Starting phenix.real_space_refine on Wed Mar 4 15:14:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rb8_24399/03_2026/7rb8_24399.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rb8_24399/03_2026/7rb8_24399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rb8_24399/03_2026/7rb8_24399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rb8_24399/03_2026/7rb8_24399.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rb8_24399/03_2026/7rb8_24399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rb8_24399/03_2026/7rb8_24399.map" } resolution = 3.63 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= 0.000 sd= 0.003 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 8 5.49 5 Mg 4 5.21 5 S 91 5.16 5 C 9000 2.51 5 N 2418 2.21 5 O 2705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14226 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 5363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5363 Classifications: {'peptide': 667} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 643} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C Time building chain proxies: 3.15, per 1000 atoms: 0.22 Number of scatterers: 14226 At special positions: 0 Unit cell: (110.21, 151.41, 139.05, 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 91 16.00 P 8 15.00 Mg 4 11.99 O 2705 8.00 N 2418 7.00 C 9000 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: 1.02 Conformation dependent library (CDL) restraints added in 509.7 milliseconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 23 sheets defined 51.7% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.515A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.021A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.807A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.954A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.613A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.776A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.555A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 286 through 296 removed outlier: 4.040A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.606A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.569A pdb=" N LEU A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.506A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'D' and resid 1210 through 1214 removed outlier: 3.726A pdb=" N GLN D1213 " --> pdb=" O ASP D1210 " (cutoff:3.500A) Processing helix chain 'D' and resid 1218 through 1232 Processing helix chain 'D' and resid 1257 through 1263 removed outlier: 4.417A pdb=" N GLN D1261 " --> pdb=" O PRO D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1268 removed outlier: 4.153A pdb=" N ALA D1267 " --> pdb=" O SER D1264 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU D1268 " --> pdb=" O GLY D1265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1264 through 1268' Processing helix chain 'D' and resid 1276 through 1290 removed outlier: 3.941A pdb=" N ASN D1280 " --> pdb=" O PHE D1276 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D1283 " --> pdb=" O ALA D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1304 through 1318 Processing helix chain 'D' and resid 1331 through 1333 No H-bonds generated for 'chain 'D' and resid 1331 through 1333' Processing helix chain 'D' and resid 1334 through 1342 Processing helix chain 'D' and resid 1379 through 1383 removed outlier: 3.679A pdb=" N ARG D1382 " --> pdb=" O GLU D1379 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D1383 " --> pdb=" O LYS D1380 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1379 through 1383' Processing helix chain 'D' and resid 1393 through 1402 removed outlier: 4.159A pdb=" N TYR D1397 " --> pdb=" O TYR D1393 " (cutoff:3.500A) Processing helix chain 'D' and resid 1404 through 1411 Processing helix chain 'D' and resid 1419 through 1424 removed outlier: 3.780A pdb=" N GLN D1424 " --> pdb=" O TYR D1420 " (cutoff:3.500A) Processing helix chain 'D' and resid 1435 through 1449 removed outlier: 3.763A pdb=" N PHE D1439 " --> pdb=" O ASP D1435 " (cutoff:3.500A) Processing helix chain 'D' and resid 1452 through 1471 removed outlier: 3.502A pdb=" N GLN D1456 " --> pdb=" O THR D1452 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN D1471 " --> pdb=" O LEU D1467 " (cutoff:3.500A) Processing helix chain 'D' and resid 1489 through 1499 removed outlier: 4.365A pdb=" N ILE D1493 " --> pdb=" O SER D1489 " (cutoff:3.500A) Processing helix chain 'D' and resid 1503 through 1512 removed outlier: 3.632A pdb=" N LEU D1507 " --> pdb=" O SER D1503 " (cutoff:3.500A) Processing helix chain 'D' and resid 1528 through 1559 removed outlier: 3.632A pdb=" N VAL D1559 " --> pdb=" O VAL D1555 " (cutoff:3.500A) Processing helix chain 'D' and resid 1583 through 1616 Processing helix chain 'D' and resid 1617 through 1620 removed outlier: 3.642A pdb=" N ARG D1620 " --> pdb=" O MET D1617 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1617 through 1620' Processing helix chain 'D' and resid 1627 through 1636 Processing helix chain 'D' and resid 1640 through 