Starting phenix.real_space_refine on Wed Mar 4 17:17:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t24_10366/03_2026/6t24_10366.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t24_10366/03_2026/6t24_10366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t24_10366/03_2026/6t24_10366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t24_10366/03_2026/6t24_10366.map" model { file = "/net/cci-nas-00/data/ceres_data/6t24_10366/03_2026/6t24_10366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t24_10366/03_2026/6t24_10366.cif" } resolution = 3.7 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= 0.012 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 70 residue(s): 0.02s 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: 3.68, per 1000 atoms: 0.25 Number of scatterers: 14910 At special positions: 0 Unit cell: (96.32, 92.96, 192.64, 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: 1.39 Conformation dependent library (CDL) restraints added in 555.9 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 53.6% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 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 126 removed outlier: 4.214A 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 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: 3.921A 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 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 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 296 removed outlier: 4.421A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.605A 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 355 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 126 removed outlier: 4.214A 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 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: 3.921A 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 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 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 296 removed outlier: 4.422A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.606A 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 355 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 126 removed outlier: 4.214A 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 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: 3.921A 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 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 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 296 removed outlier: 4.422A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.605A 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 355 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 126 removed outlier: 4.215A 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 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: 3.921A 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 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 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 296 removed outlier: 4.422A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.605A 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 355 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 126 removed outlier: 4.214A 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 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: 3.920A 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 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 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 296 removed outlier: 4.421A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.605A 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 355 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: 6.600A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.502A 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: 6.142A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.400A 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: 6.599A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.502A 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: 6.141A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.399A 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: 6.599A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.502A 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: 6.141A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.399A 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: 6.599A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.502A 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: 6.141A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.399A 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: 6.600A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.502A 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: 6.141A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.400A 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: 