Starting phenix.real_space_refine on Wed Mar 4 17:13:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t23_10365/03_2026/6t23_10365.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t23_10365/03_2026/6t23_10365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t23_10365/03_2026/6t23_10365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t23_10365/03_2026/6t23_10365.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t23_10365/03_2026/6t23_10365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t23_10365/03_2026/6t23_10365.map" } resolution = 3.1 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9425 2.51 5 N 2495 2.21 5 O 2865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 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: 14910 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.00, per 1000 atoms: 0.20 Number of scatterers: 14910 At special positions: 0 Unit cell: (96.6, 92.4, 193.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 15 15.00 Mg 5 11.99 O 2865 8.00 N 2495 7.00 C 9425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 552.0 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 30 sheets defined 53.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 124 removed outlier: 4.044A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.976A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.767A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.514A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.620A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 351 through 356 removed outlier: 4.182A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 124 removed outlier: 4.043A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.975A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.767A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.513A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.621A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 351 through 356 removed outlier: 4.181A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 124 removed outlier: 4.044A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.976A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.767A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 295 removed outlier: 4.514A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.620A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 351 through 356 removed outlier: 4.182A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 124 removed outlier: 4.044A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.976A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.767A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.514A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.620A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 351 through 356 removed outlier: 4.183A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 124 removed outlier: 4.043A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.976A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 removed outlier: 3.767A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 295 removed outlier: 4.514A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.619A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 351 through 356 removed outlier: 4.182A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.427A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.557A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.427A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.557A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.427A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.557A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.427A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.557A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.426A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.557A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 765 hydrogen bonds defined for protein. 