Starting phenix.real_space_refine on Thu Mar 5 21:41:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f1c_28793/03_2026/8f1c_28793_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f1c_28793/03_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_28793/03_2026/8f1c_28793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f1c_28793/03_2026/8f1c_28793.map" model { file = "/net/cci-nas-00/data/ceres_data/8f1c_28793/03_2026/8f1c_28793_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f1c_28793/03_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-5986/lib/python3.9/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, 88 Unusual residues: {' K': 4, ' ZN': 1, 'POV': 1, 'X9T': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 4.28, per 1000 atoms: 0.17 Number of scatterers: 25116 At special positions: 0 Unit cell: (135.24, 135.24, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 4 29.99 K 4 19.00 Cl 4 17.00 S 68 16.00 P 4 15.00 O 2208 8.00 N 2120 7.00 C 8520 6.00 H 12184 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 918.9 milliseconds 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: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.975A pdb=" N LEU A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 22 through 27' Processing helix chain 'A' and resid 32 through 39 removed outlier: 3.540A pdb=" N GLU A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.729A pdb=" N PHE A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 65 " --> pdb=" O PRO A 61 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.703A pdb=" N ASP A 100 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.697A pdb=" N TYR A 109 " --> pdb=" O CYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.905A pdb=" N ALA A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 180 removed outlier: 3.869A pdb=" N PHE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 211 removed outlier: 3.914A pdb=" N THR A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 266 removed outlier: 3.620A pdb=" N GLU A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.548A pdb=" N TYR A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 311 removed outlier: 4.456A pdb=" N ASP A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.665A pdb=" N ARG A 320 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.695A pdb=" N ARG A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 Processing helix chain 'A' and resid 341 through 367 Processing helix chain 'A' and resid 377 through 381 removed outlier: 4.179A pdb=" N HIS A 381 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 removed outlier: 4.363A pdb=" N TRP A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 431 through 452 removed outlier: 3.606A pdb=" N ILE A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.974A pdb=" N LEU B 26 " --> pdb=" O TYR B 22 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 22 through 27' Processing helix chain 'B' and resid 32 through 39 removed outlier: 3.540A pdb=" N GLU B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 74 removed outlier: 3.729A pdb=" N PHE B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N HIS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.703A pdb=" N ASP B 100 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 105 through 110 removed outlier: 3.697A pdb=" N TYR B 109 " --> pdb=" O CYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.906A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 180 removed outlier: 3.869A pdb=" N PHE B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 211 removed outlier: 3.913A pdb=" N THR B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 266 removed outlier: 3.619A pdb=" N GLU B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.548A pdb=" N TYR B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 311 removed outlier: 4.456A pdb=" N ASP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.665A pdb=" N ARG B 320 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.695A pdb=" N ARG B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 Processing helix chain 'B' and resid 341 through 367 Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.179A pdb=" N HIS B 381 " --> pdb=" O ALA B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.363A pdb=" N TRP B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 431 through 452 removed outlier: 3.606A pdb=" N ILE B 435 " --> pdb=" O PRO B 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 removed outlier: 3.975A pdb=" N LEU C 26 " --> pdb=" O TYR C 22 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG C 27 " --> pdb=" O ARG C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 22 through 27' Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.540A pdb=" N GLU C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.729A pdb=" N PHE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C 65 " --> pdb=" O PRO C 61 