2.96 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2478 1.29 - 1.43: 3885 1.43 - 1.56: 8566 1.56 - 1.69: 126 1.69 - 1.83: 185 Bond restraints: 15240 Sorted by residual: bond pdb=" C22 9ZK E 379 " pdb=" N23 9ZK E 379 " ideal model delta sigma weight residual 1.350 1.529 -0.179 2.00e-02 2.50e+03 8.03e+01 bond pdb=" C22 9ZK D 379 " pdb=" N23 9ZK D 379 " ideal model delta sigma weight residual 1.350 1.529 -0.179 2.00e-02 2.50e+03 8.01e+01 bond pdb=" C22 9ZK C 379 " pdb=" N23 9ZK C 379 " ideal model delta sigma weight residual 1.350 1.529 -0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" C22 9ZK B 379 " pdb=" N23 9ZK B 379 " ideal model delta sigma weight residual 1.350 1.528 -0.178 2.00e-02 2.50e+03 7.96e+01 bond pdb=" C22 9ZK A 379 " pdb=" N23 9ZK A 379 " ideal model delta sigma weight residual 1.350 1.528 -0.178 2.00e-02 2.50e+03 7.93e+01 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 17762 2.43 - 4.85: 2469 4.85 - 7.28: 339 7.28 - 9.70: 115 9.70 - 12.13: 5 Bond angle restraints: 20690 Sorted by residual: angle pdb=" C GLY A 366 " pdb=" N PRO A 367 " pdb=" CA PRO A 367 " ideal model delta sigma weight residual 119.56 128.07 -8.51 1.02e+00 9.61e-01 6.95e+01 angle pdb=" C GLY C 366 " pdb=" N PRO C 367 " pdb=" CA PRO C 367 " ideal model delta sigma weight residual 119.56 128.06 -8.50 1.02e+00 9.61e-01 6.95e+01 angle pdb=" C GLY E 366 " pdb=" N PRO E 367 " pdb=" CA PRO E 367 " ideal model delta sigma weight residual 119.56 128.05 -8.49 1.02e+00 9.61e-01 6.93e+01 angle pdb=" C GLY D 366 " pdb=" N PRO D 367 " pdb=" CA PRO D 367 " ideal model delta sigma weight residual 119.56 128.05 -8.49 1.02e+00 9.61e-01 6.92e+01 angle pdb=" C GLY B 366 " pdb=" N PRO B 367 " pdb=" CA PRO B 367 " ideal model delta sigma weight residual 119.56 128.05 -8.49 1.02e+00 9.61e-01 6.92e+01 ... (remaining 20685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 8970 35.87 - 71.74: 145 71.74 - 107.61: 40 107.61 - 143.48: 10 143.48 - 179.35: 75 Dihedral angle restraints: 9240 sinusoidal: 3880 harmonic: 5360 Sorted by residual: dihedral pdb=" O1B ADP A 376 " pdb=" O3A ADP A 376 " pdb=" PB ADP A 376 " pdb=" PA ADP A 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.82 -149.83 1 2.00e+01 2.50e-03 4.47e+01 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 89.80 -149.81 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 89.80 -149.80 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 9237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1353 0.074 - 0.148: 697 0.148 - 0.222: 188 0.222 - 0.296: 32 0.296 - 0.370: 10 Chirality restraints: 2280 Sorted by residual: 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 2.52 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C25 9ZK C 379 " pdb=" C26 9ZK C 379 " pdb=" C36 9ZK C 379 " pdb=" N23 9ZK C 379 " both_signs ideal model delta sigma weight residual False 2.15 2.51 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C25 9ZK B 379 " pdb=" C26 9ZK B 379 " pdb=" C36 9ZK B 379 " pdb=" N23 9ZK B 379 " both_signs ideal model delta sigma weight residual False 2.15 2.51 -0.37 2.00e-01 2.50e+01 3.39e+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 6.35e-02 4.03e+01 pdb=" C PHE A 375 " 0.110 2.00e-02 2.50e+03 pdb=" O PHE A 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE A 375 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 375 " -0.031 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C PHE E 375 " 0.110 2.00e-02 2.50e+03 pdb=" O PHE E 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE E 375 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 375 " 0.031 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C PHE B 375 " -0.110 2.00e-02 2.50e+03 pdb=" O PHE B 375 " 0.039 2.00e-02 2.50e+03 pdb=" OXT PHE B 375 " 0.039 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 490 2.66 - 3.22: 14670 3.22 - 3.78: 23581 3.78 - 4.34: 33890 4.34 - 4.90: 53672 Nonbonded interactions: 126303 Sorted by model distance: nonbonded pdb=" N SER B 14 " pdb=" O1 PO4 B 377 " model vdw 2.104 3.120 nonbonded pdb=" N SER E 14 " pdb=" O1 PO4 E 377 " model vdw 2.104 3.120 nonbonded pdb=" N SER C 14 " pdb=" O1 PO4 C 377 " model vdw 2.104 3.120 nonbonded pdb=" N SER A 14 " pdb=" O1 PO4 A 377 " model vdw 2.104 3.120 nonbonded pdb=" N SER D 14 " pdb=" O1 PO4 D 377 " model vdw 2.105 3.120 ... (remaining 126298 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.240 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.021 0.179 15240 Z= 1.128 Angle : 1.811 12.126 20690 Z= 1.165 Chirality : 0.091 0.370 2280 Planarity : 0.009 0.063 2630 Dihedral : 23.396 179.349 5810 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.74 (0.20), residues: 1830 helix: -0.66 (0.16), residues: 760 sheet: 0.72 (0.31), residues: 270 loop : 2.00 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 183 TYR 0.045 0.008 TYR B 188 PHE 0.030 0.005 PHE A 200 TRP 0.075 0.013 TRP