Starting phenix.real_space_refine on Sat Sep 12 09:54:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t24_10366/09_2026/6t24_10366.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t24_10366/09_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_10366/09_2026/6t24_10366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t24_10366/09_2026/6t24_10366.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6t24_10366/09_2026/6t24_10366.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t24_10366/09_2026/6t24_10366.cif" model { file = "/net/cci-nas-00/data/ceres_data/6t24_10366/09_2026/6t24_10366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t24_10366/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 3.01, per 1000 atoms: 0.20 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: 1.04 Conformation dependent library (CDL) restraints added in 531.1 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: 0.53 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: 2.27 Time building geometry restraints manager: 1.34 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: 1.310 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.020 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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/Z covalent geometry : bond 0.02087 / 1.13 (15240) covalent geometry : angle 1.81075 / 1.17 (20690) hydrogen bonds : bond 0.17414 / 11.43 ( 755) hydrogen bonds : angle 7.63737 / 5.44 ( 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 : 0.547 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: 0.8578 (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: 0.7838 (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: 0.7849 (mmtt) REVERT: B 157 ASP cc_start: 0.6616 (t70) cc_final: 0.5984 (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: 0.8776 (p) REVERT: C 187 ASP cc_start: 0.8049 (t70) cc_final: 0.7841 (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: 0.7427 (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: 0.7235 (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: 0.1228 time to fit residues: 110.5327 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 : 0.506 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3441 r_free = 0.3441 target = 0.125189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108853 restraints weight = 22394.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112457 restraints weight = 12219.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114896 restraints weight = 7686.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116495 restraints weight = 5354.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117705 restraints weight = 4057.159| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15240 Z= 0.142 Angle : 0.680 7.189 20690 Z= 0.333 Chirality : 0.047 0.228 2280 Planarity : 0.005 0.040 2630 Dihedral : 31.967 179.490 2330 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.62 % Allowed : 12.14 % Favored : 85.24 % 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: 1.88 (0.20), residues: 1830 helix: 0.78 (0.18), residues: 730 sheet: 1.03 (0.29), residues: 315 loop : 2.15 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 147 TYR 0.020 0.002 TYR E 294 PHE 0.013 0.001 PHE C 255 TRP 0.026 0.002 TRP A 340 HIS 0.006 0.002 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15240) covalent geometry : angle 0.68006 / 0.33 (20690) hydrogen bonds : bond 0.03822 / 2.52 ( 755) hydrogen bonds : angle 5.13281 / 3.62 ( 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 382 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 341 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7981 (mm-30) REVERT: A 154 ASP cc_start: 0.8683 (t0) cc_final: 0.8164 (t70) REVERT: A 227 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7725 (tpp) REVERT: A 259 GLU cc_start: 0.8308 (tp30) cc_final: 0.7580 (tp30) REVERT: A 283 MET cc_start: 0.7949 (mmm) cc_final: 0.7440 (mmm) REVERT: A 290 ARG cc_start: 0.7500 (mtt180) cc_final: 0.7052 (mtm180) REVERT: B 118 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7764 (mmtt) REVERT: B 244 ASP cc_start: 0.8198 (p0) cc_final: 0.7344 (t0) REVERT: