Starting phenix.real_space_refine on Mon Aug 25 05:27:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f1c_28793/08_2025/8f1c_28793_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f1c_28793/08_2025/8f1c_28793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f1c_28793/08_2025/8f1c_28793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f1c_28793/08_2025/8f1c_28793.map" model { file = "/net/cci-nas-00/data/ceres_data/8f1c_28793/08_2025/8f1c_28793_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f1c_28793/08_2025/8f1c_28793_trim.cif" } resolution = 2.92 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= 0.011 sd= 0.045 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: 9 Type Number sf(0) Gaussians K 4 8.98 5 Zn 4 6.06 5 P 4 5.49 5 S 68 5.16 5 Cl 4 4.86 5 C 8520 2.51 5 N 2120 2.21 5 O 2208 1.98 5 H 12184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25116 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6194 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 88 Unusual residues: {' K': 4, ' ZN': 1, 'POV': 1, 'X9T': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1518 SG CYS A 104 63.879 52.710 75.558 1.00 53.86 S Restraints were copied for chains: B, C, D Time building chain proxies: 6.40, per 1000 atoms: 0.25 Number of scatterers: 25116 At special positions: 0 Unit cell: (135.24, 135.24, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 4 29.99 K 4 19.00 Cl 4 17.00 S 68 16.00 P 4 15.00 O 2208 8.00 N 2120 7.00 C 8520 6.00 H 12184 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 709.6 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 104 " pdb="ZN ZN A 601 " - pdb=" SG CYS D 83 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS A 83 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS B 83 " pdb="ZN ZN C 601 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 104 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" SG CYS C 83 " 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 4 sheets defined 70.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.975A pdb=" N LEU A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 22 through 27' Processing helix chain 'A' and resid 32 through 39 removed outlier: 3.540A pdb=" N GLU A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.729A pdb=" N PHE A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 65 " --> pdb=" O PRO A 61 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.703A pdb=" N ASP A 100 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.697A pdb=" N TYR A 109 " --> pdb=" O CYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.905A pdb=" N ALA A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 180 removed outlier: 3.869A pdb=" N PHE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 211 removed outlier: 3.914A pdb=" N THR A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 266 removed outlier: 3.620A pdb=" N GLU A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.548A pdb=" N TYR A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 311 removed outlier: 4.456A pdb=" N ASP A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.665A pdb=" N ARG A 320 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.695A pdb=" N ARG A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 Processing helix chain 'A' and resid 341 through 367 Processing helix chain 'A' and resid 377 through 381 removed outlier: 4.179A pdb=" N HIS A 381 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 removed outlier: 4.363A pdb=" N TRP A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 431 through 452 removed outlier: 3.606A pdb=" N ILE A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.974A pdb=" N LEU B 26 " --> pdb=" O TYR B 22 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 22 through 27' Processing helix chain 'B' and resid 32 through 39 removed outlier: 3.540A pdb=" N GLU B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 74 removed outlier: 3.729A pdb=" N PHE B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N HIS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.703A pdb=" N ASP B 100 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 105 through 110 removed outlier: 3.697A pdb=" N TYR B 109 " --> pdb=" O CYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.906A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 180 removed outlier: 3.869A pdb=" N PHE B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 