A 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.02087 (15240) covalent geometry : angle 1.81075 (20690) hydrogen bonds : bond 0.17414 ( 755) hydrogen bonds : angle 7.63737 ( 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 619 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 619 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8886 (mt) cc_final: 0.8577 (mp) REVERT: A 226 GLU cc_start: 0.8228 (tp30) cc_final: 0.7823 (mm-30) REVERT: A 259 GLU cc_start: 0.8580 (tp30) cc_final: 0.7698 (tp30) REVERT: A 283 MET cc_start: 0.7975 (mmm) cc_final: 0.7616 (mmm) REVERT: A 290 ARG cc_start: 0.8194 (mtt180) cc_final: 0.7837 (mtm180) REVERT: B 25 ASP cc_start: 0.7361 (p0) cc_final: 0.7071 (t0) REVERT: B 118 LYS cc_start: 0.8343 (mmmt) cc_final: 0.7848 (mmtt) REVERT: B 157 ASP cc_start: 0.6616 (t70) cc_final: 0.5983 (t0) REVERT: B 269 MET cc_start: 0.7406 (mtt) cc_final: 0.7160 (mtp) REVERT: B 283 MET cc_start: 0.8554 (mmm) cc_final: 0.8336 (mmt) REVERT: B 284 LYS cc_start: 0.8204 (mttm) cc_final: 0.7868 (tptp) REVERT: B 309 ILE cc_start: 0.8527 (tp) cc_final: 0.8260 (tt) REVERT: B 316 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8174 (mm-30) REVERT: C 39 ARG cc_start: 0.6726 (ttp-170) cc_final: 0.6134 (ttp80) REVERT: C 123 MET cc_start: 0.8212 (mmt) cc_final: 0.7938 (mmm) REVERT: C 152 VAL cc_start: 0.9025 (t) cc_final: 0.8775 (p) REVERT: C 187 ASP cc_start: 0.8049 (t70) cc_final: 0.7842 (m-30) REVERT: C 190 MET cc_start: 0.8412 (mtp) cc_final: 0.8198 (mtp) REVERT: D 64 ILE cc_start: 0.8925 (tt) cc_final: 0.8691 (mt) REVERT: D 81 ASP cc_start: 0.7872 (m-30) cc_final: 0.7637 (m-30) REVERT: D 116 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7428 (mtm-85) REVERT: D 152 VAL cc_start: 0.9503 (t) cc_final: 0.9291 (p) REVERT: D 180 LEU cc_start: 0.8111 (tp) cc_final: 0.7799 (pp) REVERT: D 283 MET cc_start: 0.7688 (mmm) cc_final: 0.7236 (ttp) REVERT: D 346 LEU cc_start: 0.8679 (tp) cc_final: 0.8292 (tp) REVERT: E 104 LEU cc_start: 0.8917 (tp) cc_final: 0.8679 (tt) outliers start: 0 outliers final: 0 residues processed: 619 average time/residue: 0.1227 time to fit residues: 109.8220 Evaluate side-chains 301 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN D 225 ASN D 371 HIS E 12 ASN E 111 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110940 restraints weight = 22035.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114506 restraints weight = 12241.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116870 restraints weight = 7801.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118523 restraints weight = 5493.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119588 restraints weight = 4154.991| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15240 Z= 0.143 Angle : 0.675 7.110 20690 Z= 0.330 Chirality : 0.047 0.218 2280 Planarity : 0.005 0.042 2630 Dihedral : 31.942 179.902 2330 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.62 % Allowed : 12.27 % Favored : 85.11 % 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: 1.89 (0.20), residues: 1830 helix: 0.79 (0.18), residues: 730 sheet: 1.06 (0.29), residues: 315 loop : 2.16 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 147 TYR 0.021 0.002 TYR E 294 PHE 0.013 0.001 PHE C 255 TRP 0.025 0.002 TRP A 340 HIS 0.006 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00320 (15240) covalent geometry : angle 0.67511 (20690) hydrogen bonds : bond 0.03776 ( 755) hydrogen bonds : angle 5.13531 ( 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 385 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 344 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7985 (mm-30) REVERT: A 154 ASP cc_start: 0.8652 (t0) cc_final: 0.8127 (t70) REVERT: A 227 MET cc_start: 0.8371 (tpt) cc_final: 0.7738 (tpp) REVERT: A 259 GLU cc_start: 0.8323 (tp30) cc_final: 0.7605 (tp30) REVERT: A 283 MET cc_start: 0.7916 (mmm) cc_final: 0.7436 (mmm) REVERT: A 290 ARG cc_start: 0.7523 (mtt180) cc_final: 0.7079 (mtm180) REVERT: B 118 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7771 (mmtt) REVERT: B 244 ASP cc_start: 0.8163 (p0) cc_final: 0.7328 (t0) REVERT: B 259 GLU cc_start: 0.8101 (tp30) cc_final: 0.7650 (tp30) REVERT: B 269 MET cc_start: 0.7196 (mtt) cc_final: 0.6966 (mtp) REVERT: B 283 MET cc_start: 0.8415 (mmm) cc_final: 0.7788 (mpp) REVERT: B 284 LYS cc_start: 0.8110 (mttm) cc_final: 0.7877 (tptp) REVERT: B 299 MET cc_start: 0.7833 (mmm) cc_final: 0.7552 (mtp) REVERT: C 244 ASP cc_start: 0.8689 (p0) cc_final: 0.7558 (t0) REVERT: C 267 ILE cc_start: 0.8180 (pt) cc_final: 0.7437 (tp) REVERT: C 288 ASP cc_start: 0.7254 (m-30) cc_final: 0.6945 (m-30) REVERT: D 115 ASN cc_start: 0.8430 (t0) cc_final: 0.8222 (t0) REVERT: D 162 ASN cc_start: 0.8027 (m110) cc_final: 0.7802 (m110) REVERT: D 167 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7062 (mp0) REVERT: D 246 GLN cc_start: 0.8320 (mt0) cc_final: 0.8105 (mt0) REVERT: D 283 MET cc_start: 0.7500 (mmm) cc_final: 0.7242 (ttp) REVERT: D 346 LEU cc_start: 0.8728 (tp) cc_final: 0.8336 (tp) REVERT: E 14 SER cc_start: 0.7576 (m) cc_final: 0.7030 (p) REVERT: E 226 GLU cc_start: 0.7733 (tp30) cc_final: 0.7394 (tp30) REVERT: E 346 LEU cc_start: 0.8915 (tp) cc_final: 0.8578 (tp) REVERT: E 360 GLN cc_start: 0.8002 (pp30) cc_final: 0.7571 (pp30) outliers start: 41 outliers final: 27 residues processed: 370 average time/residue: 0.0965 time to fit residues: 56.4227 Evaluate side-chains 293 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 266 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 130 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 178 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN C 115 ASN D 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102534 restraints weight = 23023.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105947 restraints weight = 12852.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108280 restraints weight = 8214.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109864 restraints weight = 5826.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110953 restraints weight = 4462.997| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15240 Z= 0.122 Angle : 0.615 8.019 20690 Z= 0.294 Chirality : 0.044 0.164 2280 Planarity : 0.004 0.031 2630 Dihedral : 30.385 178.818 2330 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.94 % Allowed : 14.82 % Favored : 82.24 % 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: 2.18 (0.20), residues: 1830 helix: 1.19 (0.19), residues: 730 sheet: 1.21 (0.27), residues: 345 loop : 2.17 (0.25), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 372 TYR 0.014 0.001 TYR A 294 PHE 0.025 0.001 PHE E 352 TRP 0.015 0.002 TRP A 79 HIS 0.005 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00278 (15240) covalent geometry : angle 0.61540 (20690) hydrogen bonds : bond 0.03300 ( 755) hydrogen bonds : angle 4.77753 ( 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 340 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 294 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7907 (mm-30) REVERT: A 154 ASP cc_start: 0.8641 (t0) cc_final: 0.8217 (t70) REVERT: A 227 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7674 (tpp) REVERT: A 283 MET cc_start: 0.7833 (mmm) cc_final: 0.7567 (mmm) REVERT: B 47 MET cc_start: 0.3326 (ptp) cc_final: 0.1377 (tpp) REVERT: B 118 LYS cc_start: 0.8221 (mmmt) cc_final: 0.7636 (mmtp) REVERT: B 176 MET cc_start: 0.7581 (mmm) cc_final: 0.7152 (mpp) REVERT: B 244 ASP cc_start: 0.8382 (p0) cc_final: 0.7404 (t0) REVERT: B 283 MET cc_start: 0.8388 (mmm) cc_final: 0.8128 (mmt) REVERT: C 225 ASN cc_start: 0.7699 (m-40) cc_final: 0.7492 (t0) REVERT: C 244 ASP cc_start: 0.8820 (p0) cc_final: 0.7598 (t0) REVERT: C 338 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8429 (p) REVERT: D 81 ASP cc_start: 0.7564 (m-30) cc_final: 0.7210 (m-30) REVERT: D 115 ASN cc_start: 0.8318 (t0) cc_final: 0.7855 (t0) REVERT: D 162 ASN cc_start: 0.8096 (m110) cc_final: 0.7871 (m110) REVERT: D 167 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7012 (mp0) REVERT: D 283 MET cc_start: 0.7638 (mmm) cc_final: 0.7294 (ttp) REVERT: D 346 LEU cc_start: 0.8744 (tp) cc_final: 0.8351 (tp) REVERT: E 14 SER cc_start: 0.7691 (m) cc_final: 0.7148 (p) REVERT: E 226 GLU cc_start: 0.7717 (tp30) cc_final: 0.7402 (tp30) REVERT: E 346 LEU cc_start: 0.8994 (tp) cc_final: 0.8620 (tp) REVERT: E 354 GLN cc_start: 0.7410 (mt0) cc_final: 0.7069 (pm20) outliers start: 46 outliers final: 27 residues processed: 322 average time/residue: 0.0936 time to fit residues: 47.6938 Evaluate side-chains 270 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 120 optimal weight: 0.0270 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 115 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 353 GLN B 137 GLN B 162 ASN C 101 HIS ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN E 360 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106146 restraints weight = 22546.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109732 restraints weight = 12298.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112160 restraints weight = 7747.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113800 restraints weight = 5418.