Starting phenix.real_space_refine on Mon Apr 6 15:32:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu7_60892/04_2026/9iu7_60892.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu7_60892/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/9iu7_60892/04_2026/9iu7_60892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu7_60892/04_2026/9iu7_60892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iu7_60892/04_2026/9iu7_60892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu7_60892/04_2026/9iu7_60892.map" } 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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19472 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "C" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "D" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "E1" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "E2" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F1" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F2" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "G1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G2" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H2" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2429 SG CYS A 304 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: 4.32, per 1000 atoms: 0.22 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: 1.45 Conformation dependent library (CDL) restraints added in 655.2 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: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.621A pdb=" N TRP A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 118 through 151 Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 197 through 208 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 271 through 284 removed outlier: 4.122A pdb=" N LYS A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.870A pdb=" N VAL A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 423 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'B' and resid 18 through 34 Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.631A pdb=" N TRP B 64 " --> pdb=" O ASN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 118 through 151 Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 197 through 208 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 271 through 285 removed outlier: 3.757A pdb=" N LYS B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 342 through 358 Processing helix chain 'B' and resid 371 through 390 removed outlier: 3.630A pdb=" N LEU B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 423 removed outlier: 3.928A pdb=" N LEU B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 478 through 486 Processing helix chain 'C' and resid 18 through 34 Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.625A pdb=" N TRP C 64 " --> pdb=" O ASN C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 118 through 151 Processing helix chain 'C' and resid 177 through 193 Processing helix chain 'C' and resid 197 through 208 Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 271 through 283 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 342 through 358 Processing helix chain 'C' and resid 373 through 390 removed outlier: 3.694A pdb=" N LEU C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 423 Processing helix chain 'C' and resid 439 through 446 Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 478 through 486 Processing helix chain 'D' and resid 18 through 34 Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.625A pdb=" N TRP D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 86 through 100 Processing helix chain 'D' and resid 118 through 151 Processing helix chain 'D' and resid 177 through 193 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 242 through 246 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 342 through 358 Processing helix chain 'D' and resid 373 through 390 removed outlier: 3.675A pdb=" N LEU D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 422 Processing helix chain 'D' and resid 439 through 446 Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 478 through 486 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 44 removed outlier: 7.515A pdb=" N VAL A 5 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 40 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 7 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A 42 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU A 9 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU A 44 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG A 2 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL A 76 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A 4 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AA4, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 368 removed outlier: 7.086A pdb=" N ARG A 362 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 44 removed outlier: 6.790A pdb=" N ALA B 3 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ALA B 41 " --> pdb=" O ALA B 3 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 5 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASP B 43 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE B 7 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG B 2 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL B 76 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU B 4 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 168 Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 250 Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 304 Processing sheet with id=AB2, first strand: chain 'B' and resid 311 through 315 Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 368 removed outlier: 7.105A pdb=" N ARG B 362 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 36 through 44 removed outlier: 7.513A pdb=" N VAL C 5 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL C 40 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE C 7 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU C 42 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU C 9 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU C 44 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG C 2 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL C 76 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU C 4 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 249 through 250 Processing sheet with id=AB7, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AB8, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 368 removed outlier: 7.099A pdb=" N ARG C 362 " --> pdb=" O THR C 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 36 through 44 removed outlier: 7.373A pdb=" N VAL D 5 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL D 40 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE D 7 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU D 42 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU D 9 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU D 44 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG D 2 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL D 76 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU D 4 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 163 through 168 Processing sheet with id=AC3, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AC4, first strand: chain 'D' and resid 302 through 304 Processing sheet with id=AC5, first strand: chain 'D' and resid 311 through 314 Processing sheet with id=AC6, first strand: chain 'D' and resid 361 through 368 removed outlier: 7.118A pdb=" N ARG D 362 " --> pdb=" O THR D 435 " (cutoff:3.500A) 811 hydrogen bonds defined for protein. 2295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 241 hydrogen bonds 482 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 2.01 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=" 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 bond pdb=" C HIS C 321 " pdb=" N PRO C 322 " ideal model delta sigma weight residual 1.330 1.365 -0.035 1.22e-02 6.72e+03 8.21e+00 bond pdb=" C THR B 294 " pdb=" N PRO B 295 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.20e-02 6.94e+03 8.14e+00 ... (remaining 20281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 26350 3.44 - 6.89: 1859 6.89 - 10.33: 114 10.33 - 13.78: 11 13.78 - 17.22: 4 Bond angle restraints: 28338 Sorted by residual: angle pdb=" O3' DGF1 32 " pdb=" P DTF1 33 " pdb=" O5' DTF1 33 " ideal model delta sigma weight residual 104.00 86.78 17.22 1.50e+00 4.44e-01 1.32e+02 angle pdb=" O3' DGE2 32 " pdb=" P DTE2 33 " pdb=" O5' DTE2 33 " ideal model delta sigma weight residual 104.00 89.06 14.94 1.50e+00 4.44e-01 9.91e+01 angle pdb=" O3' DCH1 25 " pdb=" P DGH1 26 " pdb=" O5' DGH1 26 " ideal model delta sigma weight residual 104.00 89.27 14.73 1.50e+00 4.44e-01 9.64e+01 angle pdb=" O3' DAE1 20 " pdb=" P DCE1 21 " pdb=" O5' DCE1 21 " ideal model delta sigma weight residual 104.00 89.69 14.31 1.50e+00 4.44e-01 9.10e+01 angle pdb=" O3' DAF2 20 " pdb=" P DCF2 21 " pdb=" O5' DCF2 21 " ideal model delta sigma weight residual 104.00 90.54 13.46 1.50e+00 4.44e-01 8.05e+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 - 0.129: 2758 0.129 - 0.259: 327 0.259 - 0.388: 17 0.388 - 0.517: 2 0.517 - 0.646: 4 Chirality restraints: 3108 Sorted by residual: chirality pdb=" P DCH2 1 " pdb=" OP1 DCH2 1 " pdb=" OP2 DCH2 1 " pdb=" O5' DCH2 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DGE1 1 " pdb=" OP1 DGE1 1 " pdb=" OP2 DGE1 1 " pdb=" O5' DGE1 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+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 2.35 2.98 -0.64 2.00e-01 2.50e+01 1.01e+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: 0.500 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.110 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5742 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= 0.566 Angle : 1.852 19.798 28362 Z= 1.183 Chirality : 0.085 0.646 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 covalent geometry : bond 0.00943 (20286) covalent geometry : angle 1.83255 (28338) hydrogen bonds : bond 0.16479 ( 1052) hydrogen bonds : angle 6.04880 ( 2777) metal coordination : bond 0.05785 ( 16) metal coordination : angle 9.33634 ( 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 : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7591 (t) cc_final: 0.7265 (m) REVERT: A 21 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6862 (tpm170) REVERT: A 24 GLU cc_start: 0.8754 (tp30) cc_final: 0.7533 (tp30) REVERT: A 30 CYS cc_start: 0.7694 (m) cc_final: 0.7292 (t) REVERT: A 59 PRO cc_start: 0.7955 (Cg_endo) cc_final: 0.7697 (Cg_exo) REVERT: A 61 LEU cc_start: 0.7510 (tp) cc_final: 0.7115 (tp) REVERT: A 85 ARG cc_start: 0.5246 (OUTLIER) cc_final: 0.4885 (mmt90) REVERT: A 92 GLN cc_start: 0.8298 (tt0) cc_final: 0.8069 (tt0) REVERT: A 100 HIS cc_start: 0.7309 (m90) cc_final: 0.6870 (m90) REVERT: A 125 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7597 (tt) REVERT: A 126 MET cc_start: 0.6698 (mmm) cc_final: 0.6429 (mmp) REVERT: A 131 GLN cc_start: 0.7522 (tp40) cc_final: 0.7147 (tp40) REVERT: A 132 MET cc_start: 0.8298 (mtm) cc_final: 0.7670 (mmm) REVERT: A 138 LYS cc_start: 0.8551 (mttm) cc_final: 0.8117 (mmtp) REVERT: A 185 LEU cc_start: 0.8951 (mp) cc_final: 0.8681 (pp) REVERT: A 239 MET cc_start: 0.4986 (mmm) cc_final: 0.4413 (ptp) REVERT: A 302 LEU cc_start: 0.2851 (tp) cc_final: 0.1958 (tp) REVERT: A 312 TYR cc_start: 0.2977 (m-10) cc_final: 0.2386 (m-10) REVERT: A 329 MET cc_start: 0.0091 (mtp) cc_final: -0.1063 (tpt) REVERT: A 397 ARG cc_start: -0.1032 (OUTLIER) cc_final: -0.2543 (ttm170) REVERT: B 9 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7566 (mm) REVERT: B 11 ARG cc_start: 0.6936 (tpp80) cc_final: 0.6706 (ttm-80) REVERT: B 23 LEU cc_start: 0.7873 (tp) cc_final: 0.7658 (mt) REVERT: B 43 ASP cc_start: 0.5973 (m-30) cc_final: 0.5239 (m-30) REVERT: B 50 VAL cc_start: 0.8410 (t) cc_final: 0.8159 (m) REVERT: B 51 ASP cc_start: 0.8393 (t0) cc_final: 0.8187 (t0) REVERT: B 54 ASP cc_start: 0.5786 (t0) cc_final: 0.5415 (t0) REVERT: B 56 LYS cc_start: 0.7842 (mtmm) cc_final: 0.7574 (mtmm) REVERT: B 60 ASN cc_start: 0.7405 (m-40) cc_final: 0.6978 (m110) REVERT: B 69 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7044 (mm-30) REVERT: B 88 ARG cc_start: 0.7991 (ttt180) cc_final: 0.7647 (tpp80) REVERT: B 94 VAL cc_start: 0.7842 (t) cc_final: 0.7585 (m) REVERT: B 95 HIS cc_start: 0.7336 (m90) cc_final: 0.6462 (m90) REVERT: B 98 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7213 (mt-10) REVERT: B 99 ASP cc_start: 0.7928 (m-30) cc_final: 0.7588 (m-30) REVERT: B 100 HIS cc_start: 0.8003 (m90) cc_final: 0.7708 (m-70) REVERT: B 101 LYS cc_start: 0.8705 (mptt) cc_final: 0.8498 (mptt) REVERT: B 125 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8325 (tt) REVERT: B 133 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7400 (tp30) REVERT: B 134 LEU cc_start: 0.7640 (tp) cc_final: 0.7254 (tt) REVERT: B 148 ASN cc_start: 0.8272 (m-40) cc_final: 0.7385 (t0) REVERT: B 149 ILE cc_start: 0.8457 (mt) cc_final: 0.8133 (mm) REVERT: B 153 LYS cc_start: 0.7802 (mtmp) cc_final: 0.7136 (mtmp) REVERT: B 174 LEU cc_start: 0.7745 (mt) cc_final: 0.7340 (mt) REVERT: B 175 VAL cc_start: 0.7686 (OUTLIER) cc_final: 0.7314 (p) REVERT: B 177 ASP cc_start: 0.5827 (t0) cc_final: 0.5285 (t0) REVERT: B 187 VAL cc_start: 0.7941 (t) cc_final: 0.7738 (p) REVERT: B 188 TYR cc_start: 0.6974 (t80) cc_final: 0.6617 (t80) REVERT: B 189 HIS cc_start: 0.7189 (m-70) cc_final: 0.6842 (t-90) REVERT: B 207 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7249 (mtm-85) REVERT: B 211 LEU cc_start: 0.7658 (mt) cc_final: 0.7337 (tp) REVERT: B 214 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7832 (ttmt) REVERT: B 220 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7451 (mt) REVERT: B 236 LYS cc_start: 0.7831 (tttt) cc_final: 0.7600 (tptm) REVERT: B 257 ASP cc_start: 0.7813 (t70) cc_final: 0.6810 (p0) REVERT: B 274 GLN cc_start: 0.7257 (mt0) cc_final: 0.6832 (mt0) REVERT: B 299 LEU cc_start: 0.7297 (tp) cc_final: 0.7080 (tp) REVERT: B 302 LEU cc_start: 0.8144 (tp) cc_final: 0.7637 (tp) REVERT: B 329 MET cc_start: 0.7537 (mmt) cc_final: 0.6959 (mmt) REVERT: B 344 GLU cc_start: 0.8508 (tt0) cc_final: 0.8073 (tt0) REVERT: B 345 TRP cc_start: 0.7160 (m100) cc_final: 0.6827 (m100) REVERT: B 350 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8601 (tm-30) REVERT: B 367 TRP cc_start: 0.8016 (t-100) cc_final: 0.7373 (t-100) REVERT: B 376 GLU cc_start: 0.8782 (tt0) cc_final: 0.8273 (tt0) REVERT: B 386 ASP cc_start: 0.7591 (t70) cc_final: 0.7262 (t70) REVERT: B 416 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7786 (mtm-85) REVERT: B 441 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8197 (p0) REVERT: B 442 TRP cc_start: 0.8605 (t60) cc_final: 0.8085 (t60) REVERT: B 447 ASP cc_start: 0.8562 (t0) cc_final: 0.8185 (p0) REVERT: B 454 TRP cc_start: 0.8562 (t60) cc_final: 0.7986 (t60) REVERT: B 456 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7338 (ttm110) REVERT: C 30 CYS cc_start: 0.8242 (m) cc_final: 0.7454 (m) REVERT: C 44 LEU cc_start: 0.6765 (mp) cc_final: 0.5921 (mp) REVERT: C 90 LEU cc_start: 0.7437 (tp) cc_final: 0.7133 (tp) REVERT: C 164 LEU cc_start: 0.1281 (OUTLIER) cc_final: 0.0462 (tp) REVERT: C 199 HIS cc_start: 0.1949 (OUTLIER) cc_final: 0.1234 (m90) REVERT: C 229 GLU cc_start: 0.7621 (pt0) cc_final: 0.7056 (tt0) REVERT: C 273 GLU cc_start: 0.8380 (pt0) cc_final: 0.8171 (tp30) REVERT: D 9 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6984 (mp) REVERT: D 11 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7216 (mtp85) REVERT: D 20 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: D 24 GLU cc_start: 0.8397 (tt0) cc_final: 0.8169 (tm-30) REVERT: D 26 CYS cc_start: 0.7905 (m) cc_final: 0.6851 (p) REVERT: D 27 GLN cc_start: 0.7471 (mt0) cc_final: 0.6621 (pt0) REVERT: D 28 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7119 (tm-30) REVERT: D 33 ARG cc_start: 0.8014 (mtp180) cc_final: 0.6859 (ttm-80) REVERT: D 42 GLU cc_start: 0.6878 (tt0) cc_final: 0.6455 (tt0) REVERT: D 60 ASN cc_start: 0.8097 (m-40) cc_final: 0.7666 (m110) REVERT: D 74 VAL cc_start: 0.7716 (p) cc_final: 0.7436 (m) REVERT: D 79 ARG cc_start: 0.7059 (mtp180) cc_final: 0.6684 (mtm110) REVERT: D 81 ASP cc_start: 0.7910 (p0) cc_final: 0.7440 (p0) REVERT: D 82 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8168 (mmp80) REVERT: D 93 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7829 (mm) REVERT: D 98 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6076 (pt0) REVERT: D 125 LEU cc_start: 0.8350 (pp) cc_final: 0.8073 (pp) REVERT: D 131 GLN cc_start: 0.8079 (tt0) cc_final: 0.7604 (tt0) REVERT: D 135 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7829 (mm-30) REVERT: D 138 LYS cc_start: 0.8626 (mttt) cc_final: 0.8064 (mmmt) REVERT: D 142 ARG cc_start: 0.7596 (ttm110) cc_final: 0.7084 (ttm-80) REVERT: D 146 HIS cc_start: 0.8195 (m170) cc_final: 0.7580 (m-70) REVERT: D 153 LYS cc_start: 0.7959 (mttt) cc_final: 0.7451 (mttt) REVERT: D 182 GLU cc_start: 0.8309 (tt0) cc_final: 0.8049 (tt0) REVERT: D 193 ASP cc_start: 0.7275 (m-30) cc_final: 0.6687 (m-30) REVERT: D 214 LYS cc_start: 0.7550 (ttmt) cc_final: 0.7276 (ttmt) REVERT: D 220 LEU cc_start: 0.7889 (tt) cc_final: 0.7431 (mm) REVERT: D 225 PRO cc_start: 0.8019 (Cg_exo) cc_final: 0.7648 (Cg_endo) REVERT: D 228 ARG cc_start: 0.7275 (mtt-85) cc_final: 0.6803 (mtt-85) REVERT: D 236 LYS cc_start: 0.8556 (tttt) cc_final: 0.8160 (ttmm) REVERT: D 242 GLU cc_start: 0.8674 (mt-10) cc_final: 0.7690 (mt-10) REVERT: D 244 MET cc_start: 0.7940 (mmt) cc_final: 0.7513 (mmm) REVERT: D 245 LEU cc_start: 0.8275 (mt) cc_final: 0.7915 (mt) REVERT: D 247 TYR cc_start: 0.6348 (m-10) cc_final: 0.5853 (m-10) REVERT: D 269 ILE cc_start: 0.8204 (mm) cc_final: 0.7791 (mm) REVERT: D 270 LEU cc_start: 0.8260 (mt) cc_final: 0.8048 (mp) REVERT: D 272 ARG cc_start: 0.8110 (tpt170) cc_final: 0.7894 (mmm160) REVERT: D 278 LEU cc_start: 0.8632 (mt) cc_final: 0.8413 (mt) REVERT: D 312 TYR cc_start: 0.4065 (m-10) cc_final: 0.3779 (m-80) REVERT: D 328 SER cc_start: 0.7251 (t) cc_final: 0.6928 (p) REVERT: D 345 TRP cc_start: 0.6805 (m100) cc_final: 0.5128 (m100) REVERT: D 387 LEU cc_start: 0.9042 (mt) cc_final: 0.8701 (pp) REVERT: D 410 ILE cc_start: 0.8725 (mt) cc_final: 0.8398 (pt) REVERT: D 442 TRP cc_start: 0.7121 (t60) cc_final: 0.6697 (t60) REVERT: D 452 ASN cc_start: 0.6698 (t0) cc_final: 0.6084 (t0) REVERT: D 456 ARG cc_start: 0.8306 (mtp180) cc_final: 0.7726 (tpp80) REVERT: D 461 ARG cc_start: 0.6596 (ttm-80) cc_final: 0.6371 (ttp80) outliers start: 67 outliers final: 15 residues processed: 511 average time/residue: 0.1927 time to fit residues: 137.3942 Evaluate side-chains 429 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 396 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 0.9990 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: 20.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 251 ASN A 446 GLN B 27 GLN B 32 GLN B 131 GLN B 446 GLN C 60 ASN C 111 HIS C 148 ASN C 219 GLN C 484 GLN D 27 GLN D 111 HIS D 189 HIS D 199 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.230359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.170736 restraints weight = 45845.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.176052 restraints weight = 20993.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.179336 restraints weight = 12491.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.181346 restraints weight = 8845.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.182424 restraints weight = 7089.498| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20302 Z= 0.203 Angle : 0.634 9.427 28362 Z= 0.358 Chirality : 0.040 0.178 3108 Planarity : 0.005 0.045 3020 Dihedral : 22.857 86.622 4268 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: 2.03 (0.19), residues: 1936 helix: 2.27 (0.16), residues: 919 sheet: -0.12 (0.29), residues: 262 loop : 0.90 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 55 TYR 0.016 0.002 TYR D 396 PHE 0.025 0.002 PHE C 118 TRP 0.020 0.002 TRP D 35 HIS 0.008 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00423 (20286) covalent geometry : angle 0.62178 (28338) hydrogen bonds : bond 0.04900 ( 1052) hydrogen bonds : angle 4.00787 ( 2777) metal coordination : bond 0.00593 ( 16) metal coordination : angle 4.30851 ( 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 424 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 423 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7885 (mtp180) cc_final: 0.7221 (tpm170) REVERT: A 24 GLU cc_start: 0.8629 (tp30) cc_final: 0.7597 (tp30) REVERT: A 30 CYS cc_start: 0.7768 (m) cc_final: 0.7341 (t) REVERT: A 58 ARG cc_start: 0.7863 (ttt180) cc_final: 0.7410 (ttm110) REVERT: A 59 PRO cc_start: 0.8161 (Cg_endo) cc_final: 0.7916 (Cg_exo) REVERT: A 60 ASN cc_start: 0.7659 (t160) cc_final: 0.7247 (t0) REVERT: A 61 LEU cc_start: 0.7734 (tp) cc_final: 0.7215 (tp) REVERT: A 92 GLN cc_start: 0.8328 (tt0) cc_final: 0.7913 (tt0) REVERT: A 132 MET cc_start: 0.8069 (mtm) cc_final: 0.7672 (mtm) REVERT: A 138 LYS cc_start: 0.8546 (mttm) cc_final: 0.8097 (mmmt) REVERT: A 185 LEU cc_start: 0.8978 (mp) cc_final: 0.8706 (pp) REVERT: A 228 ARG cc_start: 0.7054 (mtt90) cc_final: 0.6551 (mtm180) REVERT: A 237 ARG cc_start: 0.3318 (ttp-170) cc_final: 0.1829 (ptm160) REVERT: A 239 MET cc_start: 0.4941 (mmm) cc_final: 0.4529 (mtp) REVERT: A 302 LEU cc_start: 0.2844 (tp) cc_final: 0.1529 (mt) REVERT: A 462 LEU cc_start: 0.6972 (mp) cc_final: 0.6714 (mp) REVERT: B 11 ARG cc_start: 0.7040 (mtt-85) cc_final: 0.6596 (tpp80) REVERT: B 21 ARG cc_start: 0.7936 (ttt-90) cc_final: 0.7351 (ptm-80) REVERT: B 24 GLU cc_start: 0.7666 (pt0) cc_final: 0.7348 (pp20) REVERT: B 28 GLN cc_start: 0.7634 (tp-100) cc_final: 0.7160 (tp-100) REVERT: B 43 ASP cc_start: 0.6579 (m-30) cc_final: 0.6310 (m-30) REVERT: B 50 VAL cc_start: 0.8470 (t) cc_final: 0.8269 (m) REVERT: B 56 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7340 (mtmm) REVERT: B 88 ARG cc_start: 0.7917 (ttt180) cc_final: 0.7670 (tpp80) REVERT: B 94 VAL cc_start: 0.8243 (t) cc_final: 0.7839 (m) REVERT: B 95 HIS cc_start: 0.7224 (m90) cc_final: 0.6860 (m90) REVERT: B 101 LYS cc_start: 0.8822 (mptt) cc_final: 0.8349 (mptt) REVERT: B 102 LYS cc_start: 0.8028 (mptt) cc_final: 0.7769 (mptt) REVERT: B 109 GLU cc_start: 0.6449 (mt-10) cc_final: 0.6045 (mp0) REVERT: B 118 PHE cc_start: 0.8009 (m-80) cc_final: 0.7730 (m-80) REVERT: B 133 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7548 (mm-30) REVERT: B 138 LYS cc_start: 0.7750 (mttt) cc_final: 0.7548 (mtmm) REVERT: B 142 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7502 (tmm-80) REVERT: B 148 ASN cc_start: 0.8176 (m-40) cc_final: 0.7584 (t0) REVERT: B 149 ILE cc_start: 0.8467 (mt) cc_final: 0.8095 (mm) REVERT: B 153 LYS cc_start: 0.7710 (mtmt) cc_final: 0.7212 (mtmt) REVERT: B 174 LEU cc_start: 0.7659 (mt) cc_final: 0.7313 (mt) REVERT: B 182 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6555 (mp0) REVERT: B 196 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6997 (mm-30) REVERT: B 236 LYS cc_start: 0.7891 (tttt) cc_final: 0.7684 (tttp) REVERT: B 282 LEU cc_start: 0.7808 (mt) cc_final: 0.7525 (mm) REVERT: B 292 VAL cc_start: 0.8489 (t) cc_final: 0.8288 (p) REVERT: B 295 PRO cc_start: 0.7879 (Cg_endo) cc_final: 0.7605 (Cg_exo) REVERT: B 298 LEU cc_start: 0.8043 (mt) cc_final: 0.7764 (mm) REVERT: B 302 LEU cc_start: 0.8229 (tp) cc_final: 0.7618 (tp) REVERT: B 329 MET cc_start: 0.7461 (mmt) cc_final: 0.6932 (mmt) REVERT: B 334 HIS cc_start: 0.6885 (p90) cc_final: 0.6273 (p90) REVERT: B 342 MET cc_start: 0.6641 (ttp) cc_final: 0.5929 (mmt) REVERT: B 344 GLU cc_start: 0.7941 (tt0) cc_final: 0.7265 (tm-30) REVERT: B 367 TRP cc_start: 0.7954 (t-100) cc_final: 0.7560 (t-100) REVERT: B 386 ASP cc_start: 0.7678 (t70) cc_final: 0.7262 (t70) REVERT: B 413 LEU cc_start: 0.8640 (mm) cc_final: 0.8279 (mm) REVERT: B 442 TRP cc_start: 0.8077 (t60) cc_final: 0.7852 (t60) REVERT: B 454 TRP cc_start: 0.8095 (t60) cc_final: 0.7573 (t60) REVERT: B 456 ARG cc_start: 0.8047 (mtp180) cc_final: 0.7660 (ttm110) REVERT: B 475 ASP cc_start: 0.6736 (t0) cc_final: 0.6477 (p0) REVERT: C 27 GLN cc_start: 0.8317 (mm110) cc_final: 0.7831 (mm110) REVERT: C 28 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7714 (tm-30) REVERT: C 43 ASP cc_start: 0.6038 (m-30) cc_final: 0.5738 (m-30) REVERT: C 90 LEU cc_start: 0.7854 (tp) cc_final: 0.7628 (tp) REVERT: C 98 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7576 (tm-30) REVERT: C 181 ARG cc_start: 0.7329 (mmm160) cc_final: 0.6971 (mmm160) REVERT: C 229 GLU cc_start: 0.7739 (pt0) cc_final: 0.7275 (tt0) REVERT: C 273 GLU cc_start: 0.8585 (pt0) cc_final: 0.8182 (tp30) REVERT: D 1 MET cc_start: 0.3762 (ttm) cc_final: 0.2606 (ttm) REVERT: D 24 GLU cc_start: 0.8168 (tt0) cc_final: 0.7880 (tp30) REVERT: D 26 CYS cc_start: 0.7992 (m) cc_final: 0.6957 (p) REVERT: D 27 GLN cc_start: 0.7411 (mt0) cc_final: 0.6610 (mt0) REVERT: D 28 GLN cc_start: 0.7542 (tm-30) cc_final: 0.7067 (tm-30) REVERT: D 33 ARG cc_start: 0.7853 (mtp180) cc_final: 0.7360 (tpp80) REVERT: D 35 TRP cc_start: 0.6308 (p90) cc_final: 0.5433 (p90) REVERT: D 60 ASN cc_start: 0.8269 (m-40) cc_final: 0.7859 (m110) REVERT: D 64 TRP cc_start: 0.8020 (m100) cc_final: 0.7366 (m100) REVERT: D 69 GLU cc_start: 0.6466 (mt-10) cc_final: 0.5986 (mp0) REVERT: D 74 VAL cc_start: 0.7892 (p) cc_final: 0.7661 (m) REVERT: D 92 GLN cc_start: 0.7701 (tt0) cc_final: 0.7463 (mt0) REVERT: D 109 GLU cc_start: 0.6812 (mp0) cc_final: 0.6609 (mp0) REVERT: D 131 GLN cc_start: 0.8106 (tt0) cc_final: 0.7741 (tt0) REVERT: D 132 MET cc_start: 0.7194 (mmm) cc_final: 0.6687 (mmm) REVERT: D 133 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7181 (mt-10) REVERT: D 135 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7582 (mm-30) REVERT: D 138 LYS cc_start: 0.8840 (mttt) cc_final: 0.8206 (mtpp) REVERT: D 139 GLU cc_start: 0.7415 (tp30) cc_final: 0.7041 (tp30) REVERT: D 140 ARG cc_start: 0.7494 (ttp-110) cc_final: 0.7198 (ttt90) REVERT: D 142 ARG cc_start: 0.7486 (ttm110) cc_final: 0.6853 (tmm-80) REVERT: D 146 HIS cc_start: 0.8248 (m170) cc_final: 0.7766 (m-70) REVERT: D 153 LYS cc_start: 0.8130 (mttt) cc_final: 0.7854 (mttt) REVERT: D 182 GLU cc_start: 0.8022 (tt0) cc_final: 0.7753 (tt0) REVERT: D 186 GLU cc_start: 0.7396 (tt0) cc_final: 0.7096 (tp30) REVERT: D 220 LEU cc_start: 0.7989 (tt) cc_final: 0.7604 (mm) REVERT: D 226 GLN cc_start: 0.7766 (mp10) cc_final: 0.7557 (mp10) REVERT: D 242 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7703 (mt-10) REVERT: D 245 LEU cc_start: 0.8479 (mt) cc_final: 0.7633 (mt) REVERT: D 247 TYR cc_start: 0.6699 (m-10) cc_final: 0.6151 (m-10) REVERT: D 269 ILE cc_start: 0.7973 (mm) cc_final: 0.7627 (mm) REVERT: D 278 LEU cc_start: 0.8441 (mt) cc_final: 0.8095 (mt) REVERT: D 302 LEU cc_start: 0.8117 (tp) cc_final: 0.7604 (tp) REVERT: D 312 TYR cc_start: 0.5069 (m-10) cc_final: 0.4706 (m-80) REVERT: D 328 SER cc_start: 0.7827 (t) cc_final: 0.7244 (p) REVERT: D 345 TRP cc_start: 0.6516 (m100) cc_final: 0.5076 (m100) REVERT: D 350 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8049 (mt-10) REVERT: D 410 ILE cc_start: 0.8715 (mt) cc_final: 0.8413 (mt) REVERT: D 416 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.7829 (ptp-110) REVERT: D 456 ARG cc_start: 0.8092 (mtp180) cc_final: 0.7758 (mmm-85) REVERT: D 459 ASN cc_start: 0.7601 (m-40) cc_final: 0.7376 (m-40) outliers start: 1 outliers final: 0 residues processed: 423 average time/residue: 0.1915 time to fit residues: 112.9978 Evaluate side-chains 374 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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: 0.0020 chunk 207 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 132 optimal weight: 50.0000 chunk 107 optimal weight: 0.4980 chunk 196 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 124 optimal weight: 0.0030 chunk 111 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 100 HIS ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN A 446 GLN B 60 ASN B 131 GLN B 189 HIS B 274 GLN C 60 ASN C 219 GLN C 221 GLN C 274 GLN ** C 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.229190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.170978 restraints weight = 45268.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.176201 restraints weight = 20778.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.179366 restraints weight = 12295.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 72)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.181320 restraints weight = 8702.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.182431 restraints weight = 6974.235| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20302 Z= 0.161 Angle : 0.575 13.042 28362 Z= 0.321 Chirality : 0.039 0.394 3108 Planarity : 0.004 0.039 3020 Dihedral : 22.876 87.450 4268 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.19), residues: 1936 helix: 2.35 (0.17), residues: 922 sheet: 0.04 (0.30), residues: 264 loop : 1.08 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 8 TYR 0.016 0.002 TYR B 324 PHE 0.013 0.001 PHE D 464 TRP 0.039 0.001 TRP D 35 HIS 0.016 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00335 (20286) covalent geometry : angle 0.56983 (28338) hydrogen bonds : bond 0.04010 ( 1052) hydrogen bonds : angle 3.83075 ( 2777) metal coordination : bond 0.00379 ( 16) metal coordination : angle 2.77690 ( 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 : 0.575 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: 0.7911 (mtp180) cc_final: 0.7293 (tpm170) REVERT: A 24 GLU cc_start: 0.8630 (tp30) cc_final: 0.7747 (tp30) REVERT: A 57 ARG cc_start: 0.7756 (mmt-90) cc_final: 0.7493 (mmt-90) REVERT: A 58 ARG cc_start: 0.7788 (ttt180) cc_final: 0.7317 (ttm170) REVERT: A 59 PRO cc_start: 0.8019 (Cg_endo) cc_final: 0.7625 (Cg_exo) REVERT: A 60 ASN cc_start: 0.7772 (t160) cc_final: 0.7303 (t0) REVERT: A 61 LEU cc_start: 0.7915 (tp) cc_final: 0.7294 (tp) REVERT: A 92 GLN cc_start: 0.8329 (tt0) cc_final: 0.8074 (tt0) REVERT: A 100 HIS cc_start: 0.7803 (m-70) cc_final: 0.7218 (m-70) REVERT: A 132 MET cc_start: 0.8006 (mtm) cc_final: 0.7384 (mtm) REVERT: A 138 LYS cc_start: 0.8583 (mttm) cc_final: 0.8111 (mmmt) REVERT: A 179 VAL cc_start: 0.7234 (t) cc_final: 0.7025 (m) REVERT: A 237 ARG cc_start: 0.3935 (ttp-110) cc_final: 0.2300 (ptm160) REVERT: A 337 ASN cc_start: -0.1028 (p0) cc_final: -0.1276 (p0) REVERT: A 462 LEU cc_start: 0.7124 (mp) cc_final: 0.6206 (tp) REVERT: B 8 ARG cc_start: 0.7497 (ttp80) cc_final: 0.7160 (ttp80) REVERT: B 11 ARG cc_start: 0.7100 (mtt-85) cc_final: 0.6732 (tpp80) REVERT: B 21 ARG cc_start: 0.7917 (ttt-90) cc_final: 0.7143 (tpt90) REVERT: B 24 GLU cc_start: 0.7774 (pt0) cc_final: 0.7508 (pt0) REVERT: B 28 GLN cc_start: 0.7619 (tp-100) cc_final: 0.6884 (tp-100) REVERT: B 43 ASP cc_start: 0.6669 (m-30) cc_final: 0.6460 (m-30) REVERT: B 50 VAL cc_start: 0.8487 (t) cc_final: 0.8183 (p) REVERT: B 56 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7435 (mtmm) REVERT: B 71 PRO cc_start: 0.7700 (Cg_exo) cc_final: 0.7457 (Cg_endo) REVERT: B 91 GLN cc_start: 0.7745 (mt0) cc_final: 0.7431 (mm-40) REVERT: B 95 HIS cc_start: 0.6881 (m90) cc_final: 0.6436 (m90) REVERT: B 96 TRP cc_start: 0.7840 (t60) cc_final: 0.7279 (t60) REVERT: B 98 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6911 (mt-10) REVERT: B 101 LYS cc_start: 0.8795 (mptt) cc_final: 0.8282 (mptt) REVERT: B 102 LYS cc_start: 0.8056 (mptt) cc_final: 0.7539 (mptt) REVERT: B 109 GLU cc_start: 0.6491 (mt-10) cc_final: 0.6155 (mt-10) REVERT: B 138 LYS cc_start: 0.7831 (mttt) cc_final: 0.7503 (ttmm) REVERT: B 142 ARG cc_start: 0.7902 (ttp-110) cc_final: 0.7596 (tmm-80) REVERT: B 143 SER cc_start: 0.8438 (t) cc_final: 0.7588 (p) REVERT: B 148 ASN cc_start: 0.8137 (m-40) cc_final: 0.7769 (t0) REVERT: B 149 ILE cc_start: 0.8508 (mt) cc_final: 0.8135 (mm) REVERT: B 174 LEU cc_start: 0.7551 (mt) cc_final: 0.7186 (mp) REVERT: B 189 HIS cc_start: 0.7163 (m90) cc_final: 0.6885 (m90) REVERT: B 196 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6929 (mm-30) REVERT: B 207 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6878 (mtm-85) REVERT: B 214 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7846 (ttmt) REVERT: B 236 LYS cc_start: 0.7821 (tttt) cc_final: 0.7604 (tttp) REVERT: B 282 LEU cc_start: 0.7789 (mt) cc_final: 0.7506 (mm) REVERT: B 292 VAL cc_start: 0.8525 (t) cc_final: 0.8240 (p) REVERT: B 295 PRO cc_start: 0.7820 (Cg_endo) cc_final: 0.7423 (Cg_exo) REVERT: B 298 LEU cc_start: 0.8132 (mt) cc_final: 0.7856 (mm) REVERT: B 302 LEU cc_start: 0.8002 (tp) cc_final: 0.7453 (tp) REVERT: B 329 MET cc_start: 0.7282 (mmt) cc_final: 0.6699 (mmt) REVERT: B 334 HIS cc_start: 0.6962 (p90) cc_final: 0.6370 (p90) REVERT: B 342 MET cc_start: 0.6414 (ttp) cc_final: 0.5849 (ttp) REVERT: B 344 GLU cc_start: 0.7961 (tt0) cc_final: 0.7657 (tt0) REVERT: B 383 GLU cc_start: 0.8265 (pt0) cc_final: 0.7663 (pp20) REVERT: B 384 LEU cc_start: 0.8864 (mt) cc_final: 0.8644 (mt) REVERT: B 386 ASP cc_start: 0.7683 (t70) cc_final: 0.7250 (t70) REVERT: B 409 ARG cc_start: 0.8224 (mtm180) cc_final: 0.7884 (mmp80) REVERT: B 413 LEU cc_start: 0.8539 (mm) cc_final: 0.8197 (mm) REVERT: B 416 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7402 (mtm-85) REVERT: B 448 THR cc_start: 0.8355 (p) cc_final: 0.7947 (p) REVERT: B 451 LYS cc_start: 0.7530 (mtmt) cc_final: 0.7193 (mtmt) REVERT: B 456 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7422 (ttm110) REVERT: B 475 ASP cc_start: 0.6808 (t0) cc_final: 0.6479 (p0) REVERT: C 28 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7631 (tm-30) REVERT: C 90 LEU cc_start: 0.7887 (tp) cc_final: 0.7663 (tp) REVERT: C 91 GLN cc_start: 0.7925 (mt0) cc_final: 0.7579 (pt0) REVERT: C 229 GLU cc_start: 0.7743 (pt0) cc_final: 0.7262 (tt0) REVERT: C 239 MET cc_start: 0.4511 (ttt) cc_final: 0.4251 (ttt) REVERT: C 271 THR cc_start: 0.7581 (p) cc_final: 0.6088 (p) REVERT: C 273 GLU cc_start: 0.8810 (pt0) cc_final: 0.8432 (pm20) REVERT: C 274 GLN cc_start: 0.6242 (pt0) cc_final: 0.5852 (pt0) REVERT: D 7 ILE cc_start: 0.8335 (mt) cc_final: 0.8087 (mm) REVERT: D 24 GLU cc_start: 0.8158 (tt0) cc_final: 0.7893 (tm-30) REVERT: D 26 CYS cc_start: 0.7985 (m) cc_final: 0.7289 (m) REVERT: D 27 GLN cc_start: 0.7414 (mt0) cc_final: 0.6768 (mt0) REVERT: D 28 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7155 (tm-30) REVERT: D 30 CYS cc_start: 0.7517 (p) cc_final: 0.7281 (p) REVERT: D 33 ARG cc_start: 0.7699 (mtp180) cc_final: 0.7405 (tpp80) REVERT: D 35 TRP cc_start: 0.6334 (p90) cc_final: 0.5883 (p90) REVERT: D 36 ASP cc_start: 0.7883 (m-30) cc_final: 0.7538 (m-30) REVERT: D 44 LEU cc_start: 0.8944 (mp) cc_final: 0.8734 (mt) REVERT: D 60 ASN cc_start: 0.8185 (m-40) cc_final: 0.7898 (m110) REVERT: D 73 ASP cc_start: 0.6200 (t0) cc_final: 0.5510 (t0) REVERT: D 92 GLN cc_start: 0.7683 (tt0) cc_final: 0.7459 (mt0) REVERT: D 105 VAL cc_start: 0.8509 (t) cc_final: 0.8091 (m) REVERT: D 109 GLU cc_start: 0.6980 (mp0) cc_final: 0.6543 (mp0) REVERT: D 131 GLN cc_start: 0.8034 (tt0) cc_final: 0.7558 (tt0) REVERT: D 132 MET cc_start: 0.7049 (mmm) cc_final: 0.6579 (mmm) REVERT: D 133 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7208 (mt-10) REVERT: D 135 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7551 (mm-30) REVERT: D 138 LYS cc_start: 0.8927 (mttt) cc_final: 0.8273 (mtpp) REVERT: D 139 GLU cc_start: 0.7404 (tp30) cc_final: 0.7051 (tp30) REVERT: D 146 HIS cc_start: 0.8268 (m170) cc_final: 0.7952 (m-70) REVERT: D 153 LYS cc_start: 0.8219 (mttt) cc_final: 0.7860 (mttt) REVERT: D 182 GLU cc_start: 0.8064 (tt0) cc_final: 0.7823 (tt0) REVERT: D 186 GLU cc_start: 0.7421 (tt0) cc_final: 0.7074 (tp30) REVERT: D 195 HIS cc_start: 0.7055 (m90) cc_final: 0.6589 (m90) REVERT: D 204 ASP cc_start: 0.7274 (t0) cc_final: 0.6389 (m-30) REVERT: D 220 LEU cc_start: 0.7991 (tt) cc_final: 0.7649 (mm) REVERT: D 226 GLN cc_start: 0.8008 (mp10) cc_final: 0.7430 (mp10) REVERT: D 242 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7472 (mt-10) REVERT: D 245 LEU cc_start: 0.8611 (mt) cc_final: 0.7761 (mt) REVERT: D 247 TYR cc_start: 0.6791 (m-10) cc_final: 0.6258 (m-10) REVERT: D 272 ARG cc_start: 0.7626 (mmm160) cc_final: 0.7356 (mmm160) REVERT: D 278 LEU cc_start: 0.8365 (mt) cc_final: 0.7958 (mt) REVERT: D 281 GLU cc_start: 0.6521 (tp30) cc_final: 0.6223 (tp30) REVERT: D 312 TYR cc_start: 0.5145 (m-10) cc_final: 0.4638 (m-80) REVERT: D 328 SER cc_start: 0.7740 (t) cc_final: 0.7059 (p) REVERT: D 331 PHE cc_start: 0.7569 (m-10) cc_final: 0.7328 (m-10) REVERT: D 345 TRP cc_start: 0.6405 (m100) cc_final: 0.4901 (m100) REVERT: D 404 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7991 (mm-30) REVERT: D 416 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7924 (mtm-85) REVERT: D 443 TRP cc_start: 0.8208 (t60) cc_final: 0.7868 (t60) REVERT: D 456 ARG cc_start: 0.8281 (mtp180) cc_final: 0.7815 (mmm-85) REVERT: D 461 ARG cc_start: 0.6751 (ttm-80) cc_final: 0.6524 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 408 average time/residue: 0.1874 time to fit residues: 107.3242 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 : 0.570 ------------------------------------------------------------------------------- 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: 0.6980 chunk 186 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 103 optimal weight: 0.0060 chunk 75 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 145 optimal weight: 0.0270 chunk 202 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 60 ASN A 100 HIS ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 131 GLN B 203 HIS B 274 GLN C 60 ASN C 274 GLN ** C 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN D 381 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.229877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.172348 restraints weight = 45510.