B 259 GLU cc_start: 0.8072 (tp30) cc_final: 0.7668 (tp30) REVERT: B 269 MET cc_start: 0.7237 (mtt) cc_final: 0.6943 (mtp) REVERT: B 284 LYS cc_start: 0.8108 (mttm) cc_final: 0.7854 (tptp) REVERT: B 299 MET cc_start: 0.7884 (mmm) cc_final: 0.7615 (mtp) REVERT: C 244 ASP cc_start: 0.8767 (p0) cc_final: 0.7599 (t0) REVERT: C 267 ILE cc_start: 0.8165 (pt) cc_final: 0.7453 (tp) REVERT: C 288 ASP cc_start: 0.7343 (m-30) cc_final: 0.7031 (m-30) REVERT: D 115 ASN cc_start: 0.8422 (t0) cc_final: 0.8213 (t0) REVERT: D 167 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7117 (mp0) REVERT: D 246 GLN cc_start: 0.8333 (mt0) cc_final: 0.8088 (mt0) REVERT: D 283 MET cc_start: 0.7484 (mmm) cc_final: 0.7213 (ttp) REVERT: D 346 LEU cc_start: 0.8733 (tp) cc_final: 0.8335 (tp) REVERT: E 14 SER cc_start: 0.7611 (m) cc_final: 0.7046 (p) REVERT: E 226 GLU cc_start: 0.7774 (tp30) cc_final: 0.7404 (tp30) REVERT: E 346 LEU cc_start: 0.8926 (tp) cc_final: 0.8571 (tp) REVERT: E 360 GLN cc_start: 0.8030 (pp30) cc_final: 0.7570 (pp30) outliers start: 41 outliers final: 27 residues processed: 366 average time/residue: 0.0975 time to fit residues: 56.7703 Evaluate side-chains 291 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 152 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 227 MET 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 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 192 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 241 GLU 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: 3.9990 chunk 98 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 163 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN C 115 ASN D 162 ASN D 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.105418 restraints weight = 22815.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108827 restraints weight = 12709.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111147 restraints weight = 8129.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112692 restraints weight = 5755.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.113826 restraints weight = 4412.748| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4590 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= 0.127 Angle : 0.622 7.800 20690 Z= 0.296 Chirality : 0.045 0.170 2280 Planarity : 0.004 0.033 2630 Dihedral : 30.314 179.315 2330 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 3.00 % Allowed : 14.38 % Favored : 82.62 % 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: 2.14 (0.20), residues: 1830 helix: 1.17 (0.19), residues: 730 sheet: 1.20 (0.27), residues: 345 loop : 2.11 (0.25), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.014 0.001 TYR A 294 PHE 0.023 0.001 PHE E 352 TRP 0.016 0.002 TRP A 79 HIS 0.005 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15240) covalent geometry : angle 0.62196 / 0.30 (20690) hydrogen bonds : bond 0.03340 / 2.18 ( 755) hydrogen bonds : angle 4.78529 / 3.39 ( 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 347 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 300 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8637 (t0) cc_final: 0.8218 (t70) REVERT: A 269 MET cc_start: 0.7713 (mtt) cc_final: 0.7484 (mtt) REVERT: A 283 MET cc_start: 0.7840 (mmm) cc_final: 0.7470 (mmm) REVERT: A 290 ARG cc_start: 0.7530 (mtt180) cc_final: 0.7316 (mtm180) REVERT: B 47 MET cc_start: 0.3076 (ptp) cc_final: 0.1369 (tpp) REVERT: B 118 LYS cc_start: 0.8272 (mmmt) cc_final: 0.7685 (mmtp) REVERT: B 176 MET cc_start: 0.7607 (mmm) cc_final: 0.7209 (mpp) REVERT: B 244 ASP cc_start: 0.8362 (p0) cc_final: 0.7486 (t0) REVERT: B 283 MET cc_start: 0.8396 (mmt) cc_final: 0.8020 (mmm) REVERT: C 44 MET cc_start: 0.3604 (mtt) cc_final: 0.3290 (mtt) REVERT: C 133 TYR cc_start: 0.8317 (t80) cc_final: 0.7885 (t80) REVERT: C 148 THR cc_start: 0.8618 (p) cc_final: 0.8350 (p) REVERT: C 207 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7135 (mm-30) REVERT: C 244 ASP cc_start: 0.8828 (p0) cc_final: 0.7562 (t0) REVERT: C 338 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8421 (p) REVERT: D 81 ASP cc_start: 0.7623 (m-30) cc_final: 0.7254 (m-30) REVERT: D 115 ASN cc_start: 