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114945 restraints weight = 4101.440| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15240 Z= 0.103 Angle : 0.587 6.708 20690 Z= 0.275 Chirality : 0.044 0.193 2280 Planarity : 0.004 0.036 2630 Dihedral : 29.302 179.531 2330 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.43 % Allowed : 15.14 % Favored : 82.43 % 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: 2.30 (0.20), residues: 1830 helix: 1.38 (0.20), residues: 730 sheet: 1.16 (0.28), residues: 345 loop : 2.19 (0.25), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 147 TYR 0.010 0.001 TYR E 169 PHE 0.026 0.001 PHE E 352 TRP 0.016 0.001 TRP A 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00231 (15240) covalent geometry : angle 0.58653 (20690) hydrogen bonds : bond 0.02911 ( 755) hydrogen bonds : angle 4.61350 ( 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 307 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 227 MET cc_start: 0.8407 (tpt) cc_final: 0.7824 (tpp) REVERT: A 270 GLU cc_start: 0.7268 (tt0) cc_final: 0.7062 (mp0) REVERT: B 12 ASN cc_start: 0.8008 (t0) cc_final: 0.7625 (t0) REVERT: B 82 MET cc_start: 0.7997 (tpt) cc_final: 0.7616 (tpt) REVERT: B 118 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7574 (mmtp) REVERT: B 244 ASP cc_start: 0.8282 (p0) cc_final: 0.7544 (t0) REVERT: B 283 MET cc_start: 0.8315 (mmm) cc_final: 0.8029 (mmt) REVERT: C 225 ASN cc_start: 0.7613 (m-40) cc_final: 0.7392 (t0) REVERT: C 244 ASP cc_start: 0.8797 (p0) cc_final: 0.7660 (t0) REVERT: C 279 TYR cc_start: 0.8137 (t80) cc_final: 0.7909 (t80) REVERT: C 338 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8460 (p) REVERT: D 81 ASP cc_start: 0.7559 (m-30) cc_final: 0.7256 (m-30) REVERT: D 115 ASN cc_start: 0.8323 (t0) cc_final: 0.7891 (t0) REVERT: D 167 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6950 (mp0) REVERT: D 269 MET cc_start: 0.8083 (mtp) cc_final: 0.7722 (ttm) REVERT: D 283 MET cc_start: 0.7525 (mmm) cc_final: 0.7216 (ttp) REVERT: D 292 ASP cc_start: 0.7843 (m-30) cc_final: 0.7600 (m-30) REVERT: D 346 LEU cc_start: 0.8741 (tp) cc_final: 0.8400 (tp) REVERT: E 14 SER cc_start: 0.7878 (m) cc_final: 0.7396 (p) REVERT: E 203 THR cc_start: 0.7513 (m) cc_final: 0.5720 (t) REVERT: E 223 PHE cc_start: 0.8664 (t80) cc_final: 0.8260 (t80) REVERT: E 226 GLU cc_start: 0.7666 (tp30) cc_final: 0.7419 (tp30) REVERT: E 271 SER cc_start: 0.8566 (m) cc_final: 0.8063 (p) REVERT: E 346 LEU cc_start: 0.8985 (tp) cc_final: 0.8661 (tp) outliers start: 38 outliers final: 23 residues processed: 295 average time/residue: 0.0890 time to fit residues: 42.1868 Evaluate side-chains 269 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 339 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN D 59 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.099339 restraints weight = 23074.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102525 restraints weight = 13029.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104718 restraints weight = 8445.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106182 restraints weight = 6036.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107269 restraints weight = 4690.262| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15240 Z= 0.190 Angle : 0.656 9.265 20690 Z= 0.311 Chirality : 0.047 0.212 2280 Planarity : 0.004 0.039 2630 Dihedral : 28.504 179.977 2330 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 3.19 % Allowed : 15.72 % Favored : 81.09 % 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: 1.83 (0.20), residues: 1830 helix: 1.17 (0.20), residues: 730 sheet: 0.67 (0.29), residues: 315 loop : 1.81 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 147 TYR 0.011 0.001 TYR A 306 PHE 0.018 0.002 PHE E 352 TRP 0.020 0.002 TRP A 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00449 (15240) covalent geometry : angle 0.65559 (20690) hydrogen bonds : bond 0.03758 ( 755) hydrogen bonds : angle 4.78039 ( 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 315 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8534 (tp) REVERT: B 103 THR cc_start: 0.8736 (m) cc_final: 0.8352 (t) REVERT: B 118 LYS cc_start: 0.8197 (mmmt) cc_final: 0.7944 (mttm) REVERT: B 244 ASP cc_start: 0.8340 (p0) cc_final: 0.7811 (t0) REVERT: C 207 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7249 (mm-30) REVERT: C 244 ASP cc_start: 0.8861 (p0) cc_final: 0.7934 (t0) REVERT: D 81 ASP cc_start: 0.7585 (m-30) cc_final: 0.7183 (m-30) REVERT: D 283 MET cc_start: 0.7589 (mmm) cc_final: 0.7285 (ttp) REVERT: D 346 LEU cc_start: 0.8938 (tp) cc_final: 0.8557 (tp) REVERT: E 14 SER cc_start: 0.8057 (m) cc_final: 0.7409 (p) REVERT: E 78 ASN cc_start: 0.8401 (t0) cc_final: 0.7860 (t0) REVERT: E 107 GLU cc_start: 0.7412 (tt0) cc_final: 0.7074 (tt0) REVERT: E 203 THR cc_start: 0.7758 (m) cc_final: 0.6159 (t) REVERT: E 346 LEU cc_start: 0.9057 (tp) cc_final: 0.8758 (tp) outliers start: 50 outliers final: 34 residues processed: 295 average time/residue: 0.0935 time to fit residues: 44.1835 Evaluate side-chains 263 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 350 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 115 optimal weight: 0.0010 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099883 restraints weight = 22902.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103134 restraints weight = 12937.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.105356 restraints weight = 8345.