Starting phenix.real_space_refine on Sun Jul 5 04:33:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f1c_28793/07_2026/8f1c_28793_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f1c_28793/07_2026/8f1c_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_28793/07_2026/8f1c_28793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f1c_28793/07_2026/8f1c_28793.map" model { file = "/net/cci-nas-00/data/ceres_data/8f1c_28793/07_2026/8f1c_28793_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f1c_28793/07_2026/8f1c_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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25116 Number of models: 1 Model: "" Number of chains: 8 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: "B" 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: "C" 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: "D" 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, 84 Ad-hoc single atom residues: {' K': 4} Unusual residues: {' ZN': 1, 'POV': 1, 'X9T': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 4 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {' ZN': 1, 'POV': 1, 'X9T': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {' ZN': 1, 'POV': 1, 'X9T': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {' ZN': 1, 'POV': 1, 'X9T': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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 ATOM 19787 SG CYS D 83 65.005 56.491 77.460 1.00 61.77 S ATOM 1205 SG CYS A 83 77.914 65.005 77.454 1.00 61.77 S ATOM 7712 SG CYS B 104 81.683 63.875 75.562 1.00 53.86 S ATOM 7399 SG CYS B 83 69.393 77.914 77.459 1.00 61.77 S ATOM 13906 SG CYS C 104 70.526 81.685 75.562 1.00 53.86 S ATOM 13593 SG CYS C 83 56.488 69.394 77.460 1.00 61.77 S ATOM 20100 SG CYS D 104 52.714 70.529 75.561 1.00 53.86 S Time building chain proxies: 4.84, per 1000 atoms: 0.19 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: 3.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.58 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: 6.60 Time building geometry restraints manager: 3.20 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: 0.180 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 32.740 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 are 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/Z covalent geometry : bond 0.00395 / 0.18 (13320) covalent geometry : angle 0.52698 / 0.25 (18136) hydrogen bonds : bond 0.16365 / 11.46 ( 700) hydrogen bonds : angle 5.51583 / 3.96 ( 2016) metal coordination : bond 0.00255 / 0.15 ( 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 : 0.680 Fit side-chains REVERT: A 412 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.7707 (p) REVERT: A 447 MET cc_start: 0.8510 (mmm) cc_final: 0.8121 (mmt) REVERT: B 412 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.7686 (p) REVERT: B 447 MET cc_start: 0.8496 (mmm) cc_final: 0.8106 (mmt) REVERT: C 412 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.7682 (p) REVERT: C 447 MET cc_start: 0.8498 (mmm) cc_final: 0.8108 (mmt) REVERT: D 412 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.7672 (p) REVERT: D 447 MET cc_start: 0.8498 (mmm) cc_final: 0.8107 (mmt) outliers start: 8 outliers final: 0 residues processed: 213 average time/residue: 1.0694 time to fit residues: 251.4192 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 : 0.474 ------------------------------------------------------------------------------- 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... 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 = 0.4064 r_free = 0.4064 target = 0.183836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.136682 restraints weight = 37619.042| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.44 r_work: 0.3162 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2028 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= 0.208 Angle : 0.570 6.321 18136 Z= 0.294 Chirality : 0.041 0.149 1960 Planarity : 0.005 0.045 2252 Dihedral : 8.648 84.385 1980 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % 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 are not related in a simple way. whole: 0.59 (0.22), residues: 1552 helix: 1.37 (0.17), residues: 936 sheet: -2.46 (0.73), residues: 40 loop : -1.00 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 317 TYR 0.008 0.001 TYR C 48 PHE 0.016 0.001 PHE A 384 TRP 0.008 0.001 TRP D 392 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (13320) covalent geometry : angle 0.57011 / 0.29 (18136) hydrogen bonds : bond 0.06337 / 4.24 ( 700) hydrogen bonds : angle 4.60542 / 3.32 ( 2016) metal coordination : bond 0.00604 / 0.40 ( 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 157 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.5022 (m-30) cc_final: 0.4821 (m-30) REVERT: A 172 TRP cc_start: 0.7157 (m100) cc_final: 0.6741 (m100) REVERT: A 262 MET cc_start: 0.8445 (mmp) cc_final: 0.8001 (mmp) REVERT: A 412 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8233 (p) REVERT: A 447 MET cc_start: 0.8564 (mmm) cc_final: 0.8138 (mmt) REVERT: B 120 ASP cc_start: 0.5035 (m-30) cc_final: 0.4829 (m-30) REVERT: B 172 TRP cc_start: 0.6813 (m100) cc_final: 0.6528 (m100) REVERT: B 262 MET cc_start: 0.8446 (mmp) cc_final: 0.7988 (mmp) REVERT: B 412 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8247 (p) REVERT: B 447 MET cc_start: 0.8558 (mmm) cc_final: 0.8124 (mmt) REVERT: C 120 ASP cc_start: 0.5060 (m-30) cc_final: 0.4852 (m-30) REVERT: C 172 TRP cc_start: 0.6909 (m100) cc_final: 0.6531 (m100) REVERT: C 262 MET cc_start: 0.8443 (mmp) cc_final: 0.7995 (mmp) REVERT: C 412 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8248 (p) REVERT: C 447 MET cc_start: 0.8573 (mmm) cc_final: 0.8147 (mmt) REVERT: D 120 ASP cc_start: 0.5025 (m-30) cc_final: 0.4824 (m-30) REVERT: D 172 TRP cc_start: 0.6804 (m100) cc_final: 0.6522 (m100) REVERT: D 262 MET cc_start: 0.8436 (mmp) cc_final: 0.7971 (mmp) REVERT: D 412 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8243 (p) REVERT: D 447 MET cc_start: 0.8562 (mmm) cc_final: 0.8132 (mmt) outliers start: 15 outliers final: 10 residues processed: 154 average time/residue: 0.8267 time to fit residues: 144.7772 Evaluate side-chains 144 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 10 ILE 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 10 ILE 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 10 ILE 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: 0.3980 chunk 51 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 33 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.187223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148467 restraints weight = 37705.389| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.39 r_work: 0.3194 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13332 Z= 0.099 Angle : 0.455 4.705 18136 Z= 0.230 Chirality : 0.037 0.133 1960 Planarity : 0.004 0.038 2252 Dihedral : 8.015 87.701 1980 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.22 % Allowed : 9.71 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.22), residues: 1552 helix: 1.71 (0.17), residues: 948 sheet: -2.24 (0.75), residues: 40 loop : -0.72 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 110 TYR 0.005 0.001 TYR A 407 PHE 0.014 0.001 PHE D 56 TRP 0.007 0.001 TRP A 255 HIS 0.001 0.000 HIS D 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (13320) covalent geometry : angle 0.45493 / 0.23 (18136) hydrogen bonds : bond 0.04793 / 3.21 ( 700) hydrogen bonds : angle 4.28461 / 3.08 ( 2016) metal coordination : bond 0.00223 / 0.15 ( 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 155 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.607 Fit side-chains REVERT: A 120 ASP cc_start: 0.5145 (m-30) cc_final: 0.4936 (m-30) REVERT: A 172 TRP cc_start: 0.7129 (m100) cc_final: 0.6745 (m100) REVERT: A 262 MET cc_start: 0.8407 (mmp) cc_final: 0.8017 (mmp) REVERT: A 447 MET cc_start: 0.8499 (mmm) cc_final: 0.8124 (mmt) REVERT: B 120 ASP cc_start: 0.5080 (m-30) cc_final: 0.4878 (m-30) REVERT: B 262 MET cc_start: 0.8395 (mmp) cc_final: 0.8006 (mmp) REVERT: B 324 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 447 MET cc_start: 0.8491 (mmm) cc_final: 0.8107 (mmt) REVERT: C 120 ASP cc_start: 0.5087 (m-30) cc_final: 0.4883 (m-30) REVERT: C 262 MET cc_start: 0.8404 (mmp) cc_final: 0.7989 (mmp) REVERT: C 324 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 447 MET cc_start: 0.8504 (mmm) cc_final: 0.8137 (mmt) REVERT: D 120 ASP cc_start: 0.5087 (m-30) cc_final: 0.4878 (m-30) REVERT: D 262 MET cc_start: 0.8393 (mmp) cc_final: 0.8008 (mmp) REVERT: D 324 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8102 (mp) REVERT: D 447 MET cc_start: 0.8477 (mmm) cc_final: 0.8099 (mmt) outliers start: 16 outliers final: 4 residues processed: 151 average time/residue: 0.7847 time to fit residues: 135.2282 Evaluate side-chains 134 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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: 0.7980 chunk 119 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.185645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.146065 restraints weight = 37446.131| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.30 r_work: 0.3187 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13332 Z= 0.119 Angle : 0.476 5.634 18136 Z= 0.240 Chirality : 0.038 0.131 1960 Planarity : 0.004 0.040 2252 Dihedral : 7.632 80.239 1976 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % 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 are not related in a simple way. whole: 1.12 (0.23), residues: 1552 helix: 1.81 (0.18), residues: 936 sheet: -1.97 (0.78), residues: 40 loop : -0.84 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 110 TYR 0.006 0.001 TYR A 407 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/Z covalent geometry : bond 0.00275 / 0.12 (13320) covalent geometry : angle 0.47623 / 0.24 (18136) hydrogen bonds : bond 0.05024 / 3.36 ( 700) hydrogen bonds : angle 4.17337 / 3.00 ( 2016) metal coordination : bond 0.00243 / 0.16 ( 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 141 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.693 Fit side-chains REVERT: A 172 TRP cc_start: 0.7070 (m100) cc_final: 0.6755 (m100) REVERT: A 262 MET cc_start: 0.8429 (mmp) cc_final: 0.8105 (mmp) REVERT: A 447 MET cc_start: 0.8608 (mmm) cc_final: 0.8272 (mmt) REVERT: B 262 MET cc_start: 0.8444 (mmp) cc_final: 0.8125 (mmp) REVERT: B 324 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8128 (mp) REVERT: C 262 MET cc_start: 0.8429 (mmp) cc_final: 0.8104 (mmp) REVERT: C 324 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8125 (mp) REVERT: C 447 MET cc_start: 0.8609 (mmm) cc_final: 0.8280 (mmt) REVERT: D 262 MET cc_start: 0.8425 (mmp) cc_final: 0.8092 (mmp) REVERT: D 324 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8128 (mp) REVERT: D 447 MET cc_start: 0.8585 (mmm) cc_final: 0.8248 (mmt) outliers start: 12 outliers final: 4 residues processed: 137 average time/residue: 0.8883 time to fit residues: 136.9506 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 : 0.677 ------------------------------------------------------------------------------- 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: 9.9990 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.184736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144636 restraints weight = 37438.582| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.32 r_work: 0.3215 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13332 Z= 0.138 Angle : 0.496 5.191 18136 Z= 0.250 Chirality : 0.038 0.127 1960 Planarity : 0.004 0.041 2252 Dihedral : 7.082 55.630 1976 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.92 % Allowed : 10.55 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.22), residues: 1552 helix: 1.74 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.85 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 317 TYR 0.006 0.001 TYR A 365 PHE 0.016 0.001 PHE B 56 TRP 0.007 0.001 TRP A 255 HIS 0.003 0.000 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13320) covalent geometry : angle 0.49584 / 0.25 (18136) hydrogen bonds : bond 0.05298 / 3.55 ( 700) hydrogen bonds : angle 4.16536 / 3.00 ( 2016) metal coordination : bond 0.00352 / 0.23 ( 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 137 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.676 Fit side-chains REVERT: A 172 TRP cc_start: 0.7045 (m100) cc_final: 0.6775 (m100) REVERT: A 262 MET cc_start: 0.8448 (mmp) cc_final: 0.8121 (mmp) REVERT: A 447 MET cc_start: 0.8618 (mmm) cc_final: 0.8290 (mmt) REVERT: B 262 MET cc_start: 0.8453 (mmp) cc_final: 0.8137 (mmp) REVERT: B 324 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8134 (mp) REVERT: C 262 MET cc_start: 0.8461 (mmp) cc_final: 0.8128 (mmp) REVERT: C 324 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8135 (mp) REVERT: C 447 MET cc_start: 0.8608 (mmm) cc_final: 0.8273 (mmt) REVERT: D 262 MET cc_start: 0.8451 (mmp) cc_final: 0.8126 (mmp) REVERT: D 324 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8139 (mp) REVERT: D 447 MET cc_start: 0.8598 (mmm) cc_final: 0.8262 (mmt) outliers start: 12 outliers final: 8 residues processed: 133 average time/residue: 0.9828 time to fit residues: 146.4847 Evaluate side-chains 132 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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: 0.8980 chunk 79 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.183782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.142196 restraints weight = 37624.836| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.35 r_work: 0.3139 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13332 Z= 0.160 Angle : 0.514 5.460 18136 Z= 0.260 Chirality : 0.039 0.125 1960 Planarity : 0.005 0.043 2252 Dihedral : 6.690 53.669 1976 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.92 % Allowed : 11.16 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.22), residues: 1552 helix: 1.66 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.86 (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 0.019 0.001 PHE A 56 TRP 0.007 0.001 TRP A 392 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (13320) covalent geometry : angle 0.51407 / 0.26 (18136) hydrogen bonds : bond 0.05665 / 3.79 ( 700) hydrogen bonds : angle 4.17097 / 3.00 ( 2016) metal coordination : bond 0.00423 / 0.28 ( 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 138 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.698 Fit side-chains REVERT: A 172 TRP cc_start: 0.7011 (m100) cc_final: 0.6781 (m100) REVERT: A 262 MET cc_start: 0.8488 (mmp) cc_final: 0.8165 (mmp) REVERT: B 262 MET cc_start: 0.8487 (mmp) cc_final: 0.8171 (mmp) REVERT: B 324 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8086 (mp) REVERT: C 262 MET cc_start: 0.8489 (mmp) cc_final: 0.8183 (mmp) REVERT: C 324 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8081 (mp) REVERT: D 262 MET cc_start: 0.8485 (mmp) cc_final: 0.8166 (mmp) REVERT: D 324 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8080 (mp) outliers start: 12 outliers final: 8 residues processed: 134 average time/residue: 0.9673 time to fit residues: 145.6433 Evaluate side-chains 135 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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: 2.9990 chunk 94 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.183662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143263 restraints weight = 37260.068| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.27 r_work: 0.3132 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13332 Z= 0.173 Angle : 0.524 5.228 18136 Z= 0.266 Chirality : 0.039 0.128 1960 Planarity : 0.005 0.043 2252 Dihedral : 6.771 53.850 1976 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.92 % Allowed : 11.62 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1552 helix: 1.59 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.87 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 72 TYR 0.008 0.001 TYR A 365 PHE 0.017 0.001 PHE D 56 TRP 0.007 0.001 TRP B 392 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (13320) covalent geometry : angle 0.52390 / 0.27 (18136) hydrogen bonds : bond 0.05820 / 3.90 ( 700) hydrogen bonds : angle 4.18673 / 3.02 ( 2016) metal coordination : bond 0.00513 / 0.34 ( 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 137 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.680 Fit side-chains REVERT: A 172 TRP cc_start: 0.6973 (m100) cc_final: 0.6771 (m100) REVERT: A 262 MET cc_start: 0.8463 (mmp) cc_final: 0.8131 (mmp) REVERT: B 262 MET cc_start: 0.8481 (mmp) cc_final: 0.8167 (mmp) REVERT: B 324 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 262 MET cc_start: 0.8490 (mmp) cc_final: 0.8180 (mmp) REVERT: C 324 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 447 MET cc_start: 0.8573 (mmm) cc_final: 0.8259 (mmt) REVERT: D 262 MET cc_start: 0.8482 (mmp) cc_final: 0.8167 (mmp) REVERT: D 324 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8096 (mp) REVERT: D 447 MET cc_start: 