0.8326 (t0) cc_final: 0.7877 (t0) REVERT: D 167 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7019 (mp0) REVERT: D 283 MET cc_start: 0.7568 (mmm) cc_final: 0.7307 (ttp) REVERT: D 346 LEU cc_start: 0.8758 (tp) cc_final: 0.8366 (tp) REVERT: D 351 THR cc_start: 0.6660 (p) cc_final: 0.5349 (p) REVERT: E 14 SER cc_start: 0.7716 (m) cc_final: 0.7157 (p) REVERT: E 47 MET cc_start: 0.4843 (mmm) cc_final: 0.4471 (mmp) REVERT: E 203 THR cc_start: 0.7532 (m) cc_final: 0.5846 (t) REVERT: E 226 GLU cc_start: 0.7688 (tp30) cc_final: 0.7389 (tp30) REVERT: E 299 MET cc_start: 0.8012 (mtp) cc_final: 0.7801 (mtp) REVERT: E 346 LEU cc_start: 0.9009 (tp) cc_final: 0.8648 (tp) REVERT: E 354 GLN cc_start: 0.7392 (mt0) cc_final: 0.7149 (pm20) outliers start: 47 outliers final: 30 residues processed: 332 average time/residue: 0.0949 time to fit residues: 49.6498 Evaluate side-chains 280 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 96 VAL 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 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 339 VAL Chi-restraints excluded: chain C residue 145 SER 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 Chi-restraints excluded: chain E residue 339 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 120 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 155 optimal weight: 0.0980 chunk 97 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 7 optimal weight: 0.3980 chunk 154 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN E 360 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106845 restraints weight = 22581.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110214 restraints weight = 12587.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112506 restraints weight = 8063.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114091 restraints weight = 5689.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115199 restraints weight = 4349.317| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15240 Z= 0.094 Angle : 0.583 6.803 20690 Z= 0.272 Chirality : 0.044 0.186 2280 Planarity : 0.004 0.037 2630 Dihedral : 29.213 179.767 2330 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.43 % Allowed : 15.34 % 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: 2.42 (0.20), residues: 1830 helix: 1.46 (0.20), residues: 725 sheet: 1.21 (0.28), residues: 345 loop : 2.28 (0.25), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 147 TYR 0.011 0.001 TYR C 294 PHE 0.027 0.001 PHE E 352 TRP 0.014 0.001 TRP A 79 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (15240) covalent geometry : angle 0.58280 / 0.27 (20690) hydrogen bonds : bond 0.02760 / 1.82 ( 755) hydrogen bonds : angle 4.59597 / 3.25 ( 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 323 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 285 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 MET cc_start: 0.7662 (mtt) cc_final: 0.7446 (mtt) REVERT: A 270 GLU cc_start: 0.7241 (tt0) cc_final: 0.7039 (mp0) REVERT: B 12 ASN cc_start: 0.7991 (t0) cc_final: 0.7579 (t0) REVERT: B 82 MET cc_start: 0.7935 (tpt) cc_final: 0.7579 (tpt) REVERT: B 103 THR cc_start: 0.8598 (m) cc_final: 0.8243 (t) REVERT: B 118 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7771 (mttm) REVERT: B 244 ASP cc_start: 0.8270 (p0) cc_final: 0.7579 (t0) REVERT: B 283 MET cc_start: 0.8372 (mmt) cc_final: 0.8162 (mmm) REVERT: C 207 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7204 (mm-30) REVERT: C 244 ASP cc_start: 0.8766 (p0) cc_final: 0.7639 (t0) REVERT: C 338 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8437 (p) REVERT: D 81 ASP cc_start: 0.7539 (m-30) cc_final: 0.7236 (m-30) REVERT: D 115 ASN cc_start: 0.8297 (t0) cc_final: 0.7870 (t0) REVERT: D 167 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6917 (mp0) REVERT: D 269 MET cc_start: 0.8067 (mtp) cc_final: 0.7695 (ttm) REVERT: D 283 MET cc_start: 0.7474 (mmm) cc_final: 0.7179 (ttp) REVERT: D 292 ASP cc_start: 0.7827 (m-30) cc_final: 0.7550 (m-30) REVERT: D 346 LEU cc_start: 0.8725 (tp) cc_final: 0.8353 (tp) REVERT: E 14 SER cc_start: 0.7746 (m) cc_final: 0.7300 (p) REVERT: E 34 ILE cc_start: 0.9147 (mt) cc_final: 