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106885 restraints weight = 5963.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107970 restraints weight = 4593.047| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5648 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= 0.137 Angle : 0.611 8.264 20690 Z= 0.286 Chirality : 0.045 0.181 2280 Planarity : 0.004 0.042 2630 Dihedral : 28.051 179.962 2330 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.88 % Allowed : 16.68 % Favored : 80.45 % 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: 1.89 (0.20), residues: 1830 helix: 1.24 (0.20), residues: 730 sheet: 0.81 (0.27), residues: 345 loop : 1.80 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 254 TYR 0.010 0.001 TYR A 306 PHE 0.031 0.001 PHE E 352 TRP 0.015 0.002 TRP A 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00322 (15240) covalent geometry : angle 0.61089 (20690) hydrogen bonds : bond 0.03161 ( 755) hydrogen bonds : angle 4.68922 ( 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 285 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.2996 (mtt) cc_final: 0.2775 (mtt) REVERT: A 224 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: B 103 THR cc_start: 0.8710 (m) cc_final: 0.8329 (t) REVERT: B 118 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7909 (mttm) REVERT: B 244 ASP cc_start: 0.8328 (p0) cc_final: 0.7840 (t0) REVERT: B 283 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7866 (mmm) REVERT: C 207 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7227 (mm-30) REVERT: D 81 ASP cc_start: 0.7429 (m-30) cc_final: 0.7020 (m-30) REVERT: D 283 MET cc_start: 0.7554 (mmm) cc_final: 0.7279 (ttp) REVERT: D 346 LEU cc_start: 0.8961 (tp) cc_final: 0.8592 (tp) REVERT: D 348 SER cc_start: 0.8015 (m) cc_final: 0.7751 (t) REVERT: E 14 SER cc_start: 0.7888 (m) cc_final: 0.7539 (p) REVERT: E 78 ASN cc_start: 0.8334 (t0) cc_final: 0.7916 (t0) REVERT: E 179 ASP cc_start: 0.7917 (t0) cc_final: 0.7672 (t0) REVERT: E 187 ASP cc_start: 0.7594 (m-30) cc_final: 0.7324 (m-30) REVERT: E 346 LEU cc_start: 0.9083 (tp) cc_final: 0.8703 (tp) outliers start: 45 outliers final: 28 residues processed: 269 average time/residue: 0.0923 time to fit residues: 39.7388 Evaluate side-chains 254 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 350 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 50 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 chunk 65 optimal weight: 0.0170 chunk 123 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 173 HIS ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102148 restraints weight = 22588.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105426 restraints weight = 12693.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107659 restraints weight = 8174.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109194 restraints weight = 5820.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110242 restraints weight = 4471.173| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15240 Z= 0.106 Angle : 0.603 9.044 20690 Z= 0.278 Chirality : 0.044 0.158 2280 Planarity : 0.004 0.055 2630 Dihedral : 27.452 179.798 2330 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.68 % Allowed : 17.76 % Favored : 79.55 % 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: 2.11 (0.20), residues: 1830 helix: 1.62 (0.20), residues: 700 sheet: 0.62 (0.27), residues: 335 loop : 1.85 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 95 TYR 0.011 0.001 TYR B 166 PHE 0.032 0.001 PHE E 352 TRP 0.013 0.001 TRP A 79 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00243 (15240) covalent geometry : angle 0.60290 (20690) hydrogen bonds : bond 0.02783 ( 755) hydrogen bonds : angle 4.56613 ( 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 287 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 245 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.8054 (mmp) cc_final: 0.7755 (mmp) REVERT: B 44 MET cc_start: 0.2494 (mtt) cc_final: 0.2253 (mtt) REVERT: B 103 THR cc_start: 0.8592 (m) cc_final: 0.8225 (t) REVERT: B 118 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7820 (mttm) REVERT: B 283 MET cc_start: 0.8017 (mmt) cc_final: 0.7729 (mmm) REVERT: D 81 ASP cc_start: 0.7297 (m-30) cc_final: 0.6956 (m-30) REVERT: D 283 MET cc_start: 0.7484 (mmm) cc_final: 0.7240 (ttp) REVERT: D 346 LEU cc_start: 0.8938 (tp) cc_final: 0.8479 (tp) REVERT: E 14 SER cc_start: 0.8029 (m) cc_final: 0.7490 (p) REVERT: E 44 MET cc_start: -0.1260 (tpp) cc_final: -0.2484 (ptm) REVERT: E 78 ASN cc_start: 0.8389 (t0) cc_final: 0.7957 (t0) REVERT: E 179 ASP cc_start: 0.7920 (t0) cc_final: 0.7693 (t0) REVERT: E 187 ASP cc_start: 0.7614 (m-30) cc_final: 0.7378 (m-30) REVERT: E 346 LEU cc_start: 0.9025 (tp) cc_final: 0.8663 (tp) outliers start: 42 outliers final: 32 residues processed: 272 average time/residue: 0.0905 time to fit residues: 39.7158 Evaluate side-chains 255 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 339 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 169 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** 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 = 0.3324 r_free = 0.3324 target = 0.115553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.099797 restraints weight = 22935.