211 removed outlier: 3.913A pdb=" N THR B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 266 removed outlier: 3.619A pdb=" N GLU B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.548A pdb=" N TYR B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 311 removed outlier: 4.456A pdb=" N ASP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.665A pdb=" N ARG B 320 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.695A pdb=" N ARG B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 Processing helix chain 'B' and resid 341 through 367 Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.179A pdb=" N HIS B 381 " --> pdb=" O ALA B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.363A pdb=" N TRP B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 431 through 452 removed outlier: 3.606A pdb=" N ILE B 435 " --> pdb=" O PRO B 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 removed outlier: 3.975A pdb=" N LEU C 26 " --> pdb=" O TYR C 22 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG C 27 " --> pdb=" O ARG C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 22 through 27' Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.540A pdb=" N GLU C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.729A pdb=" N PHE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C 65 " --> pdb=" O PRO C 61 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.703A pdb=" N ASP C 100 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.697A pdb=" N TYR C 109 " --> pdb=" O CYS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 121 removed outlier: 3.905A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 180 removed outlier: 3.869A pdb=" N PHE C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 211 removed outlier: 3.913A pdb=" N THR C 211 " --> pdb=" O PHE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 266 removed outlier: 3.619A pdb=" N GLU C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'C' and resid 278 through 285 Processing helix chain 'C' and resid 286 through 294 removed outlier: 3.548A pdb=" N TYR C 290 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 311 removed outlier: 4.456A pdb=" N ASP C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.664A pdb=" N ARG C 320 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.695A pdb=" N ARG C 326 " --> pdb=" O PHE C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 341 Processing helix chain 'C' and resid 341 through 367 Processing helix chain 'C' and resid 377 through 381 removed outlier: 4.178A pdb=" N HIS C 381 " --> pdb=" O ALA C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 399 removed outlier: 4.364A pdb=" N TRP C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 431 through 452 removed outlier: 3.606A pdb=" N ILE C 435 " --> pdb=" O PRO C 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 removed outlier: 3.974A pdb=" N LEU D 26 " --> pdb=" O TYR D 22 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 27' Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.540A pdb=" N GLU D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 74 removed outlier: 3.729A pdb=" N PHE D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA D 65 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.705A pdb=" N ASP D 100 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 101 " --> pdb=" O GLU D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.697A pdb=" N TYR D 109 " --> pdb=" O CYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.905A pdb=" N ALA D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 180 removed outlier: 3.869A pdb=" N PHE D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 211 removed outlier: 3.913A pdb=" N THR D 211 " --> pdb=" O PHE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 266 removed outlier: 3.619A pdb=" N GLU D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 276 Processing helix chain 'D' and resid 278 through 285 Processing helix chain 'D' and resid 286 through 294 removed outlier: 3.548A pdb=" N TYR D 290 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 311 removed outlier: 4.456A pdb=" N ASP D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.665A pdb=" N ARG D 320 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.695A pdb=" N ARG D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 Processing helix chain 'D' and resid 341 through 367 Processing helix chain 'D' and