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.703A pdb=" N ASP C 100 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.697A pdb=" N TYR C 109 " --> pdb=" O CYS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 121 removed outlier: 3.905A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 180 removed outlier: 3.869A pdb=" N PHE C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 211 removed outlier: 3.913A pdb=" N THR C 211 " --> pdb=" O PHE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 266 removed outlier: 3.619A pdb=" N GLU C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'C' and resid 278 through 285 Processing helix chain 'C' and resid 286 through 294 removed outlier: 3.548A pdb=" N TYR C 290 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 311 removed outlier: 4.456A pdb=" N ASP C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.664A pdb=" N ARG C 320 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.695A pdb=" N ARG C 326 " --> pdb=" O PHE C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 341 Processing helix chain 'C' and resid 341 through 367 Processing helix chain 'C' and resid 377 through 381 removed outlier: 4.178A pdb=" N HIS C 381 " --> pdb=" O ALA C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 399 removed outlier: 4.364A pdb=" N TRP C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 431 through 452 removed outlier: 3.606A pdb=" N ILE C 435 " --> pdb=" O PRO C 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 removed outlier: 3.974A pdb=" N LEU D 26 " --> pdb=" O TYR D 22 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 27' Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.540A pdb=" N GLU D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 74 removed outlier: 3.729A pdb=" N PHE D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA D 65 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.705A pdb=" N ASP D 100 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 101 " --> pdb=" O GLU D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.697A pdb=" N TYR D 109 " --> pdb=" O CYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.905A pdb=" N ALA D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 180 removed outlier: 3.869A pdb=" N PHE D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 211 removed outlier: 3.913A pdb=" N THR D 211 " --> pdb=" O PHE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 266 removed outlier: 3.619A pdb=" N GLU D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 276 Processing helix chain 'D' and resid 278 through 285 Processing helix chain 'D' and resid 286 through 294 removed outlier: 3.548A pdb=" N TYR D 290 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 311 removed outlier: 4.456A pdb=" N ASP D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.665A pdb=" N ARG D 320 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.695A pdb=" N ARG D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 Processing helix chain 'D' and resid 341 through 367 Processing helix chain 'D' and resid 377 through 381 removed outlier: 4.179A pdb=" N HIS D 381 " --> pdb=" O ALA D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 399 removed outlier: 4.363A pdb=" N TRP D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 431 through 452 removed outlier: 3.606A pdb=" N ILE D 435 " --> pdb=" O PRO D 431 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR A 21 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 10 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 49 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR B 21 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 10 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 54 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 49 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 10 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 54 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C 49 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR D 21 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 10 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU D 54 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP D 49 " --> pdb=" O GLU D 54 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.49 Time building geometry restraints manager: 3.54 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 29.800 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13332 Z= 0.183 Angle : 0.527 6.232 18136 Z= 0.247 Chirality : 0.036 0.121 1960 Planarity : 0.004 0.035 2252 Dihedral : 11.032 80.333 4768 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.61 % Allowed : 3.36 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they 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 covalent geometry : bond 0.00395 (13320) covalent geometry : angle 0.52698 (18136) hydrogen bonds : bond 0.16365 ( 700) hydrogen bonds : angle 5.51583 ( 2016) metal coordination : bond 0.00255 