1875 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: 2.72 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2490 1.30 - 1.43: 3931 1.43 - 1.56: 8550 1.56 - 1.70: 84 1.70 - 1.83: 185 Bond restraints: 15240 Sorted by residual: bond pdb=" C22 9ZK B 379 " pdb=" N23 9ZK B 379 " ideal model delta sigma weight residual 1.350 1.511 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" C22 9ZK E 379 " pdb=" N23 9ZK E 379 " ideal model delta sigma weight residual 1.350 1.511 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" C22 9ZK A 379 " pdb=" N23 9ZK A 379 " ideal model delta sigma weight residual 1.350 1.510 -0.160 2.00e-02 2.50e+03 6.44e+01 bond pdb=" C22 9ZK C 379 " pdb=" N23 9ZK C 379 " ideal model delta sigma weight residual 1.350 1.510 -0.160 2.00e-02 2.50e+03 6.43e+01 bond pdb=" C22 9ZK D 379 " pdb=" N23 9ZK D 379 " ideal model delta sigma weight residual 1.350 1.510 -0.160 2.00e-02 2.50e+03 6.40e+01 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 16839 2.09 - 4.19: 3188 4.19 - 6.28: 493 6.28 - 8.37: 120 8.37 - 10.47: 50 Bond angle restraints: 20690 Sorted by residual: angle pdb=" C GLN A 263 " pdb=" N PRO A 264 " pdb=" CA PRO A 264 " ideal model delta sigma weight residual 119.56 127.69 -8.13 1.02e+00 9.61e-01 6.35e+01 angle pdb=" C GLN E 263 " pdb=" N PRO E 264 " pdb=" CA PRO E 264 " ideal model delta sigma weight residual 119.56 127.68 -8.12 1.02e+00 9.61e-01 6.34e+01 angle pdb=" C GLN D 263 " pdb=" N PRO D 264 " pdb=" CA PRO D 264 " ideal model delta sigma weight residual 119.56 127.68 -8.12 1.02e+00 9.61e-01 6.33e+01 angle pdb=" C LEU E 171 " pdb=" N PRO E 172 " pdb=" CA PRO E 172 " ideal model delta sigma weight residual 119.87 128.13 -8.26 1.04e+00 9.25e-01 6.30e+01 angle pdb=" C GLN C 263 " pdb=" N PRO C 264 " pdb=" CA PRO C 264 " ideal model delta sigma weight residual 119.56 127.65 -8.09 1.02e+00 9.61e-01 6.29e+01 ... (remaining 20685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 8985 35.46 - 70.92: 125 70.92 - 106.39: 45 106.39 - 141.85: 10 141.85 - 177.31: 75 Dihedral angle restraints: 9240 sinusoidal: 3880 harmonic: 5360 Sorted by residual: dihedral pdb=" O1B ADP D 376 " pdb=" O3A ADP D 376 " pdb=" PB ADP D 376 " pdb=" PA ADP D 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.79 -149.79 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP C 376 " pdb=" O3A ADP C 376 " pdb=" PB ADP C 376 " pdb=" PA ADP C 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.77 -149.78 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP E 376 " pdb=" O3A ADP E 376 " pdb=" PB ADP E 376 " pdb=" PA ADP E 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.77 -149.78 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 9237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1381 0.077 - 0.154: 693 0.154 - 0.231: 170 0.231 - 0.307: 26 0.307 - 0.384: 10 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C25 9ZK D 379 " pdb=" C26 9ZK D 379 " pdb=" C36 9ZK D 379 " pdb=" N23 9ZK D 379 " both_signs ideal model delta sigma weight residual False 2.15 2.53 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" C25 9ZK E 379 " pdb=" C26 9ZK E 379 " pdb=" C36 9ZK E 379 " pdb=" N23 9ZK E 379 " both_signs ideal model delta sigma weight residual False 2.15 2.53 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" C25 9ZK A 379 " pdb=" C26 9ZK A 379 " pdb=" C36 9ZK A 379 " pdb=" N23 9ZK A 379 " both_signs ideal model delta sigma weight residual False 2.15 2.53 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 2277 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 375 " -0.031 2.00e-02 2.50e+03 6.31e-02 3.98e+01 pdb=" C PHE A 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE A 375 " -0.040 2.00e-02 2.50e+03 pdb=" OXT PHE A 375 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 375 " 0.031 2.00e-02 2.50e+03 6.30e-02 3.97e+01 pdb=" C PHE D 375 " -0.109 2.00e-02 2.50e+03 pdb=" O PHE D 375 " 0.040 2.00e-02 2.50e+03 pdb=" OXT PHE D 375 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 375 " -0.031 2.00e-02 2.50e+03 6.30e-02 3.96e+01 pdb=" C PHE C 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE C 375 " -0.040 2.00e-02 2.50e+03 pdb=" OXT PHE C 375 " -0.038 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 899 2.69 - 3.24: 14722 3.24 - 3.80: 24272 3.80 - 4.35: 33879 4.35 - 4.90: 54089 Nonbonded interactions: 127861 Sorted by model distance: nonbonded pdb=" O3 PO4 B 377 " pdb="MG MG B 378 " model vdw 2.141 2.170 nonbonded pdb=" O3 PO4 A 377 " pdb="MG MG A 378 " model vdw 2.141 2.170 nonbonded pdb=" O3 PO4 C 377 " pdb="MG MG C 378 " model vdw 2.141 2.170 nonbonded pdb=" O3 PO4 D 377 " pdb="MG MG D 378 " model vdw 2.141 2.170 nonbonded pdb=" O3 PO4 E 377 " pdb="MG MG E 378 " model vdw 2.142 2.170 ... (remaining 127856 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 375) selection = (chain 'B' and resid 5 