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.177507 restraints weight = 20786.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.180652 restraints weight = 12292.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.182457 restraints weight = 8700.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.183710 restraints weight = 7038.376| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20302 Z= 0.135 Angle : 0.541 10.410 28362 Z= 0.304 Chirality : 0.037 0.265 3108 Planarity : 0.004 0.039 3020 Dihedral : 22.874 88.299 4268 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.20), residues: 1936 helix: 2.27 (0.17), residues: 919 sheet: 0.12 (0.30), residues: 289 loop : 1.26 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 323 TYR 0.014 0.001 TYR C 216 PHE 0.016 0.001 PHE B 348 TRP 0.033 0.002 TRP D 443 HIS 0.008 0.001 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00280 (20286) covalent geometry : angle 0.53596 (28338) hydrogen bonds : bond 0.03649 ( 1052) hydrogen bonds : angle 3.78250 ( 2777) metal coordination : bond 0.00273 ( 16) metal coordination : angle 2.54326 ( 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 411 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.592 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: A 21 ARG cc_start: 0.7927 (mtp180) cc_final: 0.7254 (tpm170) REVERT: A 24 GLU cc_start: 0.8603 (tp30) cc_final: 0.7754 (tp30) REVERT: A 27 GLN cc_start: 0.8620 (mm110) cc_final: 0.8140 (mm-40) REVERT: A 58 ARG cc_start: 0.7762 (ttt180) cc_final: 0.7292 (ttm170) REVERT: A 59 PRO cc_start: 0.7944 (Cg_endo) cc_final: 0.7655 (Cg_exo) REVERT: A 60 ASN cc_start: 0.7705 (t160) cc_final: 0.7286 (t0) REVERT: A 61 LEU cc_start: 0.7887 (tp) cc_final: 0.7353 (tp) REVERT: A 92 GLN cc_start: 0.8313 (tt0) cc_final: 0.8047 (tt0) REVERT: A 132 MET cc_start: 0.7971 (mtm) cc_final: 0.7463 (mtm) REVERT: A 134 LEU cc_start: 0.8697 (tp) cc_final: 0.8357 (pp) REVERT: A 183 ARG cc_start: 0.7380 (tpp-160) cc_final: 0.7170 (mpp80) REVERT: A 237 ARG cc_start: 0.4047 (ttp-110) cc_final: 0.2414 (ptm160) REVERT: B 8 ARG cc_start: 0.7453 (ttp80) cc_final: 0.7248 (ttp80) REVERT: B 11 ARG cc_start: 0.6930 (mtt-85) cc_final: 0.6580 (tpp80) REVERT: B 21 ARG cc_start: 0.7858 (ttt-90) cc_final: 0.6700 (ptm-80) REVERT: B 24 GLU cc_start: 0.7703 (pt0) cc_final: 0.7226 (pp20) REVERT: B 28 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7274 (tp-100) REVERT: B 50 VAL cc_start: 0.8458 (t) cc_final: 0.8112 (p) REVERT: B 56 LYS cc_start: 0.7917 (mtmm) cc_final: 0.7377 (mtmm) REVERT: B 95 HIS cc_start: 0.6898 (m90) cc_final: 0.5958 (m90) REVERT: B 98 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6748 (mt-10) REVERT: B 99 ASP cc_start: 0.7803 (m-30) cc_final: 0.7238 (m-30) REVERT: B 100 HIS cc_start: 0.7840 (m170) cc_final: 0.7508 (m170) REVERT: B 101 LYS cc_start: 0.8750 (mptt) cc_final: 0.8311 (mptt) REVERT: B 102 LYS cc_start: 0.8098 (mptt) cc_final: 0.7543 (mptt) REVERT: B 103 LEU cc_start: 0.8243 (tp) cc_final: 0.7945 (mt) REVERT: B 109 GLU cc_start: 0.6438 (mt-10) cc_final: 0.6176 (mt-10) REVERT: B 138 LYS cc_start: 0.7890 (mttt) cc_final: 0.7262 (ttmm) REVERT: B 142 ARG cc_start: 0.7869 (ttp-110) cc_final: 0.7611 (tmm-80) REVERT: B 143 SER cc_start: 0.8393 (t) cc_final: 0.7580 (p) REVERT: B 148 ASN cc_start: 0.8073 (m-40) cc_final: 0.7750 (t0) REVERT: B 149 ILE cc_start: 0.8533 (mt) cc_final: 0.8226 (mm) REVERT: B 174 LEU cc_start: 0.7362 (mt) cc_final: 0.7065 (mp) REVERT: B 189 HIS cc_start: 0.7115 (m90) cc_final: 0.6804 (m90) REVERT: B 196 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6858 (mm-30) REVERT: B 199 HIS cc_start: 0.7526 (p-80) cc_final: 0.7258 (p-80) REVERT: B 214 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7775 (ttmt) REVERT: B 236 LYS cc_start: 0.7835 (tttt) cc_final: 0.7574 (tttp) REVERT: B 298 LEU cc_start: 0.8158 (mt) cc_final: 0.7365 (pp) REVERT: B 302 LEU cc_start: 0.7842 (tp) cc_final: 0.7287 (tp) REVERT: B 325 ARG cc_start: 0.6322 (mtm110) cc_final: 0.5892 (mtp85) REVERT: B 329 MET cc_start: 0.7160 (mmt) cc_final: 0.6609 (mmt) REVERT: B 334 HIS cc_start: 0.7026 (p90) cc_final: 0.6490 (p90) REVERT: B 342 MET cc_start: 0.6716 (ttp) cc_final: 0.6050 (ttp) REVERT: B 346 ASP cc_start: 0.7971 (m-30) cc_final: 0.7457 (m-30) REVERT: B 367 TRP cc_start: 0.8000 (t-100) cc_final: 0.7601 (t-100) REVERT: B 376 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7874 (mt-10) REVERT: B 383 GLU cc_start: 0.8215 (pt0) cc_final: 0.7594 (pp20) REVERT: B 384 LEU cc_start: 0.8840 (mt) cc_final: 0.8614 (mt) REVERT: B 386 ASP cc_start: 0.7562 (t70) cc_final: 0.7092 (t70) REVERT: B 409 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7801 (mmp80) REVERT: B 413 LEU cc_start: 0.8459 (mm) cc_final: 0.8191 (mm) REVERT: B 416 ARG cc_start: 0.7678 (mtm-85) cc_final: 0.7299 (mtm-85) REVERT: B 448 THR cc_start: 0.8358 (p) cc_final: 0.7990 (p) REVERT: B 451 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7521 (mtmm) REVERT: B 456 ARG cc_start: 0.7856 (mtp180) cc_final: 0.7299 (ttm110) REVERT: C 22 GLN cc_start: 0.8089 (mt0) cc_final: 0.7507 (mt0) REVERT: C 24 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7111 (tm-30) REVERT: C 28 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7624 (tm-30) REVERT: C 90 LEU cc_start: 0.8021 (tp) cc_final: 0.7819 (tp) REVERT: C 91 GLN cc_start: 0.7997 (mt0) cc_final: 0.7623 (pt0) REVERT: C 229 GLU cc_start: 0.7757 (pt0) cc_final: 0.7440 (tt0) REVERT: C 239 MET cc_start: 0.4570 (ttt) cc_final: 0.4323 (ttt) REVERT: C 273 GLU cc_start: 0.8797 (pt0) cc_final: 0.8355 (pm20) REVERT: D 7 ILE cc_start: 0.8403 (mt) cc_final: 0.8177 (mm) REVERT: D 24 GLU cc_start: 0.8135 (tt0) cc_final: 0.7858 (tp30) REVERT: D 26 CYS cc_start: 0.7922 (m) cc_final: 0.7121 (m) REVERT: D 28 GLN cc_start: 0.7479 (tm-30) cc_final: 0.6944 (tm-30) REVERT: D 36 ASP cc_start: 0.7871 (m-30) cc_final: 0.7610 (m-30) REVERT: D 57 ARG cc_start: 0.7103 (mtt90) cc_final: 0.6838 (ttm110) REVERT: D 60 ASN cc_start: 0.8116 (m-40) cc_final: 0.7808 (m110) REVERT: D 64 TRP cc_start: 0.7564 (m100) cc_final: 0.7039 (m100) REVERT: D 68 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7415 (mm-30) REVERT: D 105 VAL cc_start: 0.8439 (t) cc_final: 0.8060 (m) REVERT: D 109 GLU cc_start: 0.6989 (mp0) cc_final: 0.6607 (mp0) REVERT: D 129 VAL cc_start: 0.8456 (m) cc_final: 0.8043 (p) REVERT: D 131 GLN cc_start: 0.7935 (tt0) cc_final: 0.7442 (tt0) REVERT: D 132 MET cc_start: 0.7012 (mmm) cc_final: 0.6569 (mmm) REVERT: D 133 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7090 (mt-10) REVERT: D 135 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7531 (mm-30) REVERT: D 138 LYS cc_start: 0.8980 (mttt) cc_final: 0.8290 (mtpp) REVERT: D 142 ARG cc_start: 0.7586 (ttm170) cc_final: 0.7338 (ttm110) REVERT: D 146 HIS cc_start: 0.8292 (m170) cc_final: 0.7962 (m-70) REVERT: D 153 LYS cc_start: 0.8194 (mttt) cc_final: 0.7859 (mttt) REVERT: D 182 GLU cc_start: 0.7971 (tt0) cc_final: 0.7737 (tt0) REVERT: D 186 GLU cc_start: 0.7372 (tt0) cc_final: 0.7041 (tp30) REVERT: D 195 HIS cc_start: 0.7019 (m90) cc_final: 0.6352 (m90) REVERT: D 204 ASP cc_start: 0.7204 (t0) cc_final: 0.6323 (m-30) REVERT: D 216 TYR cc_start: 0.7369 (t80) cc_final: 0.7169 (t80) REVERT: D 220 LEU cc_start: 0.7944 (tt) cc_final: 0.7585 (mm) REVERT: D 226 GLN cc_start: 0.7763 (mp10) cc_final: 0.7238 (mp10) REVERT: D 242 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7654 (mt-10) REVERT: D 245 LEU cc_start: 0.8594 (mt) cc_final: 0.7880 (mt) REVERT: D 247 TYR cc_start: 0.6777 (m-10) cc_final: 0.6406 (m-10) REVERT: D 272 ARG cc_start: 0.7525 (mmm160) cc_final: 0.7166 (mmm160) REVERT: D 281 GLU cc_start: 0.6432 (tp30) cc_final: 0.6150 (tp30) REVERT: D 312 TYR cc_start: 0.5164 (m-10) cc_final: 0.4822 (m-80) REVERT: D 328 SER cc_start: 0.7777 (t) cc_final: 0.7122 (p) REVERT: D 342 MET cc_start: 0.7022 (ptt) cc_final: 0.6775 (ptt) REVERT: D 345 TRP cc_start: 0.6331 (m100) cc_final: 0.5262 (m100) REVERT: D 404 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7957 (mm-30) REVERT: D 419 GLU cc_start: 0.8497 (tt0) cc_final: 0.8292 (tm-30) REVERT: D 461 ARG cc_start: 0.6751 (ttm-80) cc_final: 0.6456 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.1903 time to fit residues: 109.8223 Evaluate side-chains 383 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 84 optimal weight: 0.0070 chunk 99 optimal weight: 20.0000 chunk 142 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 overall best weight: 1.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN B 274 GLN C 60 ASN C 274 GLN C 485 HIS D 352 GLN D 446 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.227232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.168038 restraints weight = 45132.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.173179 restraints weight = 20893.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.176375 restraints weight = 12565.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.178307 restraints weight = 8941.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.179386 restraints weight = 7224.763| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20302 Z= 0.167 Angle : 0.543 6.764 28362 Z= 0.308 Chirality : 0.037 0.162 3108 Planarity : 0.004 0.050 3020 Dihedral : 22.876 89.374 4268 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.19 % Allowed : 2.18 % 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: 2.15 (0.20), residues: 1936 helix: 2.21 (0.17), residues: 919 sheet: -0.02 (0.30), residues: 288 loop : 1.24 (0.26), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 323 TYR 0.017 0.002 TYR C 154 PHE 0.021 0.001 PHE C 118 TRP 0.027 0.002 TRP D 443 HIS 0.006 0.001 HIS C 485 Details of bonding type rmsd covalent geometry : bond 0.00349 (20286) covalent geometry : angle 0.53933 (28338) hydrogen bonds : bond 0.03945 ( 1052) hydrogen bonds : angle 3.77784 ( 2777) metal coordination : bond 0.00360 ( 16) metal coordination : angle 2.15298 ( 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 392 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 389 time to evaluate : 0.552 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: 0.7953 (mtp180) cc_final: 0.7189 (tpp-160) REVERT: A 24 GLU cc_start: 0.8549 (tp30) cc_final: 0.7860 (tp30) REVERT: A 27 GLN cc_start: 0.8639 (mm110) cc_final: 0.8233 (mm-40) REVERT: A 60 ASN cc_start: 0.7934 (t160) cc_final: 0.7679 (t0) REVERT: A 61 LEU cc_start: 0.8079 (tp) cc_final: 0.7778 (tp) REVERT: A 92 GLN cc_start: 0.8383 (tt0) cc_final: 0.8062 (tt0) REVERT: A 132 MET cc_start: 0.7966 (mtm) cc_final: 0.7453 (mtm) REVERT: A 134 LEU cc_start: 0.8712 (tp) cc_final: 0.8448 (pp) REVERT: A 138 LYS cc_start: 0.8642 (mttm) cc_final: 0.8103 (mttp) REVERT: A 183 ARG cc_start: 0.7481 (tpp-160) cc_final: 0.7247 (mpp80) REVERT: A 228 ARG cc_start: 0.7113 (mtt90) cc_final: 0.6726 (mtm180) REVERT: A 237 ARG cc_start: 0.4354 (ttp-110) cc_final: 0.1976 (ttt180) REVERT: A 303 PHE cc_start: 0.7416 (m-10) cc_final: 0.7106 (m-80) REVERT: B 8 ARG cc_start: 0.7351 (ttp80) cc_final: 0.7100 (ttp80) REVERT: B 11 ARG cc_start: 0.7083 (mtt-85) cc_final: 0.6790 (tpp80) REVERT: B 21 ARG cc_start: 0.7830 (ttt-90) cc_final: 0.7326 (tpt90) REVERT: B 24 GLU cc_start: 0.7796 (pt0) cc_final: 0.7445 (pt0) REVERT: B 37 VAL cc_start: 0.8091 (t) cc_final: 0.7623 (m) REVERT: B 51 ASP cc_start: 0.8124 (t0) cc_final: 0.7893 (t70) REVERT: B 67 PHE cc_start: 0.7981 (m-80) cc_final: 0.7626 (m-10) REVERT: B 95 HIS cc_start: 0.6913 (m90) cc_final: 0.5991 (m90) REVERT: B 98 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6687 (mt-10) REVERT: B 99 ASP cc_start: 0.7881 (m-30) cc_final: 0.7311 (m-30) REVERT: B 101 LYS cc_start: 0.8758 (mptt) cc_final: 0.8294 (mptt) REVERT: B 102 LYS cc_start: 0.8102 (mptt) cc_final: 0.7541 (mptt) REVERT: B 109 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6172 (mt-10) REVERT: B 133 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7553 (tp30) REVERT: B 134 LEU cc_start: 0.7829 (tt) cc_final: 0.7513 (tt) REVERT: B 138 LYS cc_start: 0.7957 (mttt) cc_final: 0.7356 (ttmm) REVERT: B 143 SER cc_start: 0.8411 (t) cc_final: 0.8109 (p) REVERT: B 148 ASN cc_start: 0.8118 (m-40) cc_final: 0.7739 (t0) REVERT: B 149 ILE cc_start: 0.8549 (mt) cc_final: 0.8198 (mm) REVERT: B 186 GLU cc_start: 0.7401 (pt0) cc_final: 0.6876 (pt0) REVERT: B 189 HIS cc_start: 0.7175 (m90) cc_final: 0.6716 (m90) REVERT: B 196 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6947 (mm-30) REVERT: B 207 ARG cc_start: 0.7250 (mtm-85) cc_final: 0.6892 (mtm-85) REVERT: B 214 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7853 (ttmt) REVERT: B 228 ARG cc_start: 0.6268 (mpp80) cc_final: 0.6033 (mpp80) REVERT: B 236 LYS cc_start: 0.7785 (tttt) cc_final: 0.7492 (tttp) REVERT: B 247 TYR cc_start: 0.7222 (m-10) cc_final: 0.6541 (m-80) REVERT: B 268 PRO cc_start: 0.8091 (Cg_endo) cc_final: 0.7840 (Cg_exo) REVERT: B 289 LYS cc_start: 0.8695 (mppt) cc_final: 0.8367 (mppt) REVERT: B 302 LEU cc_start: 0.7798 (tp) cc_final: 0.7309 (tp) REVERT: B 325 ARG cc_start: 0.6512 (mtm110) cc_final: 0.6147 (mtp85) REVERT: B 329 MET cc_start: 0.7362 (mmt) cc_final: 0.6757 (mmt) REVERT: B 334 HIS cc_start: 0.7169 (p90) cc_final: 0.6657 (p90) REVERT: B 367 TRP cc_start: 0.8219 (t-100) cc_final: 0.7718 (t-100) REVERT: B 376 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7887 (mt-10) REVERT: B 383 GLU cc_start: 0.8264 (pt0) cc_final: 0.7695 (pp20) REVERT: B 384 LEU cc_start: 0.8871 (mt) cc_final: 0.8587 (mt) REVERT: B 386 ASP cc_start: 0.7794 (t70) cc_final: 0.7291 (t70) REVERT: B 389 SER cc_start: 0.9234 (m) cc_final: 0.8772 (p) REVERT: B 391 ILE cc_start: 0.7774 (mt) cc_final: 0.7252 (mt) REVERT: B 413 LEU cc_start: 0.8512 (mm) cc_final: 0.8238 (mm) REVERT: B 416 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7379 (mtm-85) REVERT: B 448 THR cc_start: 0.8273 (p) cc_final: 0.7917 (p) REVERT: B 451 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7690 (mtmm) REVERT: B 456 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7416 (ttm110) REVERT: C 22 GLN cc_start: 0.8009 (mt0) cc_final: 0.7386 (mt0) REVERT: C 24 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7202 (tm-30) REVERT: C 28 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 30 CYS cc_start: 0.8969 (m) cc_final: 0.8717 (m) REVERT: C 90 LEU cc_start: 0.8153 (tp) cc_final: 0.7945 (tp) REVERT: C 91 GLN cc_start: 0.8078 (mt0) cc_final: 0.7665 (pt0) REVERT: C 98 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7723 (pp20) REVERT: C 99 ASP cc_start: 0.8020 (m-30) cc_final: 0.7691 (m-30) REVERT: C 100 HIS cc_start: 0.7669 (m90) cc_final: 0.7141 (m90) REVERT: C 229 GLU cc_start: 0.7787 (pt0) cc_final: 0.7467 (tp30) REVERT: C 239 MET cc_start: 0.4695 (ttt) cc_final: 0.4331 (ttt) REVERT: C 273 GLU cc_start: 0.8743 (pt0) cc_final: 0.8346 (pm20) REVERT: D 7 ILE cc_start: 0.8272 (mt) cc_final: 0.8014 (mm) REVERT: D 9 LEU cc_start: 0.8255 (tt) cc_final: 0.7907 (mt) REVERT: D 20 GLU cc_start: 0.7656 (mp0) cc_final: 0.7194 (pm20) REVERT: D 24 GLU cc_start: 0.8225 (tt0) cc_final: 0.7778 (tp30) REVERT: D 26 CYS cc_start: 0.7790 (m) cc_final: 0.7192 (m) REVERT: D 28 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7017 (tm-30) REVERT: D 33 ARG cc_start: 0.7892 (tpp80) cc_final: 0.7598 (tpp80) REVERT: D 35 TRP cc_start: 0.6113 (p90) cc_final: 0.5764 (p90) REVERT: D 36 ASP cc_start: 0.7923 (m-30) cc_final: 0.7686 (m-30) REVERT: D 57 ARG cc_start: 0.7064 (mtt90) cc_final: 0.6861 (ttm110) REVERT: D 79 ARG cc_start: 0.6795 (mtm110) cc_final: 0.6260 (mtm110) REVERT: D 92 GLN cc_start: 0.7707 (mt0) cc_final: 0.7455 (mt0) REVERT: D 105 VAL cc_start: 0.8461 (t) cc_final: 0.8167 (m) REVERT: D 109 GLU cc_start: 0.7000 (mp0) cc_final: 0.6577 (mp0) REVERT: D 129 VAL cc_start: 0.8525 (m) cc_final: 0.8187 (p) REVERT: D 133 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7201 (mt-10) REVERT: D 135 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7374 (mm-30) REVERT: D 138 LYS cc_start: 0.8971 (mttt) cc_final: 0.8369 (mttp) REVERT: D 139 GLU cc_start: 0.7465 (tp30) cc_final: 0.6989 (tp30) REVERT: D 153 LYS cc_start: 0.8214 (mttt) cc_final: 0.7852 (mttt) REVERT: D 163 TYR cc_start: 0.6037 (m-10) cc_final: 0.5678 (m-10) REVERT: D 164 LEU cc_start: 0.7977 (tp) cc_final: 0.7730 (tp) REVERT: D 182 GLU cc_start: 0.7942 (tt0) cc_final: 0.7707 (tt0) REVERT: D 186 GLU cc_start: 0.7458 (tt0) cc_final: 0.7097 (tp30) REVERT: D 189 HIS cc_start: 0.5976 (t-90) cc_final: 0.5582 (t-90) REVERT: D 195 HIS cc_start: 0.7057 (m90) cc_final: 0.6326 (m90) REVERT: D 220 LEU cc_start: 0.7910 (tt) cc_final: 0.7614 (mm) REVERT: D 226 GLN cc_start: 0.8073 (mp10) cc_final: 0.7270 (mp10) REVERT: D 242 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7666 (mt-10) REVERT: D 245 LEU cc_start: 0.8487 (mt) cc_final: 0.7675 (mt) REVERT: D 247 TYR cc_start: 0.6939 (m-10) cc_final: 0.6501 (m-10) REVERT: D 272 ARG cc_start: 0.7668 (mmm160) cc_final: 0.7230 (mmm160) REVERT: D 278 LEU cc_start: 0.8361 (mt) cc_final: 0.8139 (mt) REVERT: D 279 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7792 (tpp80) REVERT: D 281 GLU cc_start: 0.6579 (tp30) cc_final: 0.6192 (tp30) REVERT: D 309 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8088 (mm-30) REVERT: D 312 TYR cc_start: 0.5314 (m-10) cc_final: 0.4826 (m-80) REVERT: D 328 SER cc_start: 0.7690 (t) cc_final: 0.7228 (p) REVERT: D 345 TRP cc_start: 0.6647 (m100) cc_final: 0.5306 (m100) REVERT: D 381 ASN cc_start: 0.7659 (m110) cc_final: 0.7448 (m110) REVERT: D 404 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7934 (mm-30) REVERT: D 409 ARG cc_start: 0.8069 (tpt-90) cc_final: 0.7525 (mtp85) REVERT: D 416 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7889 (mtm-85) outliers start: 3 outliers final: 1 residues processed: 390 average time/residue: 0.1847 time to fit residues: 101.4733 Evaluate side-chains 359 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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: 20.0000 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 30.0000 chunk 163 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 274 GLN B 446 GLN C 89 HIS C 131 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN D 89 HIS D 100 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.223787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.177651 restraints weight = 44423.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.178458 restraints weight = 25447.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.178069 restraints weight = 18624.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.178355 restraints weight = 13723.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.178819 restraints weight = 12493.130| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20302 Z= 0.263 Angle : 0.624 8.291 28362 Z= 0.356 Chirality : 0.042 0.210 3108 Planarity : 0.005 0.096 3020 Dihedral : 22.979 89.984 4268 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 1936 helix: 1.83 (0.17), residues: 916 sheet: -0.17 (0.29), residues: 282 loop : 0.98 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 173 TYR 0.026 0.002 TYR C 154 PHE 0.023 0.002 PHE D 112 TRP 0.065 0.002 TRP D 35 HIS 0.007 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00547 (20286) covalent geometry : angle 0.61908 (28338) hydrogen bonds : bond 0.05078 ( 1052) hydrogen bonds : angle 4.14803 ( 2777) metal coordination : bond 0.00708 ( 16) metal coordination : angle 2.64054 ( 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 387 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.591 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: A 21 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7241 (tpp-160) REVERT: A 24 GLU cc_start: 0.8321 (tp30) cc_final: 0.7748 (tp30) REVERT: A 27 GLN cc_start: 0.8700 (mm110) cc_final: 0.8206 (mm-40) REVERT: A 60 ASN cc_start: 0.8040 (t0) cc_final: 0.7822 (t0) REVERT: A 61 LEU cc_start: 0.8138 (tp) cc_final: 0.7815 (tp) REVERT: A 132 MET cc_start: 0.8137 (mtm) cc_final: 0.7611 (mtm) REVERT: A 134 LEU cc_start: 0.8555 (tp) cc_final: 0.8324 (pp) REVERT: A 138 LYS cc_start: 0.8595 (mttm) cc_final: 0.8076 (tttp) REVERT: A 228 ARG cc_start: 0.6894 (mtt90) cc_final: 0.6634 (mtm180) REVERT: A 237 ARG cc_start: 0.4657 (ttp-110) cc_final: 0.1882 (ttt90) REVERT: A 303 PHE cc_start: 0.6770 (m-10) cc_final: 0.6477 (m-80) REVERT: B 11 ARG cc_start: 0.7362 (mtt-85) cc_final: 0.6883 (tpp80) REVERT: B 21 ARG cc_start: 0.8121 (ttt-90) cc_final: 0.7528 (mmm160) REVERT: B 28 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7194 (tp-100) REVERT: B 56 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7323 (mtmm) REVERT: B 67 PHE cc_start: 0.8139 (m-80) cc_final: 0.7751 (m-10) REVERT: B 95 HIS cc_start: 0.7182 (m90) cc_final: 0.6509 (m90) REVERT: B 98 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7020 (mt-10) REVERT: B 101 LYS cc_start: 0.8786 (mptt) cc_final: 0.8332 (mptt) REVERT: B 102 LYS cc_start: 0.8225 (mptt) cc_final: 0.7609 (mptt) REVERT: B 109 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6306 (mt-10) REVERT: B 131 GLN cc_start: 0.7561 (tt0) cc_final: 0.7266 (tt0) REVERT: B 138 LYS cc_start: 0.7922 (mttt) cc_final: 0.7331 (ttmm) REVERT: B 142 ARG cc_start: 0.7926 (tmm-80) cc_final: 0.7346 (tmm-80) REVERT: B 143 SER cc_start: 0.8370 (t) cc_final: 0.8126 (p) REVERT: B 148 ASN cc_start: 0.8344 (m-40) cc_final: 0.7720 (t0) REVERT: B 149 ILE cc_start: 0.8621 (mt) cc_final: 0.8282 (mm) REVERT: B 196 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 236 LYS cc_start: 0.7803 (tttt) cc_final: 0.7593 (tttp) REVERT: B 247 TYR cc_start: 0.7344 (m-10) cc_final: 0.6627 (m-80) REVERT: B 267 GLU cc_start: 0.8397 (pm20) cc_final: 0.8163 (pm20) REVERT: B 274 GLN cc_start: 0.7334 (pt0) cc_final: 0.6983 (pt0) REVERT: B 279 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7473 (mtt180) REVERT: B 302 LEU cc_start: 0.7442 (tp) cc_final: 0.6901 (tp) REVERT: B 325 ARG cc_start: 0.6885 (mtm110) cc_final: 0.6499 (mtp85) REVERT: B 329 MET cc_start: 0.7396 (mmt) cc_final: 0.6791 (mmt) REVERT: B 334 HIS cc_start: 0.7425 (p90) cc_final: 0.6960 (p90) REVERT: B 342 MET cc_start: 0.7024 (ttp) cc_final: 0.6353 (tpp) REVERT: B 367 TRP cc_start: 0.8310 (t-100) cc_final: 0.7695 (t-100) REVERT: B 379 GLU cc_start: 0.8183 (pt0) cc_final: 0.7650 (pp20) REVERT: B 383 GLU cc_start: 0.8077 (pt0) cc_final: 0.7558 (pp20) REVERT: B 386 ASP cc_start: 0.7750 (t70) cc_final: 0.7121 (t0) REVERT: B 389 SER cc_start: 0.9171 (m) cc_final: 0.8648 (p) REVERT: B 391 ILE cc_start: 0.7890 (mt) cc_final: 0.6839 (mt) REVERT: B 413 LEU cc_start: 0.8505 (mm) cc_final: 0.8212 (mm) REVERT: B 416 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7411 (mtm-85) REVERT: B 454 TRP cc_start: 0.7759 (t60) cc_final: 0.7483 (t60) REVERT: B 456 ARG cc_start: 0.7743 (mtp180) cc_final: 0.7326 (ttm110) REVERT: C 22 GLN cc_start: 0.8004 (mt0) cc_final: 0.7477 (mt0) REVERT: C 27 GLN cc_start: 0.8464 (mm110) cc_final: 0.8123 (mm110) REVERT: C 28 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7509 (tm-30) REVERT: C 30 CYS cc_start: 0.8934 (m) cc_final: 0.8613 (m) REVERT: C 90 LEU cc_start: 0.8288 (tp) cc_final: 0.7988 (tp) REVERT: C 100 HIS cc_start: 0.7445 (m90) cc_final: 0.6931 (m90) REVERT: C 229 GLU cc_start: 0.7660 (pt0) cc_final: 0.7340 (tt0) REVERT: C 271 THR cc_start: 0.7214 (p) cc_final: 0.6088 (p) REVERT: C 273 GLU cc_start: 0.8661 (pt0) cc_final: 0.8203 (pm20) REVERT: D 9 LEU cc_start: 0.8322 (tt) cc_final: 0.8109 (mt) REVERT: D 20 GLU cc_start: 0.7642 (mp0) cc_final: 0.6961 (pm20) REVERT: D 24 GLU cc_start: 0.8084 (tt0) cc_final: 0.7739 (tm-30) REVERT: D 28 GLN cc_start: 0.7417 (tm-30) cc_final: 0.7064 (tm-30) REVERT: D 36 ASP cc_start: 0.7862 (m-30) cc_final: 0.7433 (t0) REVERT: D 51 ASP cc_start: 0.7629 (t0) cc_final: 0.7359 (t0) REVERT: D 55 ARG cc_start: 0.7533 (tpt170) cc_final: 0.7310 (tpt170) REVERT: D 79 ARG cc_start: 0.6906 (mtm110) cc_final: 0.6540 (mtm110) REVERT: D 92 GLN cc_start: 0.7625 (mt0) cc_final: 0.7339 (mt0) REVERT: D 109 GLU cc_start: 0.6760 (mp0) cc_final: 0.6111 (mp0) REVERT: D 129 VAL cc_start: 0.8641 (m) cc_final: 0.8303 (p) REVERT: D 132 MET cc_start: 0.7431 (mmm) cc_final: 0.7231 (mmm) REVERT: D 135 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7231 (mm-30) REVERT: D 138 LYS cc_start: 0.8889 (mttt) cc_final: 0.8397 (mttp) REVERT: D 139 GLU cc_start: 0.7391 (tp30) cc_final: 0.7065 (tp30) REVERT: D 153 LYS cc_start: 0.8367 (mttt) cc_final: 0.7842 (mttt) REVERT: D 164 LEU cc_start: 0.8134 (tp) cc_final: 0.7861 (tp) REVERT: D 189 HIS cc_start: 0.6162 (t-90) cc_final: 0.5780 (t-90) REVERT: D 195 HIS cc_start: 0.7130 (m90) cc_final: 0.6360 (m90) REVERT: D 215 ASP cc_start: 0.7580 (m-30) cc_final: 0.7314 (m-30) REVERT: D 220 LEU cc_start: 0.7955 (tt) cc_final: 0.7634 (mm) REVERT: D 226 GLN cc_start: 0.8033 (mp10) cc_final: 0.7282 (mp10) REVERT: D 238 SER cc_start: 0.8687 (p) cc_final: 0.8410 (t) REVERT: D 242 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7617 (mt-10) REVERT: D 245 LEU cc_start: 0.8410 (mt) cc_final: 0.7340 (mt) REVERT: D 247 TYR cc_start: 0.7018 (m-10) cc_final: 0.6395 (m-10) REVERT: D 272 ARG cc_start: 0.7790 (mmm160) cc_final: 0.7209 (mmm160) REVERT: D 281 GLU cc_start: 0.6759 (tp30) cc_final: 0.6045 (tp30) REVERT: D 302 LEU cc_start: 0.8248 (tp) cc_final: 0.7913 (mt) REVERT: D 404 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7962 (mm-30) REVERT: D 409 ARG cc_start: 0.7970 (tpt-90) cc_final: 0.7179 (mtp85) REVERT: D 416 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.8067 (mtm-85) REVERT: D 458 MET cc_start: 0.6944 (mmt) cc_final: 0.6591 (mmt) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.1903 time to fit residues: 102.9627 Evaluate side-chains 357 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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: 0.4980 chunk 126 optimal weight: 40.0000 chunk 158 optimal weight: 0.9980 chunk 200 optimal weight: 20.0000 chunk 100 optimal weight: 0.0010 chunk 62 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 203 HIS B 221 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.226702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.168272 restraints weight = 44771.