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 205 time to evaluate : 0.659 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: 1.2818 time to fit residues: 297.7761 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 : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 ASN C 276 ASN D 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.183692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.144153 restraints weight = 37481.497| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.33 r_work: 0.3146 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13332 Z= 0.210 Angle : 0.578 6.669 18136 Z= 0.299 Chirality : 0.042 0.149 1960 Planarity : 0.005 0.046 2252 Dihedral : 8.702 84.506 1980 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.15 % Allowed : 9.71 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1552 helix: 1.32 (0.17), residues: 936 sheet: -2.41 (0.74), residues: 40 loop : -1.15 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 214 TYR 0.008 0.001 TYR C 365 PHE 0.015 0.001 PHE B 384 TRP 0.008 0.001 TRP B 392 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00512 (13320) covalent geometry : angle 0.57791 (18136) hydrogen bonds : bond 0.06334 ( 700) hydrogen bonds : angle 4.58381 ( 2016) metal coordination : bond 0.00621 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.642 Fit side-chains REVERT: A 120 ASP cc_start: 0.5061 (m-30) cc_final: 0.4852 (m-30) REVERT: A 172 TRP cc_start: 0.7143 (m100) cc_final: 0.6745 (m100) REVERT: A 262 MET cc_start: 0.8451 (mmp) cc_final: 0.8017 (mmp) REVERT: A 412 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8263 (p) REVERT: B 120 ASP cc_start: 0.5078 (m-30) cc_final: 0.4868 (m-30) REVERT: B 172 TRP cc_start: 0.6816 (m100) cc_final: 0.6534 (m100) REVERT: B 262 MET cc_start: 0.8460 (mmp) cc_final: 0.8033 (mmp) REVERT: B 412 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8269 (p) REVERT: B 447 MET cc_start: 0.8533 (mmm) cc_final: 0.8100 (mmt) REVERT: C 120 ASP cc_start: 0.5094 (m-30) cc_final: 0.4876 (m-30) REVERT: C 172 TRP cc_start: 0.6792 (m100) cc_final: 0.6513 (m100) REVERT: C 262 MET cc_start: 0.8454 (mmp) cc_final: 0.8031 (mmp) REVERT: C 412 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8267 (p) REVERT: D 120 ASP cc_start: 0.5076 (m-30) cc_final: 0.4870 (m-30) REVERT: D 172 TRP cc_start: 0.6820 (m100) cc_final: 0.6536 (m100) REVERT: D 262 MET cc_start: 0.8448 (mmp) cc_final: 0.8010 (mmp) REVERT: D 412 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8268 (p) outliers start: 15 outliers final: 6 residues processed: 151 average time/residue: 1.0011 time to fit residues: 169.1965 Evaluate side-chains 138 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 0.0010 chunk 51 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 33 optimal weight: 0.0670 chunk 55 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 overall best weight: 0.5928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.187408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146334 restraints weight = 37471.024| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.49 r_work: 0.3191 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13332 Z= 0.097 Angle : 0.451 4.691 18136 Z= 0.228 Chirality : 0.037 0.131 1960 Planarity : 0.004 0.037 2252 Dihedral : 7.989 88.239 1980 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.22 % Allowed : 10.02 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.22), residues: 1552 helix: 1.72 (0.17), residues: 948 sheet: -2.22 (0.76), residues: 40 loop : -0.86 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 110 TYR 0.005 0.001 TYR C 407 PHE 0.009 0.001 PHE A 384 TRP 0.007 0.001 TRP A 255 HIS 0.001 0.000 HIS D 383 Details of bonding type rmsd covalent geometry : bond 0.00201 (13320) covalent geometry : angle 0.45136 (18136) hydrogen bonds : bond 0.04714 ( 700) hydrogen bonds : angle 4.28590 ( 2016) metal coordination : bond 0.00153 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.648 Fit side-chains REVERT: A 120 ASP cc_start: 0.5083 (m-30) cc_final: 0.4878 (m-30) REVERT: A 172 TRP cc_start: 0.7114 (m100) cc_final: 0.6763 (m100) REVERT: A 262 MET cc_start: 0.8422 (mmp) cc_final: 0.8072 (mmp) REVERT: A 447 MET cc_start: 0.8511 (mmm) cc_final: 0.8145 (mmt) REVERT: B 262 MET cc_start: 0.8433 (mmp) cc_final: 0.8087 (mmp) REVERT: B 324 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8083 (mp) REVERT: B 447 MET cc_start: 0.8510 (mmm) cc_final: 0.8133 (mmt) REVERT: C 262 MET cc_start: 0.8433 (mmp) cc_final: 0.8079 (mmp) REVERT: C 324 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8077 (mp) REVERT: C 447 MET cc_start: 0.8510 (mmm) cc_final: 0.8143 (mmt) REVERT: D 120 ASP cc_start: 0.5052 (m-30) cc_final: 0.4849 (m-30) REVERT: D 262 MET cc_start: 0.8425 (mmp) cc_final: 0.8073 (mmp) REVERT: D 324 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8084 (mp) REVERT: D 447 MET cc_start: 0.8503 (mmm) cc_final: 0.8131 (mmt) outliers start: 16 