0.8939 (pt) REVERT: E 203 THR cc_start: 0.7442 (m) cc_final: 0.5804 (t) REVERT: E 271 SER cc_start: 0.8566 (m) cc_final: 0.8054 (p) REVERT: E 299 MET cc_start: 0.8090 (mtp) cc_final: 0.7868 (mtp) REVERT: E 346 LEU cc_start: 0.8935 (tp) cc_final: 0.8615 (tp) outliers start: 38 outliers final: 21 residues processed: 305 average time/residue: 0.0944 time to fit residues: 45.5839 Evaluate side-chains 270 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 153 LEU 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 176 MET 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 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 186 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 103 THR 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: 0.9980 chunk 15 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN C 101 HIS C 297 ASN D 59 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104587 restraints weight = 22844.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107861 restraints weight = 12742.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110082 restraints weight = 8156.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111565 restraints weight = 5781.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112633 restraints weight = 4434.028| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15240 Z= 0.127 Angle : 0.610 8.841 20690 Z= 0.284 Chirality : 0.045 0.194 2280 Planarity : 0.004 0.040 2630 Dihedral : 28.193 179.623 2330 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.30 % Allowed : 16.61 % 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: 2.15 (0.20), residues: 1830 helix: 1.35 (0.20), residues: 730 sheet: 1.12 (0.27), residues: 345 loop : 1.96 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 147 TYR 0.019 0.001 TYR E 166 PHE 0.018 0.001 PHE E 352 TRP 0.022 0.002 TRP A 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (15240) covalent geometry : angle 0.60989 / 0.28 (20690) hydrogen bonds : bond 0.03118 / 2.06 ( 755) hydrogen bonds : angle 4.60500 / 3.27 ( 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 294 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8507 (mttt) cc_final: 0.8192 (mptt) REVERT: A 328 LYS cc_start: 0.8476 (tttp) cc_final: 0.8243 (tttm) REVERT: B 103 THR cc_start: 0.8609 (m) cc_final: 0.8183 (t) REVERT: B 118 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7794 (mttm) REVERT: B 123 MET cc_start: 0.8225 (tpp) cc_final: 0.7950 (tpp) REVERT: B 126 THR cc_start: 0.8692 (m) cc_final: 0.8482 (m) REVERT: B 244 ASP cc_start: 0.8251 (p0) cc_final: 0.7637 (t0) REVERT: C 244 ASP cc_start: 0.8857 (p0) cc_final: 0.7830 (t0) REVERT: C 338 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8483 (p) REVERT: D 81 ASP cc_start: 0.7557 (m-30) cc_final: 0.7227 (m-30) REVERT: D 167 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6877 (mp0) REVERT: D 283 MET cc_start: 0.7588 (mmm) cc_final: 0.7281 (ttp) REVERT: D 346 LEU cc_start: 0.8867 (tp) cc_final: 0.8465 (tp) REVERT: E 14 SER cc_start: 0.8008 (m) cc_final: 0.7503 (p) REVERT: E 123 MET cc_start: 0.7685 (tpp) cc_final: 0.7222 (mtm) REVERT: E 203 THR cc_start: 0.7504 (m) cc_final: 0.5866 (t) REVERT: E 299 MET cc_start: 0.8187 (mtp) cc_final: 0.7941 (mtp) REVERT: E 346 LEU cc_start: 0.8996 (tp) cc_final: 0.8613 (tp) outliers start: 36 outliers final: 27 residues processed: 278 average time/residue: 0.0973 time to fit residues: 42.5945 Evaluate side-chains 256 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 339 VAL 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 221 LEU Chi-restraints excluded: chain C residue 236 LEU 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 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 203 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 103 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.095030 restraints weight = 23282.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.098102 restraints weight = 13250.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.100232 restraints weight = 8658.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.101656 restraints weight = 6231.