1651 removed outlier: 3.664A pdb=" N CYS D1650 " --> pdb=" O ASP D1646 " (cutoff:3.500A) Processing helix chain 'D' and resid 1655 through 1667 Processing helix chain 'D' and resid 1699 through 1703 removed outlier: 3.966A pdb=" N ASN D1703 " --> pdb=" O LEU D1700 " (cutoff:3.500A) Processing helix chain 'D' and resid 1708 through 1717 removed outlier: 3.749A pdb=" N LEU D1712 " --> pdb=" O ARG D1708 " (cutoff:3.500A) Processing helix chain 'D' and resid 1720 through 1734 removed outlier: 3.730A pdb=" N ALA D1724 " --> pdb=" O THR D1720 " (cutoff:3.500A) Processing helix chain 'D' and resid 1753 through 1772 removed outlier: 3.764A pdb=" N CYS D1772 " --> pdb=" O LYS D1768 " (cutoff:3.500A) Processing helix chain 'D' and resid 1792 through 1804 Processing helix chain 'D' and resid 1806 through 1813 removed outlier: 3.849A pdb=" N ARG D1810 " --> pdb=" O LEU D1806 " (cutoff:3.500A) Processing helix chain 'D' and resid 1821 through 1829 removed outlier: 3.650A pdb=" N PHE D1825 " --> pdb=" O PRO D1821 " (cutoff:3.500A) Processing helix chain 'D' and resid 1846 through 1854 removed outlier: 3.637A pdb=" N LEU D1850 " --> pdb=" O CYS D1846 " (cutoff:3.500A) Processing helix chain 'D' and resid 1871 through 1886 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.515A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.021A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.807A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.954A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.613A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.776A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.555A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 286 through 296 removed outlier: 4.040A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.606A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.569A pdb=" N LEU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.506A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 54 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.516A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.021A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.807A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.954A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.614A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.777A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.555A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 286 through 296 removed outlier: 4.040A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.607A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.568A pdb=" N LEU C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.505A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.278A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 132 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 4.259A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 42 removed outlier: 4.259A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.551A pdb=" N ILE A 75 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.631A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'D' and resid 1237 through 1239 removed outlier: 6.467A pdb=" N LEU D1243 " --> pdb=" O ARG D1778 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU D1780 " --> pdb=" O LEU D1243 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER D1245 " --> pdb=" O LEU D1780 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN D1293 " --> pdb=" O SER D1567 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D1569 " --> pdb=" O GLN D1293 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY D1370 " --> pdb=" O PHE D1362 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU D1364 " --> pdb=" O ILE D1368 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE D1368 " --> pdb=" O GLU D1364 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 1237 through 1239 removed outlier: 6.467A pdb=" N LEU D1243 " --> pdb=" O ARG D1778 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU D1780 " --> pdb=" O LEU D1243 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER D1245 " --> pdb=" O LEU D1780 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 1343 through 1346 removed outlier: 6.601A pdb=" N ALA D1344 " --> pdb=" O ASN D1351 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN D1351 " --> pdb=" O ALA D1344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 1513 through 1517 Processing sheet with id=AB4, first strand: chain 'D' and resid 1673 through 1674 Processing sheet with id=AB5, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.278A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 35 through 38 Processing sheet with id=AB7, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.551A pdb=" N ILE B 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.277A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 35 through 38 Processing sheet with id=AC2, first strand: chain 'C' and resid 71 through 72 removed outlier: 3.551A pdb=" N ILE C 