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.173393 restraints weight = 20814.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.176549 restraints weight = 12419.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.178526 restraints weight = 8874.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.179660 restraints weight = 7142.378| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20302 Z= 0.142 Angle : 0.551 7.255 28362 Z= 0.309 Chirality : 0.037 0.181 3108 Planarity : 0.005 0.116 3020 Dihedral : 22.991 89.652 4268 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.20), residues: 1936 helix: 2.08 (0.17), residues: 918 sheet: -0.10 (0.30), residues: 281 loop : 1.08 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 228 TYR 0.026 0.002 TYR D 312 PHE 0.016 0.001 PHE D 464 TRP 0.067 0.002 TRP D 35 HIS 0.014 0.001 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00298 (20286) covalent geometry : angle 0.54749 (28338) hydrogen bonds : bond 0.03757 ( 1052) hydrogen bonds : angle 3.85023 ( 2777) metal coordination : bond 0.00202 ( 16) metal coordination : angle 2.14119 ( 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 390 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.512 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: A 21 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7287 (tpm170) REVERT: A 24 GLU cc_start: 0.8420 (tp30) cc_final: 0.7824 (tp30) REVERT: A 27 GLN cc_start: 0.8668 (mm110) cc_final: 0.8134 (mm-40) REVERT: A 61 LEU cc_start: 0.8000 (tp) cc_final: 0.7684 (tp) REVERT: A 95 HIS cc_start: 0.7900 (m90) cc_final: 0.7680 (m90) REVERT: A 132 MET cc_start: 0.8194 (mtm) cc_final: 0.7573 (mtm) REVERT: A 134 LEU cc_start: 0.8692 (tp) cc_final: 0.8426 (pp) REVERT: A 135 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8215 (mm-30) REVERT: A 138 LYS cc_start: 0.8613 (mttm) cc_final: 0.8162 (tttp) REVERT: A 200 LEU cc_start: 0.6555 (tt) cc_final: 0.5927 (mp) REVERT: A 228 ARG cc_start: 0.7008 (mtt90) cc_final: 0.6679 (mtm180) REVERT: A 237 ARG cc_start: 0.4706 (ttp-110) cc_final: 0.3114 (ptm160) REVERT: A 303 PHE cc_start: 0.7411 (m-10) cc_final: 0.7138 (m-80) REVERT: B 8 ARG cc_start: 0.7333 (ttp80) cc_final: 0.7000 (ttp80) REVERT: B 11 ARG cc_start: 0.6979 (mtt-85) cc_final: 0.6646 (tpp80) REVERT: B 24 GLU cc_start: 0.7768 (pt0) cc_final: 0.7181 (pp20) REVERT: B 27 GLN cc_start: 0.7902 (tp40) cc_final: 0.7627 (tp40) REVERT: B 46 VAL cc_start: 0.7585 (p) cc_final: 0.7332 (p) REVERT: B 51 ASP cc_start: 0.8344 (t70) cc_final: 0.8041 (t0) REVERT: B 54 ASP cc_start: 0.6836 (t0) cc_final: 0.6336 (t0) REVERT: B 67 PHE cc_start: 0.8040 (m-80) cc_final: 0.7665 (m-10) REVERT: B 95 HIS cc_start: 0.7106 (m90) cc_final: 0.6057 (m90) REVERT: B 98 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6877 (mt-10) REVERT: B 99 ASP cc_start: 0.7747 (m-30) cc_final: 0.7334 (m-30) REVERT: B 101 LYS cc_start: 0.8725 (mptt) cc_final: 0.8489 (mptt) REVERT: B 102 LYS cc_start: 0.8196 (mptt) cc_final: 0.7990 (mmmt) REVERT: B 109 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6281 (mt-10) REVERT: B 125 LEU cc_start: 0.8467 (tt) cc_final: 0.8223 (pp) REVERT: B 133 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7475 (tp30) REVERT: B 138 LYS cc_start: 0.8026 (mttt) cc_final: 0.7550 (ttmm) REVERT: B 139 GLU cc_start: 0.6675 (tm-30) cc_final: 0.5769 (tm-30) REVERT: B 142 ARG cc_start: 0.7778 (tmm-80) cc_final: 0.7123 (tmm-80) REVERT: B 143 SER cc_start: 0.8318 (t) cc_final: 0.7937 (p) REVERT: B 148 ASN cc_start: 0.8167 (m-40) cc_final: 0.7621 (t0) REVERT: B 149 ILE cc_start: 0.8592 (mt) cc_final: 0.8228 (mm) REVERT: B 188 TYR cc_start: 0.7120 (t80) cc_final: 0.6835 (t80) REVERT: B 196 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7171 (mm-30) REVERT: B 199 HIS cc_start: 0.7543 (p-80) cc_final: 0.7310 (p-80) REVERT: B 236 LYS cc_start: 0.7755 (tttt) cc_final: 0.7504 (tttm) REVERT: B 247 TYR cc_start: 0.7259 (m-10) cc_final: 0.6639 (m-80) REVERT: B 279 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7375 (mtt180) REVERT: B 302 LEU cc_start: 0.7796 (tp) cc_final: 0.7326 (tp) REVERT: B 325 ARG cc_start: 0.6748 (mtm110) cc_final: 0.6391 (mtp85) REVERT: B 329 MET cc_start: 0.7391 (mmt) cc_final: 0.6793 (mmt) REVERT: B 334 HIS cc_start: 0.7367 (p90) cc_final: 0.7001 (p90) REVERT: B 342 MET cc_start: 0.7069 (ttp) cc_final: 0.6024 (tpp) REVERT: B 367 TRP cc_start: 0.8272 (t-100) cc_final: 0.7702 (t-100) REVERT: B 376 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7786 (tp30) REVERT: B 377 LEU cc_start: 0.8566 (tt) cc_final: 0.8298 (tt) REVERT: B 386 ASP cc_start: 0.7805 (t70) cc_final: 0.7115 (t0) REVERT: B 389 SER cc_start: 0.9146 (m) cc_final: 0.8571 (p) REVERT: B 391 ILE cc_start: 0.7817 (mt) cc_final: 0.6955 (mt) REVERT: B 416 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7381 (mtm-85) REVERT: B 456 ARG cc_start: 0.7750 (mtp180) cc_final: 0.7250 (ttm110) REVERT: C 22 GLN cc_start: 0.8072 (mt0) cc_final: 0.7432 (mt0) REVERT: C 28 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7663 (tm-30) REVERT: C 30 CYS cc_start: 0.8942 (m) cc_final: 0.8703 (m) REVERT: C 90 LEU cc_start: 0.8301 (tp) cc_final: 0.8057 (tp) REVERT: C 91 GLN cc_start: 0.8091 (mt0) cc_final: 0.7754 (pt0) REVERT: C 100 HIS cc_start: 0.7562 (m90) cc_final: 0.7014 (m90) REVERT: C 177 ASP cc_start: 0.3597 (p0) cc_final: 0.3361 (p0) REVERT: C 271 THR cc_start: 0.6995 (p) cc_final: 0.6674 (p) REVERT: C 273 GLU cc_start: 0.8567 (pt0) cc_final: 0.8184 (pm20) REVERT: C 274 GLN cc_start: 0.7236 (tt0) cc_final: 0.6689 (tt0) REVERT: D 7 ILE cc_start: 0.8164 (mt) cc_final: 0.7852 (mm) REVERT: D 9 LEU cc_start: 0.8207 (tt) cc_final: 0.7970 (mt) REVERT: D 20 GLU cc_start: 0.7668 (mp0) cc_final: 0.6988 (pm20) REVERT: D 24 GLU cc_start: 0.8082 (tt0) cc_final: 0.7711 (tm-30) REVERT: D 28 GLN cc_start: 0.7326 (tm-30) cc_final: 0.6979 (tm-30) REVERT: D 36 ASP cc_start: 0.7730 (m-30) cc_final: 0.7300 (t0) REVERT: D 51 ASP cc_start: 0.7483 (t0) cc_final: 0.7277 (t70) REVERT: D 57 ARG cc_start: 0.7279 (mtt90) cc_final: 0.7064 (ttm110) REVERT: D 79 ARG cc_start: 0.6893 (mtm110) cc_final: 0.6395 (mtm110) REVERT: D 92 GLN cc_start: 0.7608 (mt0) cc_final: 0.7129 (mt0) REVERT: D 105 VAL cc_start: 0.8317 (t) cc_final: 0.8102 (m) REVERT: D 109 GLU cc_start: 0.6734 (mp0) cc_final: 0.6324 (mp0) REVERT: D 129 VAL cc_start: 0.8671 (m) cc_final: 0.8333 (p) REVERT: D 132 MET cc_start: 0.7529 (mmm) cc_final: 0.7019 (mmm) REVERT: D 135 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7630 (mm-30) REVERT: D 138 LYS cc_start: 0.8904 (mttt) cc_final: 0.8352 (mtpp) REVERT: D 139 GLU cc_start: 0.7335 (tp30) cc_final: 0.7025 (tp30) REVERT: D 153 LYS cc_start: 0.8190 (mttt) cc_final: 0.7736 (mttt) REVERT: D 157 SER cc_start: 0.7815 (t) cc_final: 0.7213 (p) REVERT: D 163 TYR cc_start: 0.6206 (m-10) cc_final: 0.5937 (m-10) REVERT: D 164 LEU cc_start: 0.7982 (tp) cc_final: 0.7750 (tp) REVERT: D 182 GLU cc_start: 0.7932 (tt0) cc_final: 0.7687 (tt0) REVERT: D 189 HIS cc_start: 0.6135 (t-90) cc_final: 0.5699 (t-90) REVERT: D 220 LEU cc_start: 0.7938 (tt) cc_final: 0.7496 (mm) REVERT: D 226 GLN cc_start: 0.8005 (mp10) cc_final: 0.7128 (mp10) REVERT: D 242 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7646 (mt-10) REVERT: D 247 TYR cc_start: 0.6952 (m-10) cc_final: 0.6307 (m-10) REVERT: D 279 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7515 (tpp80) REVERT: D 302 LEU cc_start: 0.8152 (tp) cc_final: 0.7904 (tp) REVERT: D 312 TYR cc_start: 0.6089 (m-80) cc_final: 0.5631 (m-80) REVERT: D 328 SER cc_start: 0.7433 (t) cc_final: 0.6966 (p) REVERT: D 345 TRP cc_start: 0.6512 (m100) cc_final: 0.5136 (m100) REVERT: D 404 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7937 (mm-30) REVERT: D 409 ARG cc_start: 0.8224 (tpt-90) cc_final: 0.7484 (mtp85) REVERT: D 416 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8068 (mtm-85) REVERT: D 431 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7665 (mm-30) REVERT: D 456 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7703 (mmt90) REVERT: D 458 MET cc_start: 0.6862 (mmt) cc_final: 0.6465 (mmt) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.1872 time to fit residues: 102.8840 Evaluate side-chains 369 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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: 0.0020 chunk 97 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 40 optimal weight: 50.0000 chunk 172 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 63 optimal weight: 0.0670 chunk 199 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 106 optimal weight: 0.0770 chunk 93 optimal weight: 0.9980 overall best weight: 0.6286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 148 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 131 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.227396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.169310 restraints weight = 44790.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.174350 restraints weight = 20533.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.177499 restraints weight = 12258.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.179414 restraints weight = 8742.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.180554 restraints weight = 7076.997| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20302 Z= 0.137 Angle : 0.547 7.578 28362 Z= 0.304 Chirality : 0.037 0.202 3108 Planarity : 0.004 0.053 3020 Dihedral : 23.037 88.411 4268 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % 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: 2.02 (0.20), residues: 1936 helix: 2.14 (0.17), residues: 914 sheet: -0.05 (0.30), residues: 283 loop : 1.08 (0.25), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 173 TYR 0.013 0.001 TYR C 216 PHE 0.014 0.001 PHE B 348 TRP 0.069 0.002 TRP D 35 HIS 0.004 0.001 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00289 (20286) covalent geometry : angle 0.54404 (28338) hydrogen bonds : bond 0.03591 ( 1052) hydrogen bonds : angle 3.85117 ( 2777) metal coordination : bond 0.00139 ( 16) metal coordination : angle 1.93139 ( 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 379 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8025 (mtp180) cc_final: 0.7280 (tpp-160) REVERT: A 24 GLU cc_start: 0.8532 (tp30) cc_final: 0.7903 (tp30) REVERT: A 61 LEU cc_start: 0.7929 (tp) cc_final: 0.7624 (tp) REVERT: A 100 HIS cc_start: 0.7514 (m90) cc_final: 0.7305 (m90) REVERT: A 132 MET cc_start: 0.8213 (mtm) cc_final: 0.7539 (mtm) REVERT: A 134 LEU cc_start: 0.8705 (tp) cc_final: 0.8472 (pp) REVERT: A 135 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8247 (mm-30) REVERT: A 138 LYS cc_start: 0.8584 (mttm) cc_final: 0.8080 (tttp) REVERT: A 200 LEU cc_start: 0.6567 (tt) cc_final: 0.5938 (mp) REVERT: A 228 ARG cc_start: 0.7005 (mtt90) cc_final: 0.6679 (mtm180) REVERT: A 237 ARG cc_start: 0.4582 (ttp-110) cc_final: 0.3148 (ptm160) REVERT: A 303 PHE cc_start: 0.7429 (m-10) cc_final: 0.7153 (m-80) REVERT: B 8 ARG cc_start: 0.7469 (ttp80) cc_final: 0.7171 (ttp80) REVERT: B 11 ARG cc_start: 0.6885 (mtt-85) cc_final: 0.6674 (tpp80) REVERT: B 21 ARG cc_start: 0.7858 (ttt-90) cc_final: 0.7278 (ptm-80) REVERT: B 24 GLU