outliers final: 4 residues processed: 148 average time/residue: 0.9987 time to fit residues: 164.9682 Evaluate side-chains 135 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 62 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 146 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.185102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144572 restraints weight = 37202.324| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.35 r_work: 0.3159 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13332 Z= 0.137 Angle : 0.494 5.375 18136 Z= 0.248 Chirality : 0.038 0.130 1960 Planarity : 0.004 0.041 2252 Dihedral : 7.796 81.447 1976 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.61 % Allowed : 11.24 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1552 helix: 1.74 (0.18), residues: 936 sheet: -1.87 (0.79), residues: 40 loop : -1.04 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 214 TYR 0.006 0.001 TYR C 365 PHE 0.014 0.001 PHE B 56 TRP 0.006 0.001 TRP D 392 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00326 (13320) covalent geometry : angle 0.49387 (18136) hydrogen bonds : bond 0.05272 ( 700) hydrogen bonds : angle 4.21752 ( 2016) metal coordination : bond 0.00310 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.675 Fit side-chains REVERT: A 172 TRP cc_start: 0.7093 (m100) cc_final: 0.6764 (m100) REVERT: A 262 MET cc_start: 0.8406 (mmp) cc_final: 0.8056 (mmp) REVERT: B 262 MET cc_start: 0.8403 (mmp) cc_final: 0.8054 (mmp) REVERT: B 324 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8127 (mp) REVERT: C 262 MET cc_start: 0.8412 (mmp) cc_final: 0.8060 (mmp) REVERT: C 324 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8121 (mp) REVERT: D 262 MET cc_start: 0.8400 (mmp) cc_final: 0.8044 (mmp) REVERT: D 324 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8122 (mp) outliers start: 8 outliers final: 4 residues processed: 133 average time/residue: 1.1230 time to fit residues: 165.5617 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 : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.185045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144675 restraints weight = 37223.099| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.26 r_work: 0.3169 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13332 Z= 0.129 Angle : 0.482 5.031 18136 Z= 0.242 Chirality : 0.038 0.126 1960 Planarity : 0.004 0.041 2252 Dihedral : 7.048 56.384 1976 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.92 % Allowed : 10.93 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.22), residues: 1552 helix: 1.72 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -1.03 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 317 TYR 0.006 0.001 TYR A 407 PHE 0.016 0.001 PHE B 56 TRP 0.007 0.001 TRP A 255 HIS 0.002 0.000 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00301 (13320) covalent geometry : angle 0.48153 (18136) hydrogen bonds : bond 0.05205 ( 700) hydrogen bonds : angle 4.15592 ( 2016) metal coordination : bond 0.00333 ( 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 134 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.672 Fit side-chains REVERT: A 172 TRP cc_start: 0.7038 (m100) cc_final: 0.6766 (m100) REVERT: A 262 MET cc_start: 0.8424 (mmp) cc_final: 0.8100 (mmp) REVERT: B 262 MET cc_start: 0.8434 (mmp) cc_final: 0.8114 (mmp) REVERT: B 324 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8135 (mp) REVERT: C 262 MET cc_start: 0.8446 (mmp) cc_final: 0.8129 (mmp) REVERT: C 324 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8130 (mp) REVERT: D 262 MET cc_start: 0.8431 (mmp) cc_final: 0.8105 (mmp) REVERT: D 324 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8132 (mp) outliers start: 12 outliers final: 8 residues processed: 130 average time/residue: 1.1314 time to fit residues: 162.7139 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 : 0.639 ------------------------------------------------------------------------------- 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: 0.7980 chunk 79 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.185103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144440 restraints weight = 37421.308| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.23 r_work: 0.3157 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13332 Z= 0.130 Angle : 0.482 4.786 18136 Z= 0.243 Chirality : 0.038 0.125 1960 Planarity : 0.004 0.041 2252 Dihedral : 6.376 50.108 1976 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.59 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: 1.06 (0.22), residues: 1552 helix: 1.76 (0.18), residues: 940 sheet: None (None), residues: 0 loop : -1.00 (0.25), residues: 612 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 0.013 0.001 PHE D 384 TRP 0.007 0.001 TRP A 255 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00306 (13320) covalent geometry : angle 0.48188 (18136) hydrogen bonds : bond 0.05189 ( 