resid 377 through 381 removed outlier: 4.179A pdb=" N HIS D 381 " --> pdb=" O ALA D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 399 removed outlier: 4.363A pdb=" N TRP D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 431 through 452 removed outlier: 3.606A pdb=" N ILE D 435 " --> pdb=" O PRO D 431 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR A 21 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 10 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 49 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR B 21 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 10 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 54 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 49 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 10 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 54 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C 49 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR D 21 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 10 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU D 54 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP D 49 " --> pdb=" O GLU D 54 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12160 1.03 - 1.23: 36 1.23 - 1.42: 5800 1.42 - 1.61: 7400 1.61 - 1.81: 108 Bond restraints: 25504 Sorted by residual: bond pdb=" O12 POV A 603 " pdb=" P POV A 603 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" O12 POV C 603 " pdb=" P POV C 603 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" O12 POV D 603 " pdb=" P POV D 603 " ideal model delta sigma weight residual 1.657 1.607 0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" O12 POV B 603 " pdb=" P POV B 603 " ideal model delta sigma weight residual 1.657 1.607 0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" C11 POV A 603 " pdb=" O12 POV A 603 " ideal model delta sigma weight residual 1.408 1.455 -0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 25499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 43919 1.25 - 2.49: 1664 2.49 - 3.74: 119 3.74 - 4.99: 34 4.99 - 6.23: 8 Bond angle restraints: 45744 Sorted by residual: angle pdb=" O11 POV A 603 " pdb=" P POV A 603 " pdb=" O12 POV A 603 " ideal model delta sigma weight residual 97.67 103.90 -6.23 3.00e+00 1.11e-01 4.32e+00 angle pdb=" O11 POV C 603 " pdb=" P POV C 603 " pdb=" O12 POV C 603 " ideal model delta sigma weight residual 97.67 103.89 -6.22 3.00e+00 1.11e-01 4.30e+00 angle pdb=" O11 POV B 603 " pdb=" P POV B 603 " pdb=" O12 POV B 603 " ideal model delta sigma weight residual 97.67 103.87 -6.20 3.00e+00 1.11e-01 4.27e+00 angle pdb=" O11 POV D 603 " pdb=" P POV D 603 " pdb=" O12 POV D 603 " ideal model delta sigma weight residual 97.67 103.84 -6.17 3.00e+00 1.11e-01 4.23e+00 angle pdb=" N GLU B 181 " pdb=" CA GLU B 181 " pdb=" CB GLU B 181 " ideal model delta sigma weight residual 113.65 110.94 2.71 1.47e+00 4.63e-01 3.39e+00 ... (remaining 45739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 11211 16.07 - 32.13: 717 32.13 - 48.20: 168 48.20 - 64.27: 88 64.27 - 80.33: 16 Dihedral angle restraints: 12200 sinusoidal: 6400 harmonic: 5800 Sorted by residual: dihedral pdb=" CA ILE A 318 " pdb=" CB ILE A 318 " pdb=" CG1 ILE A 318 " pdb=" CD1 ILE A 318 " ideal model delta sinusoidal sigma weight residual 180.00 133.72 46.28 3 1.50e+01 4.44e-03 8.31e+00 dihedral pdb=" CA ILE D 318 " pdb=" CB ILE D 318 " pdb=" CG1 ILE D 318 " pdb=" CD1 ILE D 318 " ideal model delta sinusoidal sigma weight residual 180.00 133.74 46.26 3 1.50e+01 4.44e-03 8.31e+00 dihedral pdb=" CA ILE B 318 " pdb=" CB ILE B 318 " pdb=" CG1 ILE B 318 " pdb=" CD1 ILE B 318 " ideal model delta sinusoidal sigma weight residual 180.00 133.74 46.26 3 1.50e+01 4.44e-03 8.31e+00 ... (remaining 12197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1135 0.024 - 0.049: 502 0.049 - 0.073: 192 0.073 - 0.097: 90 0.097 - 0.121: 41 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CA ILE D 12 " pdb=" N ILE D 12 " pdb=" C ILE D 12 " pdb=" CB ILE D 12 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA ILE C 12 " pdb=" N ILE C 12 " pdb=" C ILE C 12 " pdb=" CB ILE C 12 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE B 12 " pdb=" N ILE B 12 " pdb=" C ILE B 12 " pdb=" CB ILE B 12 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 1957 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 102 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 103 