) REVERT: B 346 ASP cc_start: 0.7935 (m-30) cc_final: 0.7552 (m-30) REVERT: B 376 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7886 (mt-10) REVERT: B 383 GLU cc_start: 0.8240 (pt0) cc_final: 0.7730 (pp20) REVERT: B 386 ASP cc_start: 0.7686 (t70) cc_final: 0.7176 (t0) REVERT: B 389 SER cc_start: 0.8969 (m) cc_final: 0.8405 (t) REVERT: B 391 ILE cc_start: 0.7730 (mt) cc_final: 0.7276 (mt) REVERT: B 413 LEU cc_start: 0.8601 (mm) cc_final: 0.8258 (mm) REVERT: B 416 ARG cc_start: 0.7809 (mpp-170) cc_final: 0.7465 (mtm-85) REVERT: B 419 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8211 (mt-10) REVERT: B 454 TRP cc_start: 0.8146 (t60) cc_final: 0.7668 (t60) REVERT: B 456 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7428 (ttm110) REVERT: C 22 GLN cc_start: 0.8150 (mt0) cc_final: 0.7614 (mt0) REVERT: C 28 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 89 HIS cc_start: 0.8316 (m-70) cc_final: 0.8053 (m-70) REVERT: C 90 LEU cc_start: 0.8224 (tp) cc_final: 0.7902 (tp) REVERT: C 95 HIS cc_start: 0.7555 (t70) cc_final: 0.7211 (t70) REVERT: C 98 GLU cc_start: 0.8161 (pt0) cc_final: 0.7780 (pp20) REVERT: C 100 HIS cc_start: 0.7276 (m90) cc_final: 0.6938 (m90) REVERT: C 273 GLU cc_start: 0.8776 (pt0) cc_final: 0.8252 (tp30) REVERT: D 21 ARG cc_start: 0.7516 (tpp80) cc_final: 0.7092 (tpp80) REVERT: D 26 CYS cc_start: 0.7855 (m) cc_final: 0.7203 (m) REVERT: D 28 GLN cc_start: 0.7394 (tm-30) cc_final: 0.7026 (tm-30) REVERT: D 30 CYS cc_start: 0.7793 (p) cc_final: 0.7526 (p) REVERT: D 36 ASP cc_start: 0.7788 (m-30) cc_final: 0.7343 (t0) REVERT: D 64 TRP cc_start: 0.7931 (m100) cc_final: 0.7340 (m100) REVERT: D 73 ASP cc_start: 0.6972 (t0) cc_final: 0.6331 (t0) REVERT: D 88 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7354 (ttm-80) REVERT: D 92 GLN cc_start: 0.7641 (mt0) cc_final: 0.7255 (mt0) REVERT: D 101 LYS cc_start: 0.7839 (mmpt) cc_final: 0.7379 (mmpt) REVERT: D 102 LYS cc_start: 0.7649 (mmtt) cc_final: 0.7286 (mmtt) REVERT: D 109 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6591 (mm-30) REVERT: D 129 VAL cc_start: 0.8644 (m) cc_final: 0.8327 (p) REVERT: D 132 MET cc_start: 0.7429 (mmm) cc_final: 0.6914 (mmm) REVERT: D 135 GLU cc_start: 0.7474 (pp20) cc_final: 0.6409 (pp20) REVERT: D 138 LYS cc_start: 0.8976 (mttt) cc_final: 0.8276 (mttp) REVERT: D 153 LYS cc_start: 0.8535 (mttt) cc_final: 0.7938 (mttt) REVERT: D 182 GLU cc_start: 0.7937 (tt0) cc_final: 0.7663 (tt0) REVERT: D 186 GLU cc_start: 0.7689 (tt0) cc_final: 0.7413 (tp30) REVERT: D 215 ASP cc_start: 0.7487 (m-30) cc_final: 0.7109 (m-30) REVERT: D 220 LEU cc_start: 0.8061 (tt) cc_final: 0.7610 (mm) REVERT: D 226 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7972 (mp10) REVERT: D 229 GLU cc_start: 0.6910 (mp0) cc_final: 0.6451 (mp0) REVERT: D 242 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7939 (tp30) REVERT: D 302 LEU cc_start: 0.8194 (tp) cc_final: 0.7721 (mp) REVERT: D 328 SER cc_start: 0.7438 (t) cc_final: 0.7061 (p) REVERT: D 345 TRP cc_start: 0.6935 (m100) cc_final: 0.5525 (m100) REVERT: D 381 ASN cc_start: 0.7875 (m110) cc_final: 0.7666 (m110) REVERT: D 404 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7832 (mm-30) REVERT: D 409 ARG cc_start: 0.7716 (mtp85) cc_final: 0.7146 (mtp85) REVERT: D 443 TRP cc_start: 0.8079 (t60) cc_final: 0.7506 (t60) outliers start: 1 outliers final: 0 residues processed: 347 average time/residue: 0.1802 time to fit residues: 89.6223 Evaluate side-chains 331 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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: 6.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 30.0000 chunk 92 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN C 226 GLN C 274 GLN C 484 GLN D 22 GLN D 60 ASN D 334 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.227224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.168805 restraints weight = 44523.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.173937 restraints weight = 20569.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.177122 restraints weight = 12363.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.179090 restraints weight = 8797.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.180271 restraints weight = 7105.429| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20302 Z= 0.150 Angle : 0.618 10.784 28362 Z= 0.352 Chirality : 0.042 0.225 3108 Planarity : 0.005 0.088 3020 Dihedral : 23.579 88.917 4268 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1936 helix: 1.75 (0.17), residues: 914 sheet: -0.68 (0.29), residues: 290 loop : 0.81 (0.26), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 21 TYR 0.028 0.002 TYR B 188 PHE 0.033 0.002 PHE B 348 TRP 0.038 0.002 TRP A 96 HIS 0.011 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (20286) covalent geometry : angle 0.61397 / 0.35 (28338) hydrogen bonds : bond 0.04461 / 3.05 ( 1052) hydrogen bonds : angle 4.25831 / 3.15 ( 2777) metal coordination : bond 0.00277 / 0.15 ( 16) metal coordination : angle 2.45743 / 1.57 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4719.41 seconds wall clock time: 81 minutes 36.45 seconds (4896.45 seconds total)