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102723 restraints weight = 4860.100| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 15240 Z= 0.325 Angle : 0.771 8.730 20690 Z= 0.375 Chirality : 0.051 0.209 2280 Planarity : 0.005 0.052 2630 Dihedral : 28.459 179.713 2330 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.77 % Allowed : 16.87 % 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: 0.98 (0.20), residues: 1830 helix: 0.62 (0.19), residues: 735 sheet: 0.11 (0.28), residues: 305 loop : 1.21 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 95 TYR 0.022 0.002 TYR E 166 PHE 0.025 0.002 PHE E 352 TRP 0.022 0.003 TRP A 79 HIS 0.008 0.002 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.32 (15240) covalent geometry : angle 0.77079 / 0.37 (20690) hydrogen bonds : bond 0.04841 / 3.16 ( 755) hydrogen bonds : angle 5.20305 / 3.72 ( 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 307 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8542 (tp) REVERT: B 103 THR cc_start: 0.8733 (m) cc_final: 0.8437 (t) REVERT: B 118 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7941 (mttm) REVERT: B 283 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8131 (mmm) REVERT: B 305 MET cc_start: 0.7514 (mmm) cc_final: 0.7152 (tpt) REVERT: D 81 ASP cc_start: 0.7543 (m-30) cc_final: 0.7089 (m-30) REVERT: D 82 MET cc_start: 0.8340 (tpt) cc_final: 0.8000 (tpt) REVERT: D 283 MET cc_start: 0.7478 (mmm) cc_final: 0.7225 (ttp) REVERT: E 78 ASN cc_start: 0.8519 (t0) cc_final: 0.7969 (t0) REVERT: E 107 GLU cc_start: 0.7366 (tt0) cc_final: 0.7033 (tt0) REVERT: E 187 ASP cc_start: 0.7553 (m-30) cc_final: 0.7267 (m-30) REVERT: E 267 ILE cc_start: 0.8988 (pt) cc_final: 0.8770 (pt) REVERT: E 299 MET cc_start: 0.8285 (mtp) cc_final: 0.8037 (mtp) REVERT: E 346 LEU cc_start: 0.9217 (tp) cc_final: 0.8940 (tp) outliers start: 59 outliers final: 39 residues processed: 288 average time/residue: 0.0921 time to fit residues: 42.8880 Evaluate side-chains 252 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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 173 HIS 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 51 ASP 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 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 MET 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 D residue 351 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 122 ILE 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 248 ILE 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: 0.7980 chunk 138 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 154 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.094316 restraints weight = 23120.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.097592 restraints weight = 12910.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099868 restraints weight = 8319.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.101422 restraints weight = 5935.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102543 restraints weight = 4576.412| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15240 Z= 0.115 Angle : 0.618 9.090 20690 Z= 0.288 Chirality : 0.045 0.164 2280 Planarity : 0.004 0.044 2630 Dihedral : 27.757 179.986 2330 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.24 % Allowed : 18.98 % 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: 1.67 (0.20), residues: 1830 helix: 1.30 (0.20), residues: 700 sheet: 0.44 (0.27), residues: 335 loop : 1.53 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.013 0.001 TYR E 166 PHE 0.033 0.001 PHE E 352 TRP 0.014 0.001 TRP A 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (15240) covalent geometry : angle 0.61787 / 0.29 (20690) hydrogen bonds : bond 0.03021 / 1.97 ( 755) hydrogen bonds : angle 4.72392 / 3.36 ( 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 277 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.3494 (mtt) cc_final: 0.3035 (mtt) REVERT: A 227 MET cc_start: 0.8422 (tpp) cc_final: 0.8143 (tpp) REVERT: A 283 MET cc_start: 0.8074 (mmp) cc_final: 0.7675 (mmp) REVERT: B 64 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8468 (tp) REVERT: B 103 THR cc_start: 0.8654 (m) cc_final: 0.8410 (t) REVERT: B 244 ASP cc_start: 0.8192 (p0) cc_final: 0.7852 (t0) REVERT: B 283 MET cc_start: 0.8170 (mmt) cc_final: 0.7733 (mmm) REVERT: B 305 MET cc_start: 0.7626 (mmm) cc_final: 0.7246 (tpt) REVERT: C 283 MET cc_start: 0.8288 (mmt) cc_final: 0.8073 (mmt) REVERT: D 81 ASP cc_start: 0.7483 (m-30) cc_final: 0.7096 (m-30) REVERT: D 283 MET cc_start: 0.7408 (mmm) cc_final: 0.7023 (ttp) REVERT: E 14 SER cc_start: 0.7705 (m) cc_final: 0.7063 (p) REVERT: E 78 ASN cc_start: 0.8499 (t0) cc_final: 0.8012 (t0) REVERT: E 100 GLU cc_start: 0.7228 (tp30) cc_final: 0.6997 (tp30) REVERT: E 107 GLU cc_start: 0.7339 (tt0) cc_final: 0.6941 (tt0) REVERT: E 123 MET cc_start: 0.7680 (tpp) cc_final: 0.7009 (mtm) REVERT: E 179 ASP cc_start: 0.7913 (t0) cc_final: 0.7575 (t0) REVERT: E 187 ASP cc_start: 0.7692 (m-30) cc_final: 0.7416 (m-30) REVERT: E 346 LEU cc_start: 0.9045 (tp) cc_final: 0.8686 (tp) outliers start: 35 outliers final: 25 residues processed: 265 average time/residue: 0.0933 time to fit residues: 39.6401 Evaluate side-chains 239 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 147 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 THR 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 236 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 354 GLN 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: 4.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 76 optimal weight: 0.0050 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 246 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.101277 restraints weight = 22657.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104480 restraints weight = 12716.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106667 restraints weight = 8185.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108168 restraints weight = 5831.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109233 restraints weight = 4481.484| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15240 Z= 0.130 Angle : 0.629 9.875 20690 Z= 0.294 Chirality : 0.045 0.156 2280 Planarity : 0.004 0.044 2630 Dihedral : 27.380 179.159 2330 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.19 % Allowed : 19.11 % Favored : 77.70 % 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: 1.70 (0.20), residues: 1830 helix: 1.39 (0.20), residues: 700 sheet: 0.40 (0.27), residues: 335 loop : 1.51 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.012 0.001 TYR E 166 PHE 0.042 0.001 PHE E 352 TRP 0.015 0.002 TRP A 79 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (15240) covalent geometry : angle 0.62910 / 0.29 (20690) hydrogen bonds : bond 0.03185 / 2.08 ( 755) hydrogen bonds : angle 4.69342 / 3.35 ( 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 270 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.3552 (mtt) cc_final: 0.3152 (mtt) REVERT: A 283 MET cc_start: 0.8038 (mmp) cc_final: 0.7635 (mmp) REVERT: B 64 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8498 (tp) REVERT: B 82 MET cc_start: 0.7872 (tpt) cc_final: 0.7428 (tpt) REVERT: B 103 THR cc_start: 0.8611 (m) cc_final: 0.8347 (t) REVERT: B 244 ASP cc_start: 0.8167 (p0) cc_final: 0.7569 (t0) REVERT: B 283 MET cc_start: 0.8102 (mmt) cc_final: 0.7639 (mmm) REVERT: B 305 MET cc_start: 0.7559 (mmm) cc_final: 0.7167 (tpt) REVERT: C 283 MET cc_start: 0.8300 (mmt) cc_final: 0.8059 (mmt) REVERT: D 81 ASP cc_start: 0.7317 (m-30) cc_final: 0.6929 (m-30) REVERT: D 283 MET cc_start: 0.7376 (mmm) cc_final: 0.7042 (ttp) REVERT: E 14 SER cc_start: 0.7865 (m) cc_final: 0.7240 (p) REVERT: E 78 ASN cc_start: 0.8417 (t0) cc_final: 0.8000 (t0) REVERT: E 100 GLU cc_start: 0.7211 (tp30) cc_final: 0.6986 (tp30) REVERT: E 107 GLU cc_start: 0.7302 (tt0) cc_final: 0.6986 (tt0) REVERT: E 123 MET cc_start: 0.7601 (tpp) cc_final: 0.6990 (mtm) REVERT: E 179 ASP cc_start: 0.7978 (t0) cc_final: 0.7657 (t0) REVERT: E 187 ASP cc_start: 0.7651 (m-30) cc_final: 0.7399 (m-30) REVERT: E 346 LEU cc_start: 0.9072 (tp) cc_final: 0.8761 (tp) outliers start: 50 outliers final: 38 residues processed: 254 average time/residue: 0.0914 time to fit residues: 37.5678 Evaluate side-chains 252 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 