0.8551 (mmm) cc_final: 0.8233 (mmt) outliers start: 12 outliers final: 8 residues processed: 133 average time/residue: 0.9353 time to fit residues: 139.5366 Evaluate side-chains 136 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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: 2.9990 chunk 25 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 72 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.185894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.143417 restraints weight = 37390.584| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.43 r_work: 0.3177 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2846 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= 0.110 Angle : 0.472 4.393 18136 Z= 0.238 Chirality : 0.037 0.124 1960 Planarity : 0.004 0.041 2252 Dihedral : 6.312 49.242 1976 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.38 % Allowed : 11.47 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.22), residues: 1552 helix: 1.72 (0.17), residues: 956 sheet: -0.67 (0.90), residues: 40 loop : -0.74 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 110 TYR 0.006 0.001 TYR C 365 PHE 0.012 0.001 PHE D 384 TRP 0.008 0.001 TRP A 255 HIS 0.002 0.000 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (13320) covalent geometry : angle 0.47173 / 0.24 (18136) hydrogen bonds : bond 0.04889 / 3.28 ( 700) hydrogen bonds : angle 4.05352 / 2.92 ( 2016) metal coordination : bond 0.00274 / 0.18 ( 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: 18 poor density : 131 time to evaluate : 0.698 Fit side-chains REVERT: A 172 TRP cc_start: 0.6917 (m100) cc_final: 0.6710 (m100) REVERT: A 412 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 447 MET cc_start: 0.8642 (mmm) cc_final: 0.8369 (mmt) REVERT: B 324 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8077 (mp) REVERT: B 412 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8177 (p) REVERT: C 324 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8071 (mp) REVERT: C 412 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8177 (p) REVERT: C 447 MET cc_start: 0.8642 (mmm) cc_final: 0.8367 (mmt) REVERT: D 194 PHE cc_start: 0.8307 (m-10) cc_final: 0.8102 (m-10) REVERT: D 324 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8068 (mp) REVERT: D 412 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8174 (p) REVERT: D 447 MET cc_start: 0.8627 (mmm) cc_final: 0.8350 (mmt) outliers start: 18 outliers final: 8 residues processed: 145 average time/residue: 0.8628 time to fit residues: 141.2261 Evaluate side-chains 144 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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: 0.7980 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 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: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4086 r_free = 0.4086 target = 0.186216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146345 restraints weight = 37458.970| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.32 r_work: 0.3191 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13332 Z= 0.111 Angle : 0.476 4.461 18136 Z= 0.238 Chirality : 0.037 0.122 1960 Planarity : 0.004 0.041 2252 Dihedral : 6.249 48.165 1976 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.38 % Allowed : 12.31 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.23), residues: 1552 helix: 1.72 (0.17), residues: 964 sheet: -0.47 (0.94), residues: 40 loop : -0.67 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 317 TYR 0.005 0.001 TYR B 365 PHE 0.012 0.001 PHE B 194 TRP 0.007 0.001 TRP A 255 HIS 0.002 0.000 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (13320) covalent geometry : angle 0.47558 / 0.24 (18136) hydrogen bonds : bond 0.04819 / 3.23 ( 700) hydrogen bonds : angle 3.98095 / 2.86 ( 2016) metal coordination : bond 0.00269 / 0.18 ( 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 154 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.467 Fit side-chains REVERT: A 412 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8179 (p) REVERT: A 447 MET cc_start: 0.8642 (mmm) cc_final: 0.8370 (mmt) REVERT: B 324 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8083 (mp) REVERT: B 412 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8181 (p) REVERT: C 324 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8076 (mp) REVERT: C 412 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8181 (p) REVERT: C 447 MET cc_start: 0.8636 (mmm) cc_final: 0.8361 (mmt) REVERT: D 324 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8079 (mp) REVERT: D 412 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8184 (p) REVERT: D 447 MET cc_start: 0.8620 (mmm) cc_final: 0.8339 (mmt) outliers start: 18 outliers final: 8 residues processed: 150 average time/residue: 0.8130 time to fit residues: 137.2304 Evaluate side-chains 152 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 16 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4072 r_free = 0.4072 target = 0.184712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144289 restraints weight = 37220.037| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.32 r_work: 0.3160 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2943 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= 0.149 Angle : 0.508 4.830 18136 Z= 0.255 Chirality : 0.039 0.124 1960 Planarity : 0.005 0.043 2252 Dihedral : 6.561 51.727 1976 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.38 % Allowed : 12.31 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.22), residues: 1552 helix: 1.76 (0.18), residues: 940 sheet: -0.35 (0.96), residues: 40 loop : -0.93 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 72 TYR 0.007 0.001 TYR A 365 PHE 0.015 0.001 PHE D 384 TRP 0.007 0.001 TRP B 392 HIS 0.003 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (13320) covalent geometry : angle 0.50763 / 0.26 (18136) hydrogen bonds : bond 0.05398 / 3.62 ( 700) hydrogen bonds : angle 4.03138 / 2.90 ( 2016) metal coordination : bond 0.00421 / 0.28 ( 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 153 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.691 Fit side-chains REVERT: A 412 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8259 (p) REVERT: A 447 MET cc_start: 0.8620 (mmm) cc_final: 0.8325 (mmt) REVERT: B 324 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8123 (mp) REVERT: B 412 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8242 (p) REVERT: B 447 MET cc_start: 0.8613 (mmm) cc_final: 0.8380 (mmp) REVERT: C 324 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8130 (mp) REVERT: C 412 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8242 (p) REVERT: C 447 MET cc_start: 0.8627 (mmm) cc_final: 0.8329 (mmt) REVERT: D 324 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8129 (mp) REVERT: D 412 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8242 (p) REVERT: D 447 MET cc_start: 0.8617 (mmm) cc_final: 0.8317 (mmt) outliers start: 18 outliers final: 8 residues processed: 149 average time/residue: 0.9036 time to fit residues: 151.3540 Evaluate side-chains 150 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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: 0.9990 chunk 73 optimal weight: 0.9990 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: 0.8980 chunk 95 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 276 ASN C 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.186207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145914 restraints weight = 37239.596| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.32 r_work: 0.3151 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13332 Z= 0.110 Angle : 0.473 4.278 18136 Z= 0.237 Chirality : 0.037 0.122 1960 Planarity : 0.004 0.041 2252 Dihedral : 6.304 48.196 1976 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.30 % Allowed : 12.31 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.22), residues: 1552 helix: 1.75 (0.17), residues: 964 sheet: -0.27 (0.96), residues: 40 loop : -0.69 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 110 TYR 0.006 0.001 TYR A 365 PHE 0.011 0.001 PHE A 194 TRP 0.008 0.001 TRP A 255 HIS 0.002 0.000 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (13320) covalent geometry : angle 0.47314 / 0.24 (18136) hydrogen bonds : bond 0.04802 / 3.22 ( 700) hydrogen bonds : angle 3.95716 / 2.84 ( 2016) metal coordination : bond 0.00275 / 0.18 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7030.41 seconds wall clock time: 119 minutes 41.18 seconds (7181.18 seconds total)