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AC4, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.631A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 238 through 241 682 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: 2.43 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2958 1.33 - 1.45: 3299 1.45 - 1.57: 8101 1.57 - 1.69: 12 1.69 - 1.82: 153 Bond restraints: 14523 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.405 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.405 -0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.405 -0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" C GLY D1256 " pdb=" N PRO D1257 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.25e-02 6.40e+03 6.19e+00 bond pdb=" CG HIC A 73 " pdb=" CD2 HIC A 73 " ideal model delta sigma weight residual 1.369 1.413 -0.044 2.00e-02 2.50e+03 4.90e+00 ... (remaining 14518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 19209 1.92 - 3.85: 399 3.85 - 5.77: 63 5.77 - 7.69: 14 7.69 - 9.61: 2 Bond angle restraints: 19687 Sorted by residual: angle pdb=" N ILE D1865 " pdb=" CA ILE D1865 " pdb=" C ILE D1865 " ideal model delta sigma weight residual 111.56 104.82 6.74 8.60e-01 1.35e+00 6.15e+01 angle pdb=" C GLY D1256 " pdb=" N PRO D1257 " pdb=" CA PRO D1257 " ideal model delta sigma weight residual 119.56 113.04 6.52 1.01e+00 9.80e-01 4.17e+01 angle pdb=" N ASN D1320 " pdb=" CA ASN D1320 " pdb=" C ASN D1320 " ideal model delta sigma weight residual 109.76 101.09 8.67 1.64e+00 3.72e-01 2.80e+01 angle pdb=" N ILE D1242 " pdb=" CA ILE D1242 " pdb=" C ILE D1242 " ideal model delta sigma weight residual 109.55 116.54 -6.99 1.38e+00 5.25e-01 2.57e+01 angle pdb=" C ILE D1239 " pdb=" CA ILE D1239 " pdb=" CB ILE D1239 " ideal model delta sigma weight residual 113.22 108.32 4.90 1.12e+00 7.97e-01 1.92e+01 ... (remaining 19682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.36: 8235 23.36 - 46.72: 462 46.72 - 70.07: 51 70.07 - 93.43: 12 93.43 - 116.79: 4 Dihedral angle restraints: 8764 sinusoidal: 3564 harmonic: 5200 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.79 116.79 1 2.00e+01 2.50e-03 3.48e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.79 116.79 1 2.00e+01 2.50e-03 3.48e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.78 116.78 1 2.00e+01 2.50e-03 3.48e+01 ... (remaining 8761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1649 0.049 - 0.097: 416 0.097 - 0.146: 117 0.146 - 0.195: 7 0.195 - 0.244: 5 Chirality restraints: 2194 Sorted by residual: chirality pdb=" CA ILE D1242 " pdb=" N ILE D1242 " pdb=" C ILE D1242 " pdb=" CB ILE D1242 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE D1297 " pdb=" CA ILE D1297 " pdb=" CG1 ILE D1297 " pdb=" CG2 ILE D1297 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA LYS D1867 " pdb=" N LYS D1867 " pdb=" C LYS D1867 " pdb=" CB LYS D1867 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2191 not shown) Planarity restraints: 2528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D1251 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C MET D1251 " -0.056 2.00e-02 2.50e+03 pdb=" O MET D1251 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE D1252 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D1318 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C ALA D1318 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA D1318 " 0.018 2.00e-02 2.50e+03 pdb=" N MET D1319 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 243 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.023 5.00e-02 4.00e+02 ... (remaining 2525 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 50 2.52 - 3.11: 10430 3.11 - 3.71: 21558 3.71 - 4.30: 29429 4.30 - 4.90: 50324 Nonbonded interactions: 111791 Sorted by model distance: nonbonded pdb=" O LEU D1837 " pdb=" CD1 LEU D1837 " model vdw 1.921 3.460 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.186 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.186 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.186 2.170 nonbonded pdb=" O LEU D1377 " pdb=" OH TYR D1574 " model vdw 2.256 3.040 ... (remaining 111786 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 11.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.390 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14523 Z= 0.182 Angle : 0.676 9.614 19687 Z= 0.376 Chirality : 0.046 0.244 2194 Planarity : 0.004 0.041 2528 Dihedral : 14.222 116.791 5418 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % 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: -0.17 (0.21), residues: 1765 helix: 0.73 (0.19), residues: 823 sheet: -1.06 (0.30), residues: 288 loop : -0.59 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1491 TYR 0.010 0.001 TYR D1420 PHE 0.013 0.001 PHE D1699 TRP 0.026 0.002 TRP D1619 HIS 0.003 0.001 HIS D1666 Details of bonding type rmsd covalent geometry : bond 0.00368 (14523) covalent geometry : angle 0.67553 (19687) hydrogen bonds : bond 0.17364 ( 668) hydrogen bonds : angle 6.81438 ( 1875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: D 1286 MET cc_start: 0.7508 (ptp) cc_final: 0.7169 (ptm) REVERT: D 1881 MET cc_start: 0.8726 (tmm) cc_final: 0.8412 (ppp) REVERT: B 95 ARG cc_start: 0.7563 (mtt180) cc_final: 0.7180 (mmt180) REVERT: C 95 ARG cc_start: 0.7655 (mtt180) cc_final: 0.7376 (mmt180) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1102 time to fit residues: 29.8104 Evaluate side-chains 110 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** D1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1616 GLN B 115 ASN C 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.119547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084759 restraints weight = 27193.