through 375) selection = (chain 'C' and resid 5 through 375) selection = (chain 'D' and resid 5 through 375) selection = (chain 'E' and resid 5 through 375) } 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.190 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.022 0.161 15240 Z= 1.131 Angle : 1.797 10.466 20690 Z= 1.172 Chirality : 0.092 0.384 2280 Planarity : 0.009 0.063 2630 Dihedral : 23.302 177.312 5810 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.95 (0.20), residues: 1830 helix: -0.33 (0.18), residues: 735 sheet: 0.19 (0.28), residues: 290 loop : 2.16 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 183 TYR 0.054 0.009 TYR A 279 PHE 0.025 0.005 PHE A 200 TRP 0.069 0.010 TRP E 340 HIS 0.010 0.004 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.02164 (15240) covalent geometry : angle 1.79656 (20690) hydrogen bonds : bond 0.16417 ( 755) hydrogen bonds : angle 7.06369 ( 1875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8479 (mmm) cc_final: 0.8096 (mmt) REVERT: B 283 MET cc_start: 0.8209 (mmm) cc_final: 0.7967 (mmp) REVERT: C 206 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.7448 (ttm-80) REVERT: D 119 MET cc_start: 0.8643 (ttp) cc_final: 0.8413 (ttm) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.1356 time to fit residues: 71.2051 Evaluate side-chains 169 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 297 ASN C 12 ASN C 173 HIS D 12 ASN D 101 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.096290 restraints weight = 21392.327| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.68 r_work: 0.3004 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15240 Z= 0.139 Angle : 0.660 7.310 20690 Z= 0.319 Chirality : 0.047 0.166 2280 Planarity : 0.004 0.032 2630 Dihedral : 31.807 175.051 2330 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.15 % Allowed : 6.33 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.20), residues: 1830 helix: 1.22 (0.20), residues: 705 sheet: 0.77 (0.28), residues: 300 loop : 1.99 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 39 TYR 0.014 0.001 TYR C 294 PHE 0.012 0.002 PHE A 124 TRP 0.013 0.002 TRP D 340 HIS 0.003 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00317 (15240) covalent geometry : angle 0.65995 (20690) hydrogen bonds : bond 0.03451 ( 755) hydrogen bonds : angle 4.93516 ( 1875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.706 Fit side-chains REVERT: A 47 MET cc_start: 0.3567 (mmt) cc_final: 0.2864 (mmt) REVERT: B 44 MET cc_start: 0.6885 (mtm) cc_final: 0.6613 (ttm) REVERT: B 113 LYS cc_start: 0.8553 (mttt) cc_final: 0.8273 (mtmt) REVERT: B 118 LYS cc_start: 0.8621 (mttm) cc_final: 0.8021 (tptm) REVERT: C 82 MET cc_start: 0.9109 (tpt) cc_final: 0.8796 (tpt) REVERT: C 206 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7417 (ttm170) REVERT: C 314 GLN cc_start: 0.8234 (tp40) cc_final: 0.7922 (tp40) REVERT: D 82 MET cc_start: 0.9003 (tpt) cc_final: 0.8522 (mmm) REVERT: D 92 ASN cc_start: 0.7946 (m-40) cc_final: 0.7630 (m-40) REVERT: D 162 ASN cc_start: 0.8253 (m-40) cc_final: 0.8009 (m110) REVERT: D 284 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7419 (tptp) REVERT: E 44 MET cc_start: 0.2267 (tpp) cc_final: 0.1809 (tpp) REVERT: E 271 SER cc_start: 0.8576 (t) cc_final: 0.8328 (p) outliers start: 18 outliers final: 7 residues processed: 223 average time/residue: 0.1171 time to fit residues: 38.5177 Evaluate side-chains 155 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 363 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 130 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 0.0060 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS D 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.111202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.093699 restraints weight = 21509.807| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.68 r_work: 0.2955 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15240 Z= 0.126 Angle : 0.617 6.942 20690 Z= 0.291 Chirality : 0.045 0.216 2280 Planarity : 0.004 0.035 2630 Dihedral : 30.539 179.809 2330 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.15 % Allowed : 8.69 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.20), residues: 1830 helix: 1.39 (0.20), residues: 740 sheet: 0.39 (0.29), residues: 310 loop : 2.02 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 335 TYR 0.014 0.001 TYR B 294 PHE 0.011 