147 ARG Chi-restraints excluded: chain A residue 153 LEU 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 180 LEU 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 141 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 313 MET 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 132 MET Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 165 ILE 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 D residue 351 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 173 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 350 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 109 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 75 optimal weight: 0.0060 chunk 178 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 371 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS E 173 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.101604 restraints weight = 23027.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104822 restraints weight = 12910.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106996 restraints weight = 8299.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108474 restraints weight = 5910.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109555 restraints weight = 4554.748| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 15240 Z= 0.105 Angle : 0.610 10.504 20690 Z= 0.285 Chirality : 0.044 0.215 2280 Planarity : 0.004 0.043 2630 Dihedral : 26.985 179.260 2330 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.31 % Favored : 98.63 % Rotamer: Outliers : 2.43 % Allowed : 20.32 % Favored : 77.25 % 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: 1.84 (0.20), residues: 1830 helix: 1.56 (0.20), residues: 695 sheet: 0.47 (0.27), residues: 335 loop : 1.51 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.013 0.001 TYR C 166 PHE 0.040 0.001 PHE E 352 TRP 0.013 0.001 TRP A 79 HIS 0.011 0.001 HIS E 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15240) covalent geometry : angle 0.61034 / 0.28 (20690) hydrogen bonds : bond 0.02854 / 1.85 ( 755) hydrogen bonds : angle 4.60087 / 3.28 ( 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 282 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8327 (tp) REVERT: A 47 MET cc_start: 0.3205 (mtt) cc_final: 0.2907 (mtt) REVERT: B 64 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8517 (tp) REVERT: B 103 THR cc_start: 0.8660 (m) cc_final: 0.8399 (t) REVERT: B 244 ASP cc_start: 0.8122 (p0) cc_final: 0.7577 (t0) REVERT: B 283 MET cc_start: 0.8013 (mmt) cc_final: 0.7539 (mmm) REVERT: C 82 MET cc_start: 0.8306 (tpt) cc_final: 0.7896 (tmm) REVERT: C 166 TYR cc_start: 0.8266 (t80) cc_final: 0.8027 (t80) REVERT: C 283 MET cc_start: 0.8223 (mmt) cc_final: 0.7967 (mmt) REVERT: D 81 ASP cc_start: 0.7349 (m-30) cc_final: 0.7045 (m-30) REVERT: D 283 MET cc_start: 0.7433 (mmm) cc_final: 0.7139 (ttp) REVERT: D 348 SER cc_start: 0.7865 (m) cc_final: 0.7528 (t) REVERT: E 14 SER cc_start: 0.8115 (m) cc_final: 0.7520 (p) REVERT: E 47 MET cc_start: 0.2393 (mpp) cc_final: 0.2136 (mpp) REVERT: E 78 ASN cc_start: 0.8416 (t0) cc_final: 0.7960 (t0) REVERT: E 100 GLU cc_start: 0.7292 (tp30) cc_final: 0.7047 (tp30) REVERT: E 187 ASP cc_start: 0.7704 (m-30) cc_final: 0.7442 (m-30) REVERT: E 346 LEU cc_start: 0.9059 (tp) cc_final: 0.8834 (tp) outliers start: 38 outliers final: 28 residues processed: 270 average time/residue: 0.0915 time to fit residues: 39.9333 Evaluate side-chains 247 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 12 ASN Chi-restraints excluded: chain C residue 141 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 C residue 313 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 THR 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 D residue 351 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 173 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 298 VAL 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: 5.9990 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 120 optimal weight: 0.0970 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 246 GLN C 314 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.096853 restraints weight = 23339.