700) hydrogen bonds : angle 4.09328 ( 2016) metal coordination : bond 0.00326 ( 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 140 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.728 Fit side-chains REVERT: A 172 TRP cc_start: 0.6988 (m100) cc_final: 0.6783 (m100) REVERT: A 262 MET cc_start: 0.8434 (mmp) cc_final: 0.8120 (mmp) REVERT: A 447 MET cc_start: 0.8586 (mmm) cc_final: 0.8327 (mmt) REVERT: B 262 MET cc_start: 0.8439 (mmp) cc_final: 0.8125 (mmp) REVERT: B 324 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8092 (mp) REVERT: B 447 MET cc_start: 0.8585 (mmm) cc_final: 0.8326 (mmt) REVERT: C 262 MET cc_start: 0.8454 (mmp) cc_final: 0.8143 (mmp) REVERT: C 324 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8089 (mp) REVERT: C 447 MET cc_start: 0.8581 (mmm) cc_final: 0.8321 (mmt) REVERT: D 262 MET cc_start: 0.8431 (mmp) cc_final: 0.8117 (mmp) REVERT: D 324 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8093 (mp) REVERT: D 447 MET cc_start: 0.8572 (mmm) cc_final: 0.8313 (mmt) outliers start: 12 outliers final: 8 residues processed: 136 average time/residue: 1.0820 time to fit residues: 163.6697 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 : 0.674 ------------------------------------------------------------------------------- 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: 3.9990 chunk 130 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.184669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143911 restraints weight = 37049.340| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.25 r_work: 0.3152 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2679 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 : 0.491 4.891 18136 Z= 0.247 Chirality : 0.038 0.125 1960 Planarity : 0.004 0.042 2252 Dihedral : 6.397 51.458 1976 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.92 % Allowed : 11.54 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1552 helix: 1.74 (0.17), residues: 940 sheet: -1.19 (0.84), residues: 40 loop : -1.02 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 110 TYR 0.007 0.001 TYR D 365 PHE 0.013 0.001 PHE D 384 TRP 0.007 0.001 TRP A 392 HIS 0.002 0.000 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00327 (13320) covalent geometry : angle 0.49147 (18136) hydrogen bonds : bond 0.05327 ( 700) hydrogen bonds : angle 4.07708 ( 2016) metal coordination : bond 0.00374 ( 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 139 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.666 Fit side-chains REVERT: A 262 MET cc_start: 0.8442 (mmp) cc_final: 0.8141 (mmp) REVERT: A 447 MET cc_start: 0.8589 (mmm) cc_final: 0.8297 (mmt) REVERT: B 262 MET cc_start: 0.8444 (mmp) cc_final: 0.8143 (mmp) REVERT: B 324 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8104 (mp) REVERT: B 447 MET cc_start: 0.8576 (mmm) cc_final: 0.8281 (mmt) REVERT: C 262 MET cc_start: 0.8452 (mmp) cc_final: 0.8152 (mmp) REVERT: C 324 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8100 (mp) REVERT: D 262 MET cc_start: 0.8439 (mmp) cc_final: 0.8135 (mmp) REVERT: D 324 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8105 (mp) REVERT: D 447 MET cc_start: 0.8568 (mmm) cc_final: 0.8274 (mmt) outliers start: 12 outliers final: 8 residues processed: 135 average time/residue: 1.0587 time to fit residues: 158.5937 Evaluate side-chains 143 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 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: 2.9990 chunk 101 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.185118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144643 restraints weight = 37056.894| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.27 r_work: 0.3165 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13332 Z= 0.127 Angle : 0.482 4.551 18136 Z= 0.242 Chirality : 0.038 0.123 1960 Planarity : 0.004 0.041 2252 Dihedral : 6.346 50.200 1976 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.92 % Allowed : 11.85 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.22), residues: 1552 helix: 1.78 (0.18), residues: 940 sheet: -0.92 (0.86), residues: 40 loop : -0.99 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 317 TYR 0.006 0.001 TYR C 365 PHE 0.013 0.001 PHE B 384 TRP 0.007 0.001 TRP A 255 HIS 0.002 0.000 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00297 (13320) covalent geometry : angle 0.48225 (18136) hydrogen bonds : bond 0.05143 ( 700) hydrogen bonds : angle 4.02130 ( 2016) metal coordination : bond 0.00344 ( 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 146 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.642 Fit side-chains REVERT: B 262 MET cc_start: 0.8476 (mmp) cc_final: 0.8185 (mmp) REVERT: B 324 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8074 (mp) REVERT: C 262 MET cc_start: 0.8488 (mmp) cc_final: 0.8202 (mmp) REVERT: C 324 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8067 (mp) REVERT: D 262 MET cc_start: 0.8472 (mmp) cc_final: 