0.001 PHE A 200 TRP 0.010 0.002 TRP D 340 HIS 0.005 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00295 (15240) covalent geometry : angle 0.61708 (20690) hydrogen bonds : bond 0.03173 ( 755) hydrogen bonds : angle 4.60326 ( 1875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.3665 (mmt) cc_final: 0.3302 (mmt) REVERT: B 113 LYS cc_start: 0.8534 (mttt) cc_final: 0.8266 (mtmt) REVERT: B 118 LYS cc_start: 0.8675 (mttm) cc_final: 0.8047 (tptm) REVERT: B 269 MET cc_start: 0.9111 (mtt) cc_final: 0.8790 (mtt) REVERT: B 372 ARG cc_start: 0.7451 (ttp-170) cc_final: 0.7195 (ttp-170) REVERT: D 82 MET cc_start: 0.9039 (tpt) cc_final: 0.8535 (mmm) REVERT: D 95 ARG cc_start: 0.8313 (mtp85) cc_final: 0.8102 (mtm110) REVERT: D 113 LYS cc_start: 0.8679 (mttt) cc_final: 0.8056 (mmtt) REVERT: D 284 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7536 (tptp) REVERT: E 244 ASP cc_start: 0.5206 (OUTLIER) cc_final: 0.4910 (t0) outliers start: 18 outliers final: 10 residues processed: 166 average time/residue: 0.1176 time to fit residues: 29.2448 Evaluate side-chains 141 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 120 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS D 173 HIS D 353 GLN E 173 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.091015 restraints weight = 21350.288| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.68 r_work: 0.2910 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15240 Z= 0.152 Angle : 0.617 7.348 20690 Z= 0.290 Chirality : 0.046 0.178 2280 Planarity : 0.004 0.039 2630 Dihedral : 30.058 179.932 2330 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.28 % Allowed : 9.46 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.20), residues: 1830 helix: 1.68 (0.20), residues: 710 sheet: 0.31 (0.29), residues: 310 loop : 1.86 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 335 TYR 0.013 0.001 TYR B 294 PHE 0.013 0.001 PHE D 200 TRP 0.010 0.002 TRP D 340 HIS 0.005 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00363 (15240) covalent geometry : angle 0.61726 (20690) hydrogen bonds : bond 0.03226 ( 755) hydrogen bonds : angle 4.61591 ( 1875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: B 113 LYS cc_start: 0.8573 (mttt) cc_final: 0.8279 (mtmt) REVERT: B 178 LEU cc_start: 0.8647 (mp) cc_final: 0.8304 (tp) REVERT: B 269 MET cc_start: 0.9158 (mtt) cc_final: 0.8804 (mtt) REVERT: B 372 ARG cc_start: 0.7668 (ttp-170) cc_final: 0.7406 (ttp-170) REVERT: C 95 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7720 (mtm110) REVERT: C 206 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7477 (ttm170) REVERT: D 113 LYS cc_start: 0.8721 (mttt) cc_final: 0.8069 (mmtt) REVERT: D 284 LYS cc_start: 0.8196 (mtpt) cc_final: 0.7763 (tmtt) REVERT: E 224 GLU cc_start: 0.8367 (mp0) cc_final: 0.7972 (mp0) REVERT: E 244 ASP cc_start: 0.5115 (OUTLIER) cc_final: 0.4826 (t0) outliers start: 20 outliers final: 16 residues processed: 156 average time/residue: 0.1215 time to fit residues: 28.0375 Evaluate side-chains 145 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092801 restraints weight = 21217.534| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.68 r_work: 0.2938 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15240 Z= 0.118 Angle : 0.584 7.368 20690 Z= 0.270 Chirality : 0.045 0.196 2280 Planarity : 0.004 0.040 2630 Dihedral : 29.410 179.709 2330 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.21 % Allowed : 9.71 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.20), residues: 1830 helix: 1.61 (0.20), residues: 740 sheet: 0.61 (0.28), residues: 340 loop : 1.82 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 335 TYR 0.009 0.001 TYR B 294 PHE 0.009 0.001 PHE D 200 TRP 0.009 0.001 TRP C 79 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00279 (15240) covalent geometry : angle 0.58395 (20690) hydrogen bonds : bond 0.02814 ( 755) hydrogen bonds : angle 4.47731 ( 1875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.549 Fit side-chains REVERT: A 100 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8424 (mp0) REVERT: B 113 LYS cc_start: 0.8501 (mttt) cc_final: 0.8175 (mtmt) REVERT: B 178 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8307 (tp) REVERT: B 269 MET cc_start: 0.9133 (mtt) cc_final: 0.8789 (mtt) REVERT: C 51 ASP cc_start: 0.8522 (m-30) cc_final: 0.7983 (t0) REVERT: C 95 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7599 (mtm110) REVERT: C 206 ARG cc_start: 0.7759 (ttm-80) cc_final: 0.7385 (ttm-80) REVERT: D 82 MET cc_start: 0.8999 (tpt) cc_final: 0.8506 (mmm) REVERT: D 95 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8101 (mtm110) REVERT: D 113 LYS cc_start: 0.8722 (mttt) cc_final: 0.8025 (mmtt) REVERT: D 178 LEU cc_start: 0.8458 (mp) cc_final: 0.8192 (tp) REVERT: D 226 GLU cc_start: 0.8609 (tp30) cc_final: 0.8364 (mm-30) REVERT: D 284 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7787 (tmtt) REVERT: E 122 ILE cc_start: 0.8993 (mm) cc_final: 0.8586 (tt) REVERT: E 244 ASP cc_start: 0.5498 (OUTLIER) cc_final: 0.5271 (t0) outliers start: 19 outliers final: 12 residues processed: 157 average time/residue: 0.1181 time to fit residues: 28.0892 Evaluate side-chains 145 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.104903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.088468 restraints weight = 21448.055| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.56 r_work: 0.2862 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15240 Z= 0.251 Angle : 0.680 7.468 20690 Z= 0.322 Chirality : 0.049 0.226 2280 Planarity : 0.004 0.039 2630 Dihedral : 29.795 179.403 2330 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.21 % Allowed : 10.10 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.20), residues: 1830 helix: 1.59 (0.20), residues: 705 sheet: 0.27 (0.27), residues: 350 loop : 1.57 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 335 TYR 0.014 0.001 TYR B 198 PHE 0.017 0.002 PHE A 200 TRP 0.012 0.002 TRP D 340 HIS 0.006 0.002 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00606 (15240) covalent geometry : angle 0.68033 (20690) hydrogen bonds : bond 0.03831 ( 755) hydrogen bonds : angle 4.78407 ( 1875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.450 Fit side-chains REVERT: A 82 MET cc_start: 0.8819 (tpt) cc_final: 0.8511 (tpt) REVERT: A 100 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: B 113 LYS cc_start: 0.8612 (mttt) cc_final: 0.8308 (mtmt) REVERT: C 206 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7391 (ttm-80) REVERT: D 95 ARG cc_start: 0.8296 (mtp85) cc_final: 0.8024 (mtm110) REVERT: D 178 LEU cc_start: 0.8505 (mp) cc_final: 0.8226 (tp) REVERT: D 284 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7953 (tmtt) REVERT: D 355 MET cc_start: 0.7861 (mtt) cc_final: 0.7545 (mtt) REVERT: E 122 ILE cc_start: 0.8985 (mm) cc_final: 0.8610 (tt) REVERT: E 125 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: E 244 ASP cc_start: 0.5285 (OUTLIER) cc_final: 0.4952 (t0) REVERT: E 355 MET cc_start: 0.8169 (ttm) cc_final: 0.7558 (mtp) outliers start: 19 outliers final: 13 residues processed: 144 average time/residue: 0.1207 time to fit residues: 25.9809 Evaluate side-chains 137 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 50 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.090988 restraints weight = 21061.910| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.66 r_work: 0.2910 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15240 Z= 0.118 Angle : 0.583 6.920 20690 Z= 0.270 Chirality : 0.045 0.202 2280 Planarity : 0.004 0.039 2630 Dihedral : 29.059 179.873 2330 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.02 % Allowed : 10.35 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.20), residues: 1830 helix: 1.80 (0.20), residues: 710 sheet: 0.17 (0.29), residues: 310 loop : 1.66 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 335 TYR 0.009 0.001 TYR B 294 PHE 0.010 0.001 PHE B 200 TRP 0.010 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00281 (15240) covalent geometry : angle 0.58317 (20690) hydrogen bonds : bond 0.02835 ( 755) hydrogen bonds : angle 4.52488 ( 1875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.546 Fit side-chains REVERT: A 82 MET cc_start: 0.8741 (tpt) cc_final: 0.8479 (tpt) REVERT: A 100 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: B 44 MET cc_start: 0.6901 (ttm) cc_final: 0.6560 (ttm) REVERT: B 113 LYS cc_start: 0.8562 (mttt) cc_final: 0.8232 (mtmt) REVERT: B 178 LEU cc_start: 0.8605 (mp) cc_final: 0.8260 (tp) REVERT: B 269 MET cc_start: 0.9173 (mtt) cc_final: 0.8846 (mtt) REVERT: B 314 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7346 (tp40) REVERT: C 206 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7435 (ttm-80) REVERT: C 355 MET cc_start: 0.8064 (ttm) cc_final: 