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 102 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO D 103 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 102 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO C 103 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 103 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 103 " -0.020 5.00e-02 4.00e+02 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.36: 8096 2.36 - 3.06: 68417 3.06 - 3.75: 85403 3.75 - 4.45: 132921 4.45 - 5.14: 203943 Nonbonded interactions: 498780 Sorted by model distance: nonbonded pdb=" OD2 ASP A 100 " pdb=" HZ1 LYS D 458 " model vdw 1.667 2.450 nonbonded pdb=" HZ1 LYS A 458 " pdb=" OD2 ASP B 100 " model vdw 1.668 2.450 nonbonded pdb=" HZ1 LYS B 458 " pdb=" OD2 ASP C 100 " model vdw 1.672 2.450 nonbonded pdb=" HZ1 LYS C 458 " pdb=" OD2 ASP D 100 " model vdw 1.673 2.450 nonbonded pdb=" O GLU B 210 " pdb="HD21 ASN B 216 " model vdw 1.693 2.450 ... (remaining 498775 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' and resid 7 through 603) 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 individual isotropic 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: 2.030 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: 0.150 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.800 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.004 0.051 13332 Z= 0.183 Angle : 0.527 6.232 18136 Z= 0.247 Chirality : 0.036 0.121 1960 Planarity : 0.004 0.035 2252 Dihedral : 11.032 80.333 4768 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.61 % Allowed : 3.36 % Favored : 96.02 % 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 aren not related in a simple way. whole: 0.84 (0.22), residues: 1552 helix: 1.68 (0.18), residues: 908 sheet: -2.91 (0.85), residues: 40 loop : -0.95 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.005 0.001 TYR C 71 PHE 0.006 0.001 PHE C 328 TRP 0.006 0.001 TRP C 255 HIS 0.001 0.000 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00395 (13320) covalent geometry : angle 0.52698 (18136) hydrogen bonds : bond 0.16365 ( 700) hydrogen bonds : angle 5.51583 ( 2016) metal coordination : bond 0.00255 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 205 time to evaluate : 0.622 Fit side-chains REVERT: A 412 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.7712 (p) REVERT: A 447 MET cc_start: 0.8507 (mmm) cc_final: 0.8121 (mmt) REVERT: B 412 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 447 MET cc_start: 0.8497 (mmm) cc_final: 0.8107 (mmt) REVERT: C 412 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.7690 (p) REVERT: C 447 MET cc_start: 0.8499 (mmm) cc_final: 0.8110 (mmt) REVERT: D 412 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.7681 (p) REVERT: D 447 MET cc_start: 0.8499 (mmm) cc_final: 0.8112 (mmt) outliers start: 8 outliers final: 0 residues processed: 213 average time/residue: 1.2035 time to fit residues: 280.6360 Evaluate side-chains 145 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 ASN C 276 ASN D 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.183692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.144153 restraints weight = 37481.497| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.33 r_work: 0.3146 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13332 Z= 0.210 Angle : 0.578 6.669 18136 Z= 0.299 Chirality : 0.042 0.149 1960 Planarity : 0.005 0.046 2252 Dihedral : 8.702 84.506 1980 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.15 % Allowed : 9.71 % Favored : 89.14 % 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 aren not related in a simple way. whole: 0.47 (0.22), residues: 1552 helix: 1.32 (0.17), residues: 936 sheet: -2.41 (0.74), residues: 40 loop : -1.15 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 214 TYR 0.008 0.001 TYR C 365 PHE 0.015 0.001 PHE B 384 TRP 0.008 0.001 TRP B 392 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00512 (13320) covalent geometry : angle 0.57791 (18136) hydrogen bonds : bond 0.06334 ( 700) hydrogen bonds : angle 4.58381 ( 2016) metal coordination : bond 0.00621 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.425 Fit side-chains REVERT: A 120 ASP cc_start: 0.5058 (m-30) cc_final: 0.4849 (m-30) REVERT: A 172 TRP cc_start: 0.7140 (m100) cc_final: 0.6743 (m100) REVERT: A 262 MET cc_start: 0.8453 (mmp) cc_final: 0.8017 (mmp) REVERT: A 412 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8257 (p) REVERT: B 120 ASP cc_start: 0.5083 (m-30) cc_final: 0.4873 (m-30) REVERT: B 172 TRP cc_start: 0.6816 (m100) cc_final: 0.6533 (m100) REVERT: B 262 MET cc_start: 0.8458 (mmp) cc_final: 0.8032 (mmp) REVERT: B 412 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8258 (p) REVERT: B 447 MET cc_start: 0.8539 (mmm) cc_final: 0.8104 (mmt) REVERT: C 120 ASP cc_start: 0.5092 (m-30) cc_final: 0.4874 (m-30) REVERT: C 172 TRP cc_start: 0.6795 (m100) cc_final: 0.6516 (m100) REVERT: C 262 MET cc_start: 0.8452 (mmp) cc_final: 0.8030 (mmp) REVERT: C 412 SER cc_start: 0.8758 (OUTLIER) cc_final: 0.8259 (p) REVERT: D 120 ASP cc_start: 0.5073 (m-30) cc_final: 0.4865 (m-30) REVERT: D 172 TRP cc_start: 0.6818 (m100) cc_final: 0.6535 (m100) REVERT: D 262 MET cc_start: 0.8449 (mmp) cc_final: 0.8010 (mmp) REVERT: D 412 SER cc_start: 0.8758 (OUTLIER) cc_final: 0.8262 (p) outliers start: 15 outliers final: 6 residues processed: 151 average time/residue: 0.8572 time to fit residues: 145.5452 Evaluate side-chains 138 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 0.0010 chunk 51 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 33 optimal weight: 0.0670 chunk 55 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 overall best weight: 0.5928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.187408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146334 restraints weight = 37471.022| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.49 r_work: 0.3190 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13332 Z= 0.097 Angle : 0.451 4.691 18136 Z= 0.228 Chirality : 0.037 0.131 1960 Planarity : 0.004 0.037 2252 Dihedral : 7.989 88.239 1980 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.22 % Allowed : 10.02 % Favored : 88.76 % 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 aren not related in a simple way. whole: 1.04 (0.22), residues: 1552 helix: 1.72 (0.17), residues: 948 sheet: -2.22 (0.76), residues: 40 loop : -0.86 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 110 TYR 0.005 0.001 TYR C 407 PHE 0.009 0.001 PHE A 384 TRP 0.007 0.001 TRP A 255 HIS 0.001 0.000 HIS D 383 Details of bonding type rmsd covalent geometry : bond 0.00201 (13320) covalent geometry : angle 0.45136 (18136) hydrogen bonds : bond 0.04714 ( 700) hydrogen bonds : angle 4.28590 ( 2016) metal coordination : bond 0.00153 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.746 Fit side-chains REVERT: A 120 ASP cc_start: 0.5106 (m-30) cc_final: 0.4898 (m-30) REVERT: A 172 TRP cc_start: 0.7118 (m100) cc_final: 0.6757 (m100) REVERT: A 262 MET cc_start: 0.8415 (mmp) cc_final: 0.8061 (mmp) REVERT: A 447 MET cc_start: 0.8525 (mmm) cc_final: 0.8165 (mmt) REVERT: B 262 MET cc_start: 0.8421 (mmp) cc_final: 0.8065 (mmp) REVERT: B 324 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8093 (mp) REVERT: B 447 MET cc_start: 0.8519 (mmm) cc_final: 0.8145 (mmt) REVERT: C 262 MET cc_start: 0.8416 (mmp) cc_final: 0.8057 (mmp) REVERT: C 324 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8090 (mp) REVERT: C 447 MET cc_start: 0.8522 (mmm) cc_final: 0.8162 (mmt) REVERT: D 120 ASP cc_start: 0.5079 (m-30) cc_final: 0.4875 (m-30) REVERT: D 262 MET cc_start: 0.8412 (mmp) cc_final: 0.8051 (mmp) REVERT: D 324 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8096 (mp) REVERT: D 447 MET cc_start: 0.8514 (mmm) cc_final: 0.8149 (mmt) outliers start: 16 outliers final: 4 residues processed: 148 average time/residue: 0.9739 time to fit residues: 162.2393 Evaluate side-chains 135 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 62 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 146 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.185113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144563 restraints weight = 37212.737| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.36 r_work: 0.3167 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13332 Z= 0.137 Angle : 0.493 5.350 18136 Z= 0.248 Chirality : 0.038 0.130 1960 Planarity : 0.004 0.041 2252 Dihedral : 7.778 81.223 1976 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.61 % Allowed : 11.16 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.22), residues: 1552 helix: 1.74 (0.18), residues: 936 sheet: -1.87 (0.79), residues: 40 loop : -1.04 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 317 TYR 0.006 0.001 TYR D 365 PHE 0.014 0.001 PHE B 56 TRP 0.006 0.001 TRP D 392 