0.8184 (mmp) REVERT: D 324 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8073 (mp) outliers start: 12 outliers final: 8 residues processed: 142 average time/residue: 1.0204 time to fit residues: 160.6038 Evaluate side-chains 145 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 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: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.185717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144950 restraints weight = 37216.726| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.22 r_work: 0.3182 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2770 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= 0.117 Angle : 0.478 4.490 18136 Z= 0.239 Chirality : 0.038 0.122 1960 Planarity : 0.004 0.041 2252 Dihedral : 6.289 49.084 1976 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.92 % Allowed : 12.23 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.22), residues: 1552 helix: 1.71 (0.17), residues: 964 sheet: -0.68 (0.89), residues: 40 loop : -0.79 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 110 TYR 0.006 0.001 TYR B 365 PHE 0.012 0.001 PHE A 194 TRP 0.007 0.001 TRP C 255 HIS 0.002 0.000 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00270 (13320) covalent geometry : angle 0.47773 (18136) hydrogen bonds : bond 0.04973 ( 700) hydrogen bonds : angle 3.98481 ( 2016) metal coordination : bond 0.00301 ( 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 147 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.692 Fit side-chains REVERT: B 324 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8094 (mp) REVERT: C 324 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8089 (mp) REVERT: D 324 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8093 (mp) outliers start: 12 outliers final: 8 residues processed: 143 average time/residue: 1.0530 time to fit residues: 167.3884 Evaluate side-chains 145 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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=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: 0.9990 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.185486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145175 restraints weight = 37054.593| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.29 r_work: 0.3152 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13332 Z= 0.128 Angle : 0.492 4.810 18136 Z= 0.245 Chirality : 0.038 0.123 1960 Planarity : 0.004 0.041 2252 Dihedral : 6.354 49.625 1976 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.99 % Allowed : 12.46 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.22), residues: 1552 helix: 1.82 (0.17), residues: 940 sheet: -0.51 (0.92), residues: 40 loop : -0.99 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 317 TYR 0.006 0.001 TYR D 365 PHE 0.013 0.001 PHE D 384 TRP 0.007 0.001 TRP D 392 HIS 0.002 0.000 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00300 (13320) covalent geometry : angle 0.49222 (18136) hydrogen bonds : bond 0.05094 ( 700) hydrogen bonds : angle 3.98458 ( 2016) metal coordination : bond 0.00352 ( 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 147 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.657 Fit side-chains REVERT: B 324 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8100 (mp) REVERT: C 324 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8094 (mp) REVERT: D 324 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8094 (mp) outliers start: 13 outliers final: 8 residues processed: 143 average time/residue: 1.1291 time to fit residues: 178.7839 Evaluate side-chains 147 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 29 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 ASN D 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.185756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144991 restraints weight = 37070.810| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.29 r_work: 0.3190 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2848 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= 0.118 Angle : 0.482 4.740 18136 Z= 0.240 Chirality : 0.038 0.122 1960 Planarity : 0.004 0.041 2252 Dihedral : 6.305 48.633 1976 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.99 % Allowed : 12.61 % 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: 1.22 (0.22), residues: 1552 helix: 1.74 (0.17), residues: 964 sheet: -0.33 (0.95), residues: 40 loop : -0.78 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 317 TYR 0.006 0.001 TYR D 365 PHE 0.014 0.001 PHE A 194 TRP 0.007 0.001 TRP A 255 HIS 0.002 0.000 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00274 (13320) covalent geometry : angle 0.48168 (18136) hydrogen bonds : bond 0.04939 ( 700) hydrogen bonds : angle 3.95277 ( 2016) metal coordination : bond 0.00306 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7681.05 seconds wall clock time: 130 minutes 22.62 seconds (7822.62 seconds total)