0.7734 (mtt) REVERT: D 95 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7979 (mtm-85) REVERT: D 178 LEU cc_start: 0.8469 (mp) cc_final: 0.8213 (tp) REVERT: D 226 GLU cc_start: 0.8653 (tp30) cc_final: 0.8393 (mm-30) REVERT: D 284 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7933 (tmtt) REVERT: D 355 MET cc_start: 0.7912 (mtt) cc_final: 0.7637 (mtt) REVERT: E 122 ILE cc_start: 0.8966 (mm) cc_final: 0.8614 (tt) REVERT: E 244 ASP cc_start: 0.5580 (OUTLIER) cc_final: 0.5331 (t0) outliers start: 16 outliers final: 12 residues processed: 145 average time/residue: 0.1192 time to fit residues: 25.9094 Evaluate side-chains 142 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 169 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 0.2980 chunk 39 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.091951 restraints weight = 21173.989| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.53 r_work: 0.2918 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15240 Z= 0.122 Angle : 0.582 6.659 20690 Z= 0.269 Chirality : 0.045 0.194 2280 Planarity : 0.004 0.038 2630 Dihedral : 28.598 179.960 2330 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.21 % Allowed : 10.48 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.20), residues: 1830 helix: 1.66 (0.20), residues: 740 sheet: 0.21 (0.29), residues: 310 loop : 1.63 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 335 TYR 0.008 0.001 TYR D 294 PHE 0.010 0.001 PHE B 200 TRP 0.010 0.001 TRP B 79 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00289 (15240) covalent geometry : angle 0.58182 (20690) hydrogen bonds : bond 0.02814 ( 755) hydrogen bonds : angle 4.46098 ( 1875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.530 Fit side-chains REVERT: A 82 MET cc_start: 0.8692 (tpt) cc_final: 0.8457 (tpt) REVERT: A 100 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: B 44 MET cc_start: 0.6911 (ttm) cc_final: 0.6635 (ttm) REVERT: B 113 LYS cc_start: 0.8556 (mttt) cc_final: 0.8224 (mtmt) REVERT: B 178 LEU cc_start: 0.8562 (mp) cc_final: 0.8250 (tp) REVERT: B 314 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7277 (tp40) REVERT: C 47 MET cc_start: 0.4255 (OUTLIER) cc_final: 0.3272 (mtt) REVERT: C 206 ARG cc_start: 0.7825 (ttm-80) cc_final: 0.7419 (ttm-80) REVERT: C 326 LYS cc_start: 0.8711 (tttp) cc_final: 0.8303 (mtpp) REVERT: C 355 MET cc_start: 0.8200 (ttm) cc_final: 0.7893 (mtt) REVERT: D 44 MET cc_start: 0.3128 (ttt) cc_final: 0.2494 (ttt) REVERT: D 95 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7957 (mtm-85) REVERT: D 178 LEU cc_start: 0.8441 (mp) cc_final: 0.8189 (tp) REVERT: D 226 GLU cc_start: 0.8652 (tp30) cc_final: 0.8395 (mm-30) REVERT: D 284 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7973 (tmtt) REVERT: D 355 MET cc_start: 0.7916 (mtt) cc_final: 0.7662 (mtt) REVERT: E 244 ASP cc_start: 0.5611 (OUTLIER) cc_final: 0.5384 (t0) outliers start: 19 outliers final: 13 residues processed: 147 average time/residue: 0.1202 time to fit residues: 26.4348 Evaluate side-chains 145 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 109 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 32 optimal weight: 0.0050 chunk 75 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.089097 restraints weight = 21466.231| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.54 r_work: 0.2886 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15240 Z= 0.184 Angle : 0.624 6.840 20690 Z= 0.292 Chirality : 0.047 0.205 2280 Planarity : 0.004 0.037 2630 Dihedral : 28.825 179.756 2330 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.34 % Allowed : 10.54 % Favored : 88.12 % 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: 1.94 (0.20), residues: 1830 helix: 1.78 (0.20), residues: 705 sheet: 0.32 (0.27), residues: 350 loop : 1.57 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 335 TYR 0.010 0.001 TYR B 198 PHE 0.013 0.001 PHE A 200 TRP 0.011 0.002 TRP D 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00443 (15240) covalent geometry : angle 0.62419 (20690) hydrogen bonds : bond 0.03304 ( 755) hydrogen bonds : angle 4.61386 ( 1875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.461 Fit side-chains REVERT: A 100 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: B 44 MET cc_start: 0.7073 (ttm) cc_final: 0.6653 (ttm) REVERT: B 113 LYS cc_start: 0.8538 (mttt) cc_final: 0.8192 (mtmt) REVERT: B 178 