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00327 (13320) covalent geometry : angle 0.49318 (18136) hydrogen bonds : bond 0.05262 ( 700) hydrogen bonds : angle 4.21118 ( 2016) metal coordination : bond 0.00317 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.701 Fit side-chains REVERT: A 172 TRP cc_start: 0.7098 (m100) cc_final: 0.6762 (m100) REVERT: A 262 MET cc_start: 0.8381 (mmp) cc_final: 0.8022 (mmp) REVERT: B 262 MET cc_start: 0.8379 (mmp) cc_final: 0.8022 (mmp) REVERT: B 324 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8123 (mp) REVERT: C 262 MET cc_start: 0.8395 (mmp) cc_final: 0.8035 (mmp) REVERT: C 324 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8117 (mp) REVERT: D 262 MET cc_start: 0.8377 (mmp) cc_final: 0.8011 (mmp) REVERT: D 324 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8119 (mp) outliers start: 8 outliers final: 4 residues processed: 133 average time/residue: 1.0083 time to fit residues: 149.4839 Evaluate side-chains 132 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 155 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.184056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.143323 restraints weight = 37207.550| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.23 r_work: 0.3166 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13332 Z= 0.153 Angle : 0.506 5.343 18136 Z= 0.256 Chirality : 0.039 0.127 1960 Planarity : 0.004 0.043 2252 Dihedral : 7.239 54.358 1976 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.92 % Allowed : 11.01 % Favored : 88.07 % 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 aren not related in a simple way. whole: 0.88 (0.22), residues: 1552 helix: 1.62 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -1.07 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 214 TYR 0.007 0.001 TYR A 365 PHE 0.016 0.001 PHE B 56 TRP 0.007 0.001 TRP A 255 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00366 (13320) covalent geometry : angle 0.50585 (18136) hydrogen bonds : bond 0.05615 ( 700) hydrogen bonds : angle 4.20257 ( 2016) metal coordination : bond 0.00413 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.652 Fit side-chains REVERT: A 172 TRP cc_start: 0.7056 (m100) cc_final: 0.6768 (m100) REVERT: A 262 MET cc_start: 0.8459 (mmp) cc_final: 0.8120 (mmp) REVERT: B 262 MET cc_start: 0.8441 (mmp) cc_final: 0.8101 (mmp) REVERT: B 324 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8123 (mp) REVERT: C 262 MET cc_start: 0.8447 (mmp) cc_final: 0.8110 (mmp) REVERT: C 324 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8121 (mp) REVERT: D 262 MET cc_start: 0.8458 (mmp) cc_final: 0.8113 (mmp) REVERT: D 324 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8123 (mp) outliers start: 12 outliers final: 8 residues processed: 131 average time/residue: 1.1222 time to fit residues: 163.0063 Evaluate side-chains 134 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 23 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.180504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138172 restraints weight = 37512.366| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.23 r_work: 0.3097 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 13332 Z= 0.320 Angle : 0.657 8.477 18136 Z= 0.341 Chirality : 0.046 0.174 1960 Planarity : 0.006 0.049 2252 Dihedral : 8.043 63.576 1976 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.92 % Allowed : 10.93 % Favored : 88.15 % 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 aren not related in a simple way. whole: 0.07 (0.21), residues: 1552 helix: 1.00 (0.17), residues: 936 sheet: -1.49 (0.79), residues: 40 loop : -1.41 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.013 0.002 TYR C 365 PHE 0.022 0.002 PHE B 384 TRP 0.009 0.002 TRP A 255 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00798 (13320) covalent geometry : angle 0.65663 (18136) hydrogen bonds : bond 0.07727 ( 700) hydrogen bonds : angle 4.54084 ( 2016) metal coordination : bond 0.00975 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.547 Fit side-chains REVERT: A 88 GLU cc_start: 0.7753 (tt0) cc_final: 0.7519 (tt0) REVERT: A 172 TRP cc_start: 0.7077 (m100) cc_final: 0.6804 (m100) REVERT: A 262 MET cc_start: 0.8496 (mmp) cc_final: 0.8103 (mmp) REVERT: B 88 GLU cc_start: 0.7775 (tt0) cc_final: 0.7544 (tt0) REVERT: B 262 MET cc_start: 0.8503 (mmp) cc_final: 0.8117 (mmp) REVERT: B 324 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8094 (mp) REVERT: C 88 GLU cc_start: 0.7784 (tt0) cc_final: 0.7582 (tt0) REVERT: C 262 MET cc_start: 0.8513 (mmp) cc_final: 0.8128 (mmp) REVERT: C 324 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8094 (mp) REVERT: D 88 GLU cc_start: 0.7782 (tt0) cc_final: 0.7576 (tt0) REVERT: D 262 MET cc_start: 0.8502 (mmp) cc_final: 0.8117 (mmp) REVERT: D 324 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8097 (mp) outliers start: 12 outliers final: 8 residues processed: 140 average time/residue: 0.9855 time to fit residues: 153.2863 Evaluate side-chains 140 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 113 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.185471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137865 restraints weight = 37200.095| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.43 r_work: 0.3200 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13332 Z= 0.106 Angle : 0.474 5.204 18136 Z= 0.239 Chirality : 0.038 0.124 1960 Planarity : 0.005 0.042 2252 Dihedral : 6.738 53.387 1976 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.84 % Allowed : 11.54 % Favored : 87.61 % 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 aren not related in a simple way. whole: 0.82 (0.22), residues: 1552 helix: 1.50 (0.17), residues: 956 sheet: -1.23 (0.84), residues: 40 loop : -0.99 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 311 TYR 0.006 0.001 TYR D 407 PHE 0.012 0.001 PHE C 384 TRP 0.010 0.001 TRP A 255 HIS 0.002 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00231 (13320) covalent geometry : angle 0.47448 (18136) hydrogen bonds : bond 0.04991 ( 700) hydrogen bonds : angle 4.19253 ( 2016) metal coordination : bond 0.00238 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.643 Fit side-chains REVERT: B 324 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8117 (mp) REVERT: C 262 MET cc_start: 0.8589 (mmp) cc_final: 0.8325 (mmp) REVERT: C 324 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8114 (mp) REVERT: D 324 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8114 (mp) outliers start: 11 outliers final: 8 residues processed: 138 average time/residue: 0.9482 time to fit residues: 145.7522 Evaluate side-chains 140 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.183668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.142768 restraints weight = 37175.816| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.22 r_work: 0.3162 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13332 Z= 0.164 Angle : 0.523 5.730 18136 Z= 0.264 Chirality : 0.039 0.127 1960 Planarity : 0.005 0.044 2252 Dihedral : 6.896 54.449 1976 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.22 % Allowed : 11.47 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.22), residues: 1552 helix: 1.51 (0.17), residues: 940 sheet: -1.01 (0.87), residues: 40 loop : -1.10 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 317 TYR 0.008 0.001 TYR D 365 PHE 0.015 0.001 PHE D 384 TRP 0.008 0.001 TRP C 392 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00396 (13320) covalent geometry : angle 0.52274 (18136) hydrogen bonds : bond 0.05756 ( 700) hydrogen bonds : angle 4.19811 ( 2016) metal coordination : bond 0.00470 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.469 Fit side-chains REVERT: A 412 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8256 (p) REVERT: B 324 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8119 (mp) REVERT: B 412 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8256 (p) REVERT: C 262 MET cc_start: 0.8488 (mmp) cc_final: 0.8193 (mmp) REVERT: C 324 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8110 (mp) REVERT: C 412 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8255 (p) REVERT: D 324 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8117 (mp) REVERT: D 412 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8259 (p) outliers start: 16 outliers final: 8 residues processed: 145 average time/residue: 0.8925 time to fit residues: 144.5014 Evaluate side-chains 148 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.186048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.146147 restraints weight = 37265.601| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.38 r_work: 0.3206 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13332 Z= 0.104 Angle : 0.469 4.492 18136 Z= 0.235 Chirality : 0.037 0.123 1960 Planarity : 0.005 0.042 2252 Dihedral : 