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102983 restraints weight = 12939.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105167 restraints weight = 8357.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106586 restraints weight = 5977.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107709 restraints weight = 4658.756| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15240 Z= 0.158 Angle : 0.639 7.624 20690 Z= 0.298 Chirality : 0.045 0.160 2280 Planarity : 0.004 0.044 2630 Dihedral : 27.249 179.108 2330 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.00 % Allowed : 17.64 % Favored : 79.36 % 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: 1.49 (0.20), residues: 700 sheet: 0.48 (0.28), residues: 315 loop : 1.70 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.010 0.001 TYR A 306 PHE 0.034 0.001 PHE E 352 TRP 0.014 0.002 TRP A 79 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00377 (15240) covalent geometry : angle 0.63925 (20690) hydrogen bonds : bond 0.03285 ( 755) hydrogen bonds : angle 4.66360 ( 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 275 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.8048 (mmp) cc_final: 0.7602 (mmp) REVERT: B 64 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8537 (tp) REVERT: B 103 THR cc_start: 0.8658 (m) cc_final: 0.8345 (t) REVERT: B 118 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7836 (mttm) REVERT: B 244 ASP cc_start: 0.8222 (p0) cc_final: 0.7603 (t0) REVERT: B 283 MET cc_start: 0.8153 (mmt) cc_final: 0.7722 (mmm) REVERT: C 207 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7260 (mm-30) REVERT: D 81 ASP cc_start: 0.7365 (m-30) cc_final: 0.6953 (m-30) REVERT: D 283 MET cc_start: 0.7406 (mmm) cc_final: 0.7129 (ttp) REVERT: D 346 LEU cc_start: 0.8995 (tp) cc_final: 0.8629 (tp) REVERT: D 355 MET cc_start: 0.8323 (mmp) cc_final: 0.8083 (mmt) REVERT: E 14 SER cc_start: 0.8016 (m) cc_final: 0.7562 (p) REVERT: E 44 MET cc_start: -0.1415 (tpp) cc_final: -0.2384 (ptm) REVERT: E 78 ASN cc_start: 0.8532 (t0) cc_final: 0.8018 (t0) REVERT: E 132 MET cc_start: 0.7041 (ttt) cc_final: 0.6823 (ttt) REVERT: E 179 ASP cc_start: 0.7883 (t0) cc_final: 0.7597 (t0) REVERT: E 187 ASP cc_start: 0.7704 (m-30) cc_final: 0.7356 (m-30) REVERT: E 346 LEU cc_start: 0.9081 (tp) cc_final: 0.8741 (tp) outliers start: 47 outliers final: 37 residues processed: 261 average time/residue: 0.0891 time to fit residues: 37.7694 Evaluate side-chains 257 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 354 GLN 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: 3.9990 chunk 99 optimal weight: 0.0370 chunk 32 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103216 restraints weight = 22797.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106465 restraints weight = 12754.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108686 restraints weight = 8168.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110166 restraints weight = 5807.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111279 restraints weight = 4459.366| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15240 Z= 0.112 Angle : 0.609 10.523 20690 Z= 0.282 Chirality : 0.044 0.146 2280 Planarity : 0.004 0.043 2630 Dihedral : 26.850 179.328 2330 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.36 % Allowed : 18.40 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.20), residues: 1830 helix: 1.67 (0.20), residues: 695 sheet: 0.31 (0.29), residues: 305 loop : 1.73 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 95 TYR 0.009 0.001 TYR C 143 PHE 0.034 0.001 PHE E 352 TRP 0.012 0.001 TRP A 79 HIS 0.003 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00262 (15240) covalent geometry : angle 0.60859 (20690) hydrogen bonds : bond 0.02820 ( 755) hydrogen bonds : angle 4.53605 ( 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 269 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.8008 (mmp) cc_final: 0.7631 (mmp) REVERT: B 64 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8519 (tp) REVERT: B 103 THR cc_start: 0.8673 (m) cc_final: 0.8316 (t) REVERT: B 118 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7851 (mttm) REVERT: B 283 MET cc_start: 0.7986 (mmt) cc_final: 0.7669 (mmm) REVERT: C 207 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7106 (mm-30) REVERT: D 81 ASP cc_start: 0.7316 (m-30) cc_final: 0.7011 (m-30) REVERT: D 283 MET cc_start: 0.7318 (mmm) cc_final: 0.6942 (ttp) REVERT: D 346 LEU cc_start: 0.8939 (tp) cc_final: 0.8527 (tp) REVERT: E 14 SER cc_start: 0.8113 (m) cc_final: 0.7480 (p) REVERT: E 78 ASN cc_start: 0.8498 (t0) cc_final: 0.8180 (t0) REVERT: E 187 ASP cc_start: 0.7748 (m-30) cc_final: 0.7367 (m-30) REVERT: E 346 LEU cc_start: 0.9022 (tp) cc_final: 0.8756 (tp) outliers start: 37 outliers final: 26 residues processed: 260 average time/residue: 0.0911 time to fit residues: 38.1420 Evaluate side-chains 246 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 173 HIS Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 350 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 0.0070 chunk 96 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.102005 restraints weight = 22957.