LEU cc_start: 0.8648 (mp) cc_final: 0.8237 (tp) REVERT: B 314 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7305 (tp40) REVERT: C 47 MET cc_start: 0.4236 (OUTLIER) cc_final: 0.3656 (mtt) REVERT: C 206 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7359 (ttm-80) REVERT: C 326 LYS cc_start: 0.8699 (tttp) cc_final: 0.8332 (mtpp) REVERT: C 355 MET cc_start: 0.8365 (ttm) cc_final: 0.8063 (mtt) REVERT: D 95 ARG cc_start: 0.8302 (mtp85) cc_final: 0.8012 (mtm-85) REVERT: D 178 LEU cc_start: 0.8473 (mp) cc_final: 0.8214 (tp) REVERT: D 226 GLU cc_start: 0.8704 (tp30) cc_final: 0.8452 (mm-30) REVERT: D 284 LYS cc_start: 0.8320 (mtpt) cc_final: 0.8023 (tmtt) REVERT: D 355 MET cc_start: 0.7928 (mtt) cc_final: 0.7662 (mtt) REVERT: E 122 ILE cc_start: 0.8986 (mm) cc_final: 0.8611 (tt) REVERT: E 244 ASP cc_start: 0.5358 (OUTLIER) cc_final: 0.5108 (t0) outliers start: 21 outliers final: 16 residues processed: 143 average time/residue: 0.1184 time to fit residues: 25.1967 Evaluate side-chains 145 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.088827 restraints weight = 21410.714| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.54 r_work: 0.2884 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15240 Z= 0.189 Angle : 0.627 7.044 20690 Z= 0.294 Chirality : 0.047 0.209 2280 Planarity : 0.004 0.037 2630 Dihedral : 28.888 179.892 2330 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.47 % Allowed : 10.61 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.20), residues: 1830 helix: 1.76 (0.20), residues: 705 sheet: 0.36 (0.27), residues: 345 loop : 1.45 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 335 TYR 0.010 0.001 TYR B 198 PHE 0.013 0.001 PHE A 200 TRP 0.011 0.002 TRP D 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00457 (15240) covalent geometry : angle 0.62723 (20690) hydrogen bonds : bond 0.03304 ( 755) hydrogen bonds : angle 4.61869 ( 1875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.492 Fit side-chains REVERT: A 100 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: B 44 MET cc_start: 0.7098 (ttm) cc_final: 0.6675 (ttm) REVERT: B 113 LYS cc_start: 0.8582 (mttt) cc_final: 0.8243 (mtmt) REVERT: B 178 LEU cc_start: 0.8656 (mp) cc_final: 0.8228 (tp) REVERT: B 269 MET cc_start: 0.9146 (mtt) cc_final: 0.8845 (mtt) REVERT: B 314 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7276 (tp40) REVERT: C 206 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7363 (ttm-80) REVERT: C 326 LYS cc_start: 0.8728 (tttp) cc_final: 0.8351 (mtpp) REVERT: D 44 MET cc_start: 0.3106 (ttt) cc_final: 0.2501 (ttt) REVERT: D 95 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7984 (mtm-85) REVERT: D 178 LEU cc_start: 0.8352 (mp) cc_final: 0.8101 (tp) REVERT: D 226 GLU cc_start: 0.8719 (tp30) cc_final: 0.8459 (mm-30) REVERT: D 284 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7995 (tmtt) REVERT: D 355 MET cc_start: 0.7920 (mtt) cc_final: 0.7636 (mtt) REVERT: E 122 ILE cc_start: 0.8973 (mm) cc_final: 0.8608 (tt) REVERT: E 244 ASP cc_start: 0.5350 (OUTLIER) cc_final: 0.5082 (t0) outliers start: 23 outliers final: 16 residues processed: 140 average time/residue: 0.1285 time to fit residues: 26.7024 Evaluate side-chains 143 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 76 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 143 optimal weight: 0.0270 chunk 63 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.092709 restraints weight = 21103.302| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.62 r_work: 0.2945 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15240 Z= 0.094 Angle : 0.560 6.431 20690 Z= 0.257 Chirality : 0.044 0.185 2280 Planarity : 0.004 0.038 2630 Dihedral : 27.916 179.211 2330 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.02 % Allowed : 10.80 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.20), residues: 1830 helix: 1.80 (0.20), residues: 740 sheet: 0.58 (0.28), residues: 335 loop : 1.58 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 335 TYR 0.007 0.001 TYR B 294 PHE 0.008 0.001 PHE B 255 TRP 0.010 0.001 TRP B 79 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00215 (15240) covalent geometry : angle 0.55979 (20690) hydrogen bonds : bond 0.02506 ( 755) hydrogen bonds : angle 4.37318 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3241.18 seconds wall clock time: 56 minutes 16.68 seconds (3376.68 seconds total)