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.099980 restraints weight = 13212.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.102114 restraints weight = 8585.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103592 restraints weight = 6174.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.104649 restraints weight = 4785.148| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15240 Z= 0.145 Angle : 0.638 8.346 20690 Z= 0.301 Chirality : 0.045 0.186 2280 Planarity : 0.004 0.044 2630 Dihedral : 26.884 179.499 2330 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.62 % Allowed : 20.89 % Favored : 76.49 % 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: 1.77 (0.20), residues: 1830 helix: 1.53 (0.20), residues: 695 sheet: 0.24 (0.29), residues: 295 loop : 1.48 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.016 0.001 TYR C 166 PHE 0.035 0.002 PHE E 352 TRP 0.015 0.001 TRP A 79 HIS 0.010 0.001 HIS E 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (15240) covalent geometry : angle 0.63848 / 0.30 (20690) hydrogen bonds : bond 0.03267 / 2.13 ( 755) hydrogen bonds : angle 4.66905 / 3.33 ( 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 256 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8754 (m-80) cc_final: 0.8145 (m-80) REVERT: B 64 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8531 (tp) REVERT: B 103 THR cc_start: 0.8708 (m) cc_final: 0.8433 (t) REVERT: B 244 ASP cc_start: 0.8158 (p0) cc_final: 0.7533 (t0) REVERT: B 283 MET cc_start: 0.8039 (mmt) cc_final: 0.7576 (mmm) REVERT: D 81 ASP cc_start: 0.7347 (m-30) cc_final: 0.6962 (m-30) REVERT: D 283 MET cc_start: 0.7433 (mmm) cc_final: 0.7122 (ttp) REVERT: E 14 SER cc_start: 0.8150 (m) cc_final: 0.7456 (p) REVERT: E 78 ASN cc_start: 0.8439 (t0) cc_final: 0.7970 (t0) REVERT: E 100 GLU cc_start: 0.7234 (tp30) cc_final: 0.7012 (tp30) REVERT: E 187 ASP cc_start: 0.7708 (m-30) cc_final: 0.7476 (m-30) REVERT: E 346 LEU cc_start: 0.9118 (tp) cc_final: 0.8827 (tp) REVERT: E 355 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.6130 (mmt) outliers start: 41 outliers final: 36 residues processed: 242 average time/residue: 0.0891 time to fit residues: 35.4844 Evaluate side-chains 247 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 65 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 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 339 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 12 ASN 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 C residue 313 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 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 76 optimal weight: 0.4980 chunk 137 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 63 optimal weight: 0.0570 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.099888 restraints weight = 22975.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103187 restraints weight = 12675.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105452 restraints weight = 8073.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107006 restraints weight = 5704.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108109 restraints weight = 4362.820| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.6348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 15240 Z= 0.184 Angle : 0.886 59.199 20690 Z= 0.497 Chirality : 0.046 0.553 2280 Planarity : 0.005 0.155 2630 Dihedral : 26.900 179.495 2330 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.09 % Rotamer: Outliers : 2.81 % Allowed : 20.83 % Favored : 76.36 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.77 (0.20), residues: 1830 helix: 1.55 (0.20), residues: 695 sheet: 0.26 (0.29), residues: 295 loop : 1.46 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.020 0.001 TYR C 294 PHE 0.033 0.001 PHE E 352 TRP 0.014 0.001 TRP A 79 HIS 0.006 0.001 HIS E 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (15240) covalent geometry : angle 0.88648 / 0.50 (20690) hydrogen bonds : bond 0.03376 / 2.13 ( 755) hydrogen bonds : angle 4.67388 / 3.33 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2189.97 seconds wall clock time: 38 minutes 50.70 seconds (2330.70 seconds total)