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105279 restraints weight = 12546.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107550 restraints weight = 7971.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109100 restraints weight = 5608.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110195 restraints weight = 4281.056| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15240 Z= 0.115 Angle : 0.613 10.211 20690 Z= 0.286 Chirality : 0.044 0.143 2280 Planarity : 0.004 0.042 2630 Dihedral : 26.689 179.490 2330 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.24 % Allowed : 19.11 % Favored : 78.66 % 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: 1.68 (0.20), residues: 695 sheet: 0.32 (0.29), residues: 305 loop : 1.69 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.012 0.001 TYR E 169 PHE 0.034 0.001 PHE E 352 TRP 0.013 0.001 TRP A 79 HIS 0.005 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00269 (15240) covalent geometry : angle 0.61336 (20690) hydrogen bonds : bond 0.02860 ( 755) hydrogen bonds : angle 4.52032 ( 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 264 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8727 (m-80) cc_final: 0.8077 (m-10) REVERT: A 283 MET cc_start: 0.8074 (mmp) cc_final: 0.7665 (mmp) REVERT: B 64 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8532 (tp) REVERT: B 103 THR cc_start: 0.8656 (m) cc_final: 0.8347 (t) REVERT: B 118 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7826 (mttm) REVERT: B 244 ASP cc_start: 0.8414 (p0) cc_final: 0.7497 (t0) REVERT: B 283 MET cc_start: 0.7999 (mmt) cc_final: 0.7671 (mmm) REVERT: C 314 GLN cc_start: 0.8682 (tm-30) cc_final: 0.7342 (tt0) REVERT: D 81 ASP cc_start: 0.7345 (m-30) cc_final: 0.7006 (m-30) REVERT: D 93 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7399 (mp0) REVERT: D 283 MET cc_start: 0.7317 (mmm) cc_final: 0.6909 (ttp) REVERT: D 346 LEU cc_start: 0.8948 (tp) cc_final: 0.8515 (tp) REVERT: E 14 SER cc_start: 0.8183 (m) cc_final: 0.7493 (p) REVERT: E 78 ASN cc_start: 0.8503 (t0) cc_final: 0.7993 (t0) REVERT: E 173 HIS cc_start: 0.7118 (OUTLIER) cc_final: 0.6726 (p-80) REVERT: E 187 ASP cc_start: 0.7811 (m-30) cc_final: 0.7473 (m-30) REVERT: E 346 LEU cc_start: 0.9055 (tp) cc_final: 0.8798 (tp) outliers start: 35 outliers final: 27 residues processed: 257 average time/residue: 0.0885 time to fit residues: 36.9458 Evaluate side-chains 253 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 173 HIS Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 350 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 76 optimal weight: 0.0670 chunk 137 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 96 optimal weight: 0.0570 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 147 optimal weight: 0.2980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN E 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104255 restraints weight = 22735.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107604 restraints weight = 12400.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109831 restraints weight = 7816.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111444 restraints weight = 5498.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112425 restraints weight = 4163.227| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15240 Z= 0.096 Angle : 0.595 9.957 20690 Z= 0.277 Chirality : 0.043 0.135 2280 Planarity : 0.004 0.041 2630 Dihedral : 26.440 179.931 2330 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.66 % Allowed : 19.55 % Favored : 78.79 % 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: 2.16 (0.20), residues: 1830 helix: 1.82 (0.20), residues: 695 sheet: 0.43 (0.29), residues: 305 loop : 1.76 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.009 0.001 TYR E 306 PHE 0.031 0.001 PHE E 352 TRP 0.011 0.001 TRP A 79 HIS 0.005 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00216 (15240) covalent geometry : angle 0.59498 (20690) hydrogen bonds : bond 0.02571 ( 755) hydrogen bonds : angle 4.45200 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2061.98 seconds wall clock time: 36 minutes 32.53 seconds (2192.53 seconds total)