6.382 49.588 1976 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.07 % Allowed : 12.08 % Favored : 86.85 % 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 aren not related in a simple way. whole: 1.06 (0.22), residues: 1552 helix: 1.67 (0.17), residues: 956 sheet: -0.79 (0.89), residues: 40 loop : -0.88 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 110 TYR 0.006 0.001 TYR B 403 PHE 0.012 0.001 PHE A 194 TRP 0.008 0.001 TRP C 255 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00231 (13320) covalent geometry : angle 0.46869 (18136) hydrogen bonds : bond 0.04779 ( 700) hydrogen bonds : angle 4.03742 ( 2016) metal coordination : bond 0.00229 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.697 Fit side-chains REVERT: B 324 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 412 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8135 (p) REVERT: C 324 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8097 (mp) REVERT: C 412 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8136 (p) REVERT: D 324 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8102 (mp) REVERT: D 412 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8130 (p) outliers start: 14 outliers final: 8 residues processed: 148 average time/residue: 0.8054 time to fit residues: 134.1147 Evaluate side-chains 149 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.183105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142731 restraints weight = 37090.475| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.28 r_work: 0.3127 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13332 Z= 0.197 Angle : 0.550 6.366 18136 Z= 0.279 Chirality : 0.040 0.134 1960 Planarity : 0.005 0.045 2252 Dihedral : 7.081 55.252 1976 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.22 % Allowed : 12.31 % Favored : 86.47 % 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 aren not related in a simple way. whole: 0.74 (0.22), residues: 1552 helix: 1.54 (0.17), residues: 928 sheet: -0.71 (0.92), residues: 40 loop : -1.14 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 368 TYR 0.009 0.001 TYR A 365 PHE 0.018 0.001 PHE D 384 TRP 0.008 0.001 TRP C 392 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00482 (13320) covalent geometry : angle 0.55045 (18136) hydrogen bonds : bond 0.06073 ( 700) hydrogen bonds : angle 4.15471 ( 2016) metal coordination : bond 0.00562 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.486 Fit side-chains REVERT: A 412 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8271 (p) REVERT: B 324 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8103 (mp) REVERT: B 412 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8270 (p) REVERT: C 324 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8100 (mp) REVERT: C 412 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8270 (p) REVERT: D 324 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8110 (mp) REVERT: D 412 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8274 (p) outliers start: 16 outliers final: 8 residues processed: 144 average time/residue: 0.8840 time to fit residues: 141.2393 Evaluate side-chains 146 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 29 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.185338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145004 restraints weight = 37070.430| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.29 r_work: 0.3183 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13332 Z= 0.118 Angle : 0.485 4.325 18136 Z= 0.243 Chirality : 0.038 0.123 1960 Planarity : 0.005 0.042 2252 Dihedral : 6.622 51.118 1976 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.22 % Allowed : 12.23 % Favored : 86.54 % 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 aren not related in a simple way. whole: 1.01 (0.22), residues: 1552 helix: 1.61 (0.17), residues: 956 sheet: -0.59 (0.93), residues: 40 loop : -0.88 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 110 TYR 0.006 0.001 TYR D 403 PHE 0.012 0.001 PHE D 384 TRP 0.008 0.001 TRP A 255 HIS 0.002 0.000 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00272 (13320) covalent geometry : angle 0.48460 (18136) hydrogen bonds : bond 0.05054 ( 700) hydrogen bonds : angle 4.03880 ( 2016) metal coordination : bond 0.00291 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6962.13 seconds wall clock time: 118 minutes 25.45 seconds (7105.45 seconds total)