cc_start: 0.7822 (pt0) cc_final: 0.7448 (pt0) REVERT: B 27 GLN cc_start: 0.7912 (tp40) cc_final: 0.7654 (tp40) REVERT: B 28 GLN cc_start: 0.7375 (tm-30) cc_final: 0.6775 (tm-30) REVERT: B 46 VAL cc_start: 0.7640 (p) cc_final: 0.7302 (p) REVERT: B 67 PHE cc_start: 0.7994 (m-80) cc_final: 0.7718 (m-10) REVERT: B 95 HIS cc_start: 0.6937 (m90) cc_final: 0.6057 (m90) REVERT: B 98 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6841 (mt-10) REVERT: B 99 ASP cc_start: 0.7723 (m-30) cc_final: 0.7250 (m-30) REVERT: B 101 LYS cc_start: 0.8709 (mptt) cc_final: 0.8419 (mptt) REVERT: B 102 LYS cc_start: 0.8208 (mptt) cc_final: 0.7979 (mmmt) REVERT: B 138 LYS cc_start: 0.7990 (mttt) cc_final: 0.7323 (mtpp) REVERT: B 139 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6236 (tm-30) REVERT: B 143 SER cc_start: 0.8327 (t) cc_final: 0.8106 (p) REVERT: B 148 ASN cc_start: 0.8108 (m-40) cc_final: 0.7711 (t0) REVERT: B 149 ILE cc_start: 0.8620 (mt) cc_final: 0.8271 (mm) REVERT: B 196 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7040 (mm-30) REVERT: B 226 GLN cc_start: 0.7454 (tp-100) cc_final: 0.6989 (tp40) REVERT: B 247 TYR cc_start: 0.7272 (m-10) cc_final: 0.6213 (m-80) REVERT: B 267 GLU cc_start: 0.8425 (pm20) cc_final: 0.8189 (pm20) REVERT: B 279 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7428 (mtt180) REVERT: B 281 GLU cc_start: 0.6533 (pp20) cc_final: 0.5712 (pp20) REVERT: B 284 LYS cc_start: 0.7885 (ptpp) cc_final: 0.7619 (ptpp) REVERT: B 289 LYS cc_start: 0.8624 (mppt) cc_final: 0.7949 (mmtm) REVERT: B 302 LEU cc_start: 0.7494 (tp) cc_final: 0.7069 (tp) REVERT: B 325 ARG cc_start: 0.6837 (mtm110) cc_final: 0.6374 (mtp85) REVERT: B 329 MET cc_start: 0.7313 (mmt) cc_final: 0.6737 (mmt) REVERT: B 334 HIS cc_start: 0.7330 (p90) cc_final: 0.7036 (p90) REVERT: B 339 THR cc_start: 0.8166 (p) cc_final: 0.7963 (t) REVERT: B 342 MET cc_start: 0.7233 (ttp) cc_final: 0.5878 (tpp) REVERT: B 346 ASP cc_start: 0.7994 (m-30) cc_final: 0.7470 (m-30) REVERT: B 367 TRP cc_start: 0.8254 (t-100) cc_final: 0.7680 (t-100) REVERT: B 376 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8040 (mt-10) REVERT: B 379 GLU cc_start: 0.8297 (pt0) cc_final: 0.7887 (pp20) REVERT: B 383 GLU cc_start: 0.8262 (pt0) cc_final: 0.7706 (pp20) REVERT: B 384 LEU cc_start: 0.8840 (mt) cc_final: 0.8586 (mt) REVERT: B 386 ASP cc_start: 0.7818 (t70) cc_final: 0.7114 (t0) REVERT: B 389 SER cc_start: 0.9203 (m) cc_final: 0.8691 (p) REVERT: B 391 ILE cc_start: 0.7849 (mt) cc_final: 0.7149 (mt) REVERT: B 413 LEU cc_start: 0.8530 (mm) cc_final: 0.7435 (mm) REVERT: B 416 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7057 (mtm-85) REVERT: B 456 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7348 (ttm110) REVERT: B 458 MET cc_start: 0.7501 (mpp) cc_final: 0.7089 (mpp) REVERT: C 22 GLN cc_start: 0.8047 (mt0) cc_final: 0.7494 (mt0) REVERT: C 28 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7567 (tm-30) REVERT: C 30 CYS cc_start: 0.8950 (m) cc_final: 0.8710 (m) REVERT: C 90 LEU cc_start: 0.8355 (tp) cc_final: 0.8134 (tp) REVERT: C 91 GLN cc_start: 0.8169 (mt0) cc_final: 0.7827 (pt0) REVERT: C 100 HIS cc_start: 0.7455 (m90) cc_final: 0.7034 (m90) REVERT: C 177 ASP cc_start: 0.3634 (p0) cc_final: 0.3415 (p0) REVERT: C 271 THR cc_start: 0.7281 (p) cc_final: 0.6670 (p) REVERT: C 273 GLU cc_start: 0.8655 (pt0) cc_final: 0.8178 (pm20) REVERT: C 274 GLN cc_start: 0.6676 (tt0) cc_final: 0.5518 (tt0) REVERT: D 7 ILE cc_start: 0.8318 (mt) cc_final: 0.7482 (mm) REVERT: D 9 LEU cc_start: 0.8193 (tt) cc_final: 0.7956 (mt) REVERT: D 20 GLU cc_start: 0.7671 (mp0) cc_final: 0.6962 (pm20) REVERT: D 24 GLU cc_start: 0.8078 (tt0) cc_final: 0.7619 (tp30) REVERT: D 28 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7139 (tm-30) REVERT: D 36 ASP cc_start: 0.7761 (m-30) cc_final: 0.7427 (t0) REVERT: D 42 GLU cc_start: 0.7638 (tt0) cc_final: 0.6727 (tp30) REVERT: D 51 ASP cc_start: 0.7430 (t0) cc_final: 0.7184 (t70) REVERT: D 57 ARG cc_start: 0.7164 (mtt90) cc_final: 0.6899 (ttm110) REVERT: D 79 ARG cc_start: 0.6856 (mtm110) cc_final: 0.6634 (mtm110) REVERT: D 92 GLN cc_start: 0.7641 (mt0) cc_final: 0.7094 (mt0) REVERT: D 105 VAL cc_start: 0.8283 (t) cc_final: 0.8044 (m) REVERT: D 109 GLU cc_start: 0.6646 (mp0) cc_final: 0.6027 (mp0) REVERT: D 129 VAL cc_start: 0.8616 (m) cc_final: 0.8250 (p) REVERT: D 131 GLN cc_start: 0.7996 (tt0) cc_final: 0.7678 (tp40) REVERT: D 132 MET cc_start: 0.7392 (mmm) cc_final: 0.7100 (mmm) REVERT: D 133 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7290 (mt-10) REVERT: D 135 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7601 (mm-30) REVERT: D 138 LYS cc_start: 0.8885 (mttt) cc_final: 0.8364 (mtpp) REVERT: D 139 GLU cc_start: 0.7327 (tp30) cc_final: 0.7050 (tp30) REVERT: D 157 SER cc_start: 0.7751 (t) cc_final: 0.7146 (p) REVERT: D 164 LEU cc_start: 0.7898 (tp) cc_final: 0.7694 (tp) REVERT: D 182 GLU cc_start: 0.7996 (tt0) cc_final: 0.7699 (tt0) REVERT: D 186 GLU cc_start: 0.7367 (tp30) cc_final: 0.7116 (tp30) REVERT: D 189 HIS cc_start: 0.6184 (t-90) cc_final: 0.5768 (t-90) REVERT: D 220 LEU cc_start: 0.7947 (tt) cc_final: 0.7466 (mm) REVERT: D 226 GLN cc_start: 0.8050 (mp10) cc_final: 0.7339 (mp10) REVERT: D 242 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7933 (mt-10) REVERT: D 247 TYR cc_start: 0.6975 (m-10) cc_final: 0.6605 (m-10) REVERT: D 279 ARG cc_start: 0.7887 (mmm-85) cc_final: 0.7358 (tpp80) REVERT: D 328 SER cc_start: 0.7564 (t) cc_final: 0.7056 (p) REVERT: D 345 TRP cc_start: 0.6563 (m100) cc_final: 0.5206 (m100) REVERT: D 346 ASP cc_start: 0.7455 (t0) cc_final: 0.7157 (t70) REVERT: D 404 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7893 (mm-30) REVERT: D 409 ARG cc_start: 0.8205 (tpt-90) cc_final: 0.7519 (mtp85) REVERT: D 431 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7693 (mm-30) REVERT: D 458 MET cc_start: 0.6837 (mmt) cc_final: 0.6452 (mmt) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1892 time to fit residues: 100.8735 Evaluate side-chains 364 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 60 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 160 optimal weight: 0.2980 chunk 18 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.225668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.166630 restraints weight = 44075.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.171697 restraints weight = 20426.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.174807 restraints weight = 12321.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.176695 restraints weight = 8831.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.177849 restraints weight = 7209.608| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20302 Z= 0.194 Angle : 0.581 7.897 28362 Z= 0.325 Chirality : 0.039 0.159 3108 Planarity : 0.005 0.046 3020 Dihedral : 23.007 86.841 4268 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 1.81 (0.20), residues: 1936 helix: 1.96 (0.17), residues: 912 sheet: -0.11 (0.30), residues: 286 loop : 0.99 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 207 TYR 0.010 0.001 TYR C 216 PHE 0.019 0.001 PHE B 348 TRP 0.071 0.002 TRP D 35 HIS 0.005 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00405 (20286) covalent geometry : angle 0.57861 (28338) hydrogen bonds : bond 0.04232 ( 1052) hydrogen bonds : angle 4.01596 ( 2777) metal coordination : bond 0.00423 ( 16) metal coordination : angle 1.97157 ( 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 378 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8029 (mtp180) cc_final: 0.7346 (tpm170) REVERT: A 24 GLU cc_start: 0.8340 (tp30) cc_final: 0.7769 (tp30) REVERT: A 61 LEU cc_start: 0.8091 (tp) cc_final: 0.7805 (tp) REVERT: A 100 HIS cc_start: 0.7155 (m90) cc_final: 0.6899 (m90) REVERT: A 128 THR cc_start: 0.8449 (p) cc_final: 0.7966 (p) REVERT: A 132 MET cc_start: 0.8376 (mtm) cc_final: 0.7764 (mtm) REVERT: A 134 LEU cc_start: 0.8710 (tp) cc_final: 0.8480 (pp) REVERT: A 135 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8264 (mm-30) REVERT: A 138 LYS cc_start: 0.8584 (mttm) cc_final: 0.8094 (tttp) REVERT: A 237 ARG cc_start: 0.4723 (ttp-110) cc_final: 0.2439 (ttt180) REVERT: A 303 PHE cc_start: 0.7493 (m-10) cc_final: 0.7225 (m-80) REVERT: A 337 ASN cc_start: 0.0319 (p0) cc_final: 0.0012 (p0) REVERT: B 8 ARG cc_start: 0.7549 (ttp80) cc_final: 0.7065 (ttp80) REVERT: B 21 ARG cc_start: 0.8100 (ttt-90) cc_final: 0.7504 (mmm160) REVERT: B 32 GLN cc_start: 0.8035 (mp10) cc_final: 0.7784 (mp10) REVERT: B 46 VAL cc_start: 0.7731 (p) cc_final: 0.7443 (p) REVERT: B 67 PHE cc_start: 0.8127 (m-80) cc_final: 0.7776 (m-10) REVERT: B 91 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7874 (mm-40) REVERT: B 95 HIS cc_start: 0.7195 (m90) cc_final: 0.6150 (m90) REVERT: B 98 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6963 (mt-10) REVERT: B 99 ASP cc_start: 0.7811 (m-30) cc_final: 0.7340 (m-30) REVERT: B 101 LYS cc_start: 0.8749 (mptt) cc_final: 0.8410 (mptt) REVERT: B 102 LYS cc_start: 0.8270 (mptt) cc_final: 0.8019 (mmmt) REVERT: B 138 LYS cc_start: 0.8059 (mttt) cc_final: 0.7799 (mtmt) REVERT: B 139 GLU cc_start: 0.6838 (tm-30) cc_final: 0.6327 (tm-30) REVERT: B 148 ASN cc_start: 0.8209 (m-40) cc_final: 0.7716 (t0) REVERT: B 149 ILE cc_start: 0.8648 (mt) cc_final: 0.8354 (mm) REVERT: B 196 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7133 (mm-30) REVERT: B 247 TYR cc_start: 0.7206 (m-10) cc_final: 0.6207 (m-80) REVERT: B 267 GLU cc_start: 0.8382 (pm20) cc_final: 0.8126 (pm20) REVERT: B 279 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7438 (mtt180) REVERT: B 284 LYS cc_start: 0.7782 (ptpp) cc_final: 0.7570 (ptpp) REVERT: B 289 LYS cc_start: 0.8570 (mppt) cc_final: 0.8165 (mppt) REVERT: B 302 LEU cc_start: 0.7675 (tp) cc_final: 0.7230 (tp) REVERT: B 325 ARG cc_start: 0.6997 (mtm110) cc_final: 0.6528 (mtp85) REVERT: B 329 MET cc_start: 0.7453 (mmt) cc_final: 0.6749 (mmt) REVERT: B 334 HIS cc_start: 0.7279 (p90) cc_final: 0.7031 (p90) REVERT: B 339 THR cc_start: 0.8213 (p) cc_final: 0.7873 (t) REVERT: B 342 MET cc_start: 0.7176 (ttp) cc_final: 0.5997 (tpp) REVERT: B 345 TRP cc_start: 0.7259 (m100) cc_final: 0.6812 (m100) REVERT: B 346 ASP cc_start: 0.7967 (m-30) cc_final: 0.7407 (m-30) REVERT: B 367 TRP cc_start: 0.8404 (t-100) cc_final: 0.7841 (t-100) REVERT: B 376 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8033 (mt-10) REVERT: B 379 GLU cc_start: 0.8337 (pt0) cc_final: 0.7911 (pp20) REVERT: B 383 GLU cc_start: 0.8303 (pt0) cc_final: 0.7787 (pp20) REVERT: B 384 LEU cc_start: 0.8880 (mt) cc_final: 0.8626 (mt) REVERT: B 386 ASP cc_start: 0.7918 (t70) cc_final: 0.7223 (t0) REVERT: B 389 SER cc_start: 0.9173 (m) cc_final: 0.8554 (p) REVERT: B 391 ILE cc_start: 0.7918 (mt) cc_final: 0.6977 (mt) REVERT: B 413 LEU cc_start: 0.8637 (mm) cc_final: 0.7407 (mm) REVERT: B 416 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7198 (mtm-85) REVERT: B 456 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7441 (ttm110) REVERT: B 458 MET cc_start: 0.7451 (mpp) cc_final: 0.6991 (mpp) REVERT: B 478 ASP cc_start: 0.8062 (m-30) cc_final: 0.7543 (m-30) REVERT: C 22 GLN cc_start: 0.8103 (mt0) cc_final: 0.7569 (mt0) REVERT: C 28 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7561 (tm-30) REVERT: C 89 HIS cc_start: 0.8118 (m90) cc_final: 0.7859 (m90) REVERT: C 90 LEU cc_start: 0.8398 (tp) cc_final: 0.8134 (tp) REVERT: C 100 HIS cc_start: 0.7546 (m90) cc_final: 0.7011 (m90) REVERT: C 273 GLU cc_start: 0.8740 (pt0) cc_final: 0.8284 (pm20) REVERT: D 7 ILE cc_start: 0.8143 (mt) cc_final: 0.7822 (mm) REVERT: D 9 LEU cc_start: 0.8164 (tt) cc_final: 0.7902 (mt) REVERT: D 11 ARG cc_start: 0.7763 (mtp85) cc_final: 0.7449 (mtm110) REVERT: D 20 GLU cc_start: 0.7705 (mp0) cc_final: 0.7011 (pm20) REVERT: D 24 GLU cc_start: 0.8122 (tt0) cc_final: 0.7698 (tm-30) REVERT: D 28 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7258 (tm-30) REVERT: D 36 ASP cc_start: 0.7804 (m-30) cc_final: 0.7418 (t0) REVERT: D 42 GLU cc_start: 0.7715 (tt0) cc_final: 0.6875 (tt0) REVERT: D 44 LEU cc_start: 0.8916 (mp) cc_final: 0.8638 (mp) REVERT: D 79 ARG cc_start: 0.6901 (mtm110) cc_final: 0.6652 (mtm110) REVERT: D 92 GLN cc_start: 0.7625 (mt0) cc_final: 0.7084 (mt0) REVERT: D 109 GLU cc_start: 0.6663 (mp0) cc_final: 0.6263 (mp0) REVERT: D 129 VAL cc_start: 0.8664 (m) cc_final: 0.8338 (p) REVERT: D 133 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7344 (mt-10) REVERT: D 135 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7387 (mm-30) REVERT: D 138 LYS cc_start: 0.8925 (mttt) cc_final: 0.8406 (mttp) REVERT: D 149 ILE cc_start: 0.8802 (pt) cc_final: 0.8441 (tp) REVERT: D 153 LYS cc_start: 0.8261 (mttt) cc_final: 0.7820 (mttt) REVERT: D 157 SER cc_start: 0.7803 (t) cc_final: 0.7126 (p) REVERT: D 164 LEU cc_start: 0.7979 (tp) cc_final: 0.7682 (tp) REVERT: D 182 GLU cc_start: 0.8003 (tt0) cc_final: 0.7776 (tt0) REVERT: D 186 GLU cc_start: 0.7462 (tp30) cc_final: 0.7176 (tp30) REVERT: D 189 HIS cc_start: 0.6168 (t-90) cc_final: 0.5863 (t-90) REVERT: D 195 HIS cc_start: 0.7096 (m90) cc_final: 0.6411 (m90) REVERT: D 220 LEU cc_start: 0.7905 (tt) cc_final: 0.7581 (mm) REVERT: D 226 GLN cc_start: 0.7925 (mp10) cc_final: 0.7215 (mp10) REVERT: D 242 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7827 (mt-10) REVERT: D 247 TYR cc_start: 0.7023 (m-10) cc_final: 0.6388 (m-10) REVERT: D 279 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7477 (tpp80) REVERT: D 302 LEU cc_start: 0.8320 (tp) cc_final: 0.8019 (tp) REVERT: D 326 CYS cc_start: 0.5082 (t) cc_final: 0.4774 (t) REVERT: D 328 SER cc_start: 0.7512 (t) cc_final: 0.7035 (p) REVERT: D 345 TRP cc_start: 0.6764 (m100) cc_final: 0.5367 (m100) REVERT: D 350 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7326 (mt-10) REVERT: D 381 ASN cc_start: 0.7991 (m110) cc_final: 0.7774 (m110) REVERT: D 383 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7224 (pp20) REVERT: D 404 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7927 (mm-30) REVERT: D 409 ARG cc_start: 0.8173 (tpt-90) cc_final: 0.7546 (mtp85) REVERT: D 413 LEU cc_start: 0.8609 (mt) cc_final: 0.7792 (pp) REVERT: D 416 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.8061 (ptp-110) REVERT: D 431 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7491 (mm-30) REVERT: D 458 MET cc_start: 0.6855 (mmt) cc_final: 0.6346 (mmt) outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 0.1853 time to fit residues: 98.8776 Evaluate side-chains 360 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 71 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 39 optimal weight: 40.0000 chunk 51 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 30.0000 chunk 159 optimal weight: 0.8980 chunk 205 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 131 GLN C 95 HIS ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.225545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.166239 restraints weight = 44085.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.171336 restraints weight = 20509.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.174480 restraints weight = 12342.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.176360 restraints weight = 8874.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.177496 restraints weight = 7202.964| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20302 Z= 0.198 Angle : 0.584 7.177 28362 Z= 0.328 Chirality : 0.039 0.151 3108 Planarity : 0.005 0.043 3020 Dihedral : 23.061 85.091 4268 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.20), residues: 1936 helix: 1.93 (0.17), residues: 907 sheet: -0.12 (0.29), residues: 306 loop : 0.88 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 207 TYR 0.024 0.002 TYR B 188 PHE 0.017 0.001 PHE B 348 TRP 0.075 0.002 TRP D 35 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00413 (20286) covalent geometry : angle 0.57993 (28338) hydrogen bonds : bond 0.04240 ( 1052) hydrogen bonds : angle 4.02100 ( 2777) metal coordination : bond 0.00416 ( 16) metal coordination : angle 2.33251 ( 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 386 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.614 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: 0.8043 (mtp180) cc_final: 0.7245 (tpp-160) REVERT: A 24 GLU cc_start: 0.8337 (tp30) cc_final: 0.7820 (tp30) REVERT: A 61 LEU cc_start: 0.8132 (tp) cc_final: 0.7871 (tp) REVERT: A 132 MET cc_start: 0.8386 (mtm) cc_final: 0.7706 (mtm) REVERT: A 134 LEU cc_start: 0.8687 (tp) cc_final: 0.8466 (pp) REVERT: A 135 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8261 (mm-30) REVERT: A 138 LYS cc_start: 0.8570 (mttm) cc_final: 0.8084 (tttp) REVERT: A 237 ARG cc_start: 0.5060 (ttp-110) cc_final: 0.2838 (ttt90) REVERT: A 239 MET cc_start: 0.4767 (mmp) cc_final: 0.4366 (ptp) REVERT: A 303 PHE cc_start: 0.7663 (m-10) cc_final: 0.7453 (m-80) REVERT: B 8 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7228 (ttp80) REVERT: B 21 ARG cc_start: 0.8121 (ttt-90) cc_final: 0.7526 (mmm160) REVERT: B 28 GLN cc_start: 0.7520 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 46 VAL cc_start: 0.7845 (p) cc_final: 0.7558 (p) REVERT: B 54 ASP cc_start: 0.6941 (t70) cc_final: 0.6407 (t0) REVERT: B 56 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7455 (mtmm) REVERT: B 67 PHE cc_start: 0.8135 (m-80) cc_final: 0.7786 (m-10) REVERT: B 91 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7856 (mm-40) REVERT: B 95 HIS cc_start: 0.7184 (m90) cc_final: 0.6018 (m90) REVERT: B 98 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6921 (mt-10) REVERT: B 99 ASP cc_start: 0.7785 (m-30) cc_final: 0.7295 (m-30) REVERT: B 101 LYS cc_start: 0.8751 (mptt) cc_final: 0.8404 (mptt) REVERT: B 102 LYS cc_start: 0.8274 (mptt) cc_final: 0.8017 (mmmt) REVERT: B 138 LYS cc_start: 0.8095 (mttt) cc_final: 0.7570 (ttmm) REVERT: B 139 GLU cc_start: 0.6883 (tm-30) cc_final: 0.5917 (tm-30) REVERT: B 142 ARG cc_start: 0.7907 (tmm-80) cc_final: 0.7245 (tmm-80) REVERT: B 148 ASN cc_start: 0.8211 (m-40) cc_final: 0.7634 (t0) REVERT: B 149 ILE cc_start: 0.8687 (mt) cc_final: 0.8318 (mm) REVERT: B 196 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7132 (mm-30) REVERT: B 226 GLN cc_start: 0.7545 (tp-100) cc_final: 0.7131 (tp40) REVERT: B 247 TYR cc_start: 0.7231 (m-10) cc_final: 0.6210 (m-80) REVERT: B 279 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7400 (mtt180) REVERT: B 289 LYS cc_start: 0.8552 (mppt) cc_final: 0.8135 (mppt) REVERT: B 302 LEU cc_start: 0.7699 (tp) cc_final: 0.7273 (tp) REVERT: B 325 ARG cc_start: 0.7086 (mtm110) cc_final: 0.6612 (mtp85) REVERT: B 329 MET cc_start: 0.7502 (mmt) cc_final: 0.6767 (mmt) REVERT: B 334 HIS cc_start: 0.7229 (p90) cc_final: 0.7019 (p90) REVERT: B 339 THR cc_start: 0.8156 (p) cc_final: 0.7904 (t) REVERT: B 342 MET cc_start: 0.7268 (ttp) cc_final: 0.6046 (tpp) REVERT: B 345 TRP cc_start: 0.7244 (m100) cc_final: 0.6770 (m100) REVERT: B 346 ASP cc_start: 0.7968 (m-30) cc_final: 0.7375 (m-30) REVERT: B 350 GLU cc_start: 0.7870 (pp20) cc_final: 0.7661 (pp20) REVERT: B 367 TRP cc_start: 0.8431 (t-100) cc_final: 0.7891 (t-100) REVERT: B 379 GLU cc_start: 0.8352 (pt0) cc_final: 0.7915 (pp20) REVERT: B 383 GLU cc_start: 0.8326 (pt0) cc_final: 0.7797 (pp20) REVERT: B 384 LEU cc_start: 0.8891 (mt) cc_final: 0.8635 (mt) REVERT: B 386 ASP cc_start: 0.7935 (t70) cc_final: 0.7237 (t0) REVERT: B 389 SER cc_start: 0.9169 (m) cc_final: 0.8677 (p) REVERT: B 391 ILE cc_start: 0.7884 (mt) cc_final: 0.7043 (mt) REVERT: B 413 LEU cc_start: 0.8653 (mm) cc_final: 0.7482 (mm) REVERT: B 416 ARG cc_start: 0.7947 (mtm-85) cc_final: 0.7294 (mtm-85) REVERT: B 456 ARG cc_start: 0.7740 (mtp180) cc_final: 0.7341 (ttm110) REVERT: B 458 MET cc_start: 0.7409 (mpp) cc_final: 0.6574 (mpp) REVERT: B 459 ASN cc_start: 0.8453 (m-40) cc_final: 0.8234 (m-40) REVERT: B 478 ASP cc_start: 0.8054 (m-30) cc_final: 0.7500 (m-30) REVERT: C 22 GLN cc_start: 0.8224 (mt0) cc_final: 0.7665 (mt0) REVERT: C 28 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7566 (tm-30) REVERT: C 30 CYS cc_start: 0.8967 (m) cc_final: 0.8764 (m) REVERT: C 89 HIS cc_start: 0.8092 (m90) cc_final: 0.7846 (m90) REVERT: C 90 LEU cc_start: 0.8376 (tp) cc_final: 0.8120 (tp) REVERT: C 100 HIS cc_start: 0.7516 (m90) cc_final: 0.6957 (m90) REVERT: C 177 ASP cc_start: 0.3453 (p0) cc_final: 0.3144 (p0) REVERT: C 273 GLU cc_start: 0.8555 (pt0) cc_final: 0.8194 (pm20) REVERT: D 7 ILE cc_start: 0.8159 (mt) cc_final: 0.7938 (mm) REVERT: D 20 GLU cc_start: 0.7728 (mp0) cc_final: 0.6966 (pm20) REVERT: D 21 ARG cc_start: 0.7579 (tpp80) cc_final: 0.6987 (tpp80) REVERT: D 24 GLU cc_start: 0.8131 (tt0) cc_final: 0.7652 (tm-30) REVERT: D 28 GLN cc_start: 0.7593 (tm-30) cc_final: 0.7256 (tm-30) REVERT: D 33 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7332 (tpp80) REVERT: D 35 TRP cc_start: 0.5810 (p90) cc_final: 0.5598 (p90) REVERT: D 36 ASP cc_start: 0.7857 (m-30) cc_final: 0.7481 (t0) REVERT: D 42 GLU cc_start: 0.7827 (tt0) cc_final: 0.7102 (tt0) REVERT: D 44 LEU cc_start: 0.8948 (mp) cc_final: 0.8679 (mp) REVERT: D 68 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7095 (mt-10) REVERT: D 79 ARG cc_start: 0.6942 (mtm110) cc_final: 0.6672 (mtm110) REVERT: D 92 GLN cc_start: 0.7674 (mt0) cc_final: 0.7113 (mt0) REVERT: D 109 GLU cc_start: 0.6728 (mp0) cc_final: 0.6298 (mp0) REVERT: D 129 VAL cc_start: 0.8670 (m) cc_final: 0.8121 (p) REVERT: D 132 MET cc_start: 0.7593 (mmm) cc_final: 0.6920 (mmm) REVERT: D 133 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7266 (mt-10) REVERT: D 135 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7703 (mm-30) REVERT: D 138 LYS cc_start: 0.8941 (mttt) cc_final: 0.8319 (mtpp) REVERT: D 146 HIS cc_start: 0.8165 (m170) cc_final: 0.7935 (m-70) REVERT: D 149 ILE cc_start: 0.8807 (pt) cc_final: 0.8466 (tp) REVERT: D 153 LYS cc_start: 0.8260 (mttt) cc_final: 0.7865 (mttt) REVERT: D 157 SER cc_start: 0.7821 (t) cc_final: 0.7199 (p) REVERT: D 164 LEU cc_start: 0.7944 (tp) cc_final: 0.7698 (tp) REVERT: D 182 GLU cc_start: 0.8030 (tt0) cc_final: 0.7779 (tt0) REVERT: D 186 GLU cc_start: 0.7455 (tp30) cc_final: 0.7149 (tp30) REVERT: D 189 HIS cc_start: 0.6134 (t-90) cc_final: 0.5864 (t-90) REVERT: D 195 HIS cc_start: 0.7092 (m90) cc_final: 0.6497 (m90) REVERT: D 220 LEU cc_start: 0.7913 (tt) cc_final: 0.7580 (mm) REVERT: D 226 GLN cc_start: 0.7909 (mp10) cc_final: 0.7259 (mp10) REVERT: D 242 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7877 (mt-10) REVERT: D 247 TYR cc_start: 0.7082 (m-10) cc_final: 0.6473 (m-10) REVERT: D 279 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7549 (tpp80) REVERT: D 281 GLU cc_start: 0.6883 (tp30) cc_final: 0.6270 (tp30) REVERT: D 302 LEU cc_start: 0.8171 (tp) cc_final: 0.7876 (tp) REVERT: D 328 SER cc_start: 0.7435 (t) cc_final: 0.6982 (p) REVERT: D 345 TRP cc_start: 0.7011 (m100) cc_final: 0.5608 (m100) REVERT: D 350 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7369 (mt-10) REVERT: D 383 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7233 (pp20) REVERT: D 404 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7967 (mm-30) REVERT: D 409 ARG cc_start: 0.8198 (tpt-90) cc_final: 0.7536 (mtp85) REVERT: D 413 LEU cc_start: 0.8592 (mt) cc_final: 0.7824 (pp) REVERT: D 416 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.8038 (ptp-110) REVERT: D 458 MET cc_start: 0.7135 (mmt) cc_final: 0.6705 (mmt) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.1841 time to fit residues: 100.2858 Evaluate side-chains 367 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 115 optimal weight: 30.0000 chunk 32 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 178 optimal weight: 0.4980 chunk 64 optimal weight: 0.0040 chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.228992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.172258 restraints weight = 44672.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.177303 restraints weight = 20579.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.180434 restraints weight = 12298.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.182321 restraints weight = 8759.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.183507 restraints weight = 7072.847| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.6242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20302 Z= 0.129 Angle : 0.547 7.924 28362 Z= 0.304 Chirality : 0.037 0.211 3108 Planarity : 0.004 0.046 3020 Dihedral : 23.086 82.738 4268 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.20), residues: 1936 helix: 2.18 (0.17), residues: 905 sheet: -0.01 (0.29), residues: 306 loop : 1.07 (0.26), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 323 TYR 0.022 0.001 TYR B 188 PHE 0.014 0.001 PHE A 314 TRP 0.087 0.002 TRP B 454 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00268 (20286) covalent geometry : angle 0.54425 (28338) hydrogen bonds : bond 0.03515 ( 1052) hydrogen bonds : angle 3.83287 ( 2777) metal coordination : bond 0.00159 ( 16) metal coordination : angle 1.92221 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4645.46 seconds wall clock time: 80 minutes 13.55 seconds (4813.55 seconds total)