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.083882 restraints weight = 17044.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.084557 restraints weight = 12252.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.085084 restraints weight = 10091.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.085364 restraints weight = 8219.141| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14523 Z= 0.130 Angle : 0.614 8.733 19687 Z= 0.304 Chirality : 0.045 0.208 2194 Planarity : 0.004 0.040 2528 Dihedral : 7.030 104.512 1997 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.39 % Allowed : 6.61 % Favored : 93.00 % 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: 0.06 (0.21), residues: 1765 helix: 1.00 (0.19), residues: 807 sheet: -0.99 (0.30), residues: 292 loop : -0.53 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1491 TYR 0.014 0.001 TYR D1665 PHE 0.011 0.001 PHE D1252 TRP 0.029 0.002 TRP D1550 HIS 0.004 0.001 HIS D1666 Details of bonding type rmsd covalent geometry : bond 0.00306 (14523) covalent geometry : angle 0.61433 (19687) hydrogen bonds : bond 0.03856 ( 668) hydrogen bonds : angle 4.96783 ( 1875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: D 1286 MET cc_start: 0.7677 (ptp) cc_final: 0.7357 (ptm) REVERT: D 1647 ASP cc_start: 0.8016 (m-30) cc_final: 0.7618 (m-30) REVERT: D 1881 MET cc_start: 0.8651 (tmm) cc_final: 0.8374 (ppp) REVERT: B 95 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7259 (mmt180) REVERT: B 370 VAL cc_start: 0.9364 (p) cc_final: 0.9119 (p) REVERT: C 95 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7306 (mmt180) REVERT: C 184 ASP cc_start: 0.7532 (t0) cc_final: 0.7312 (t0) outliers start: 6 outliers final: 3 residues processed: 129 average time/residue: 0.1055 time to fit residues: 21.6339 Evaluate side-chains 114 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain B residue 6 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 0 optimal weight: 6.9990 chunk 125 optimal weight: 0.0770 chunk 96 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 172 optimal weight: 0.0870 chunk 100 optimal weight: 20.0000 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 115 optimal weight: 0.7980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1274 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.120769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.086154 restraints weight = 27222.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.085657 restraints weight = 15430.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.086532 restraints weight = 10553.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086965 restraints weight = 9356.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086958 restraints weight = 7728.395| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14523 Z= 0.097 Angle : 0.564 7.877 19687 Z= 0.272 Chirality : 0.043 0.222 2194 Planarity : 0.004 0.039 2528 Dihedral : 6.549 94.978 1997 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.78 % Allowed : 8.31 % Favored : 90.91 % 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: 0.31 (0.21), residues: 1765 helix: 1.15 (0.19), residues: 801 sheet: -0.81 (0.29), residues: 306 loop : -0.33 (0.27), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1408 TYR 0.021 0.001 TYR D1255 PHE 0.010 0.001 PHE D1822 TRP 0.033 0.002 TRP D1550 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00213 (14523) covalent geometry : angle 0.56400 (19687) hydrogen bonds : bond 0.03270 ( 668) hydrogen bonds : angle 4.60182 ( 1875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: D 1286 MET cc_start: 0.7715 (ptp) cc_final: 0.7434 (ptm) REVERT: D 1881 MET cc_start: 0.8639 (tmm) cc_final: 0.8343 (ppp) REVERT: B 95 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7254 (mmt180) REVERT: B 353 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7692 (tm-30) REVERT: B 370 VAL cc_start: 0.9321 (p) cc_final: 0.9082 (p) REVERT: C 95 ARG cc_start: 0.7715 (mtt180) cc_final: 0.7338 (mmt180) outliers start: 12 outliers final: 5 residues processed: 133 average time/residue: 0.1059 time to fit residues: 22.0683 Evaluate side-chains 118 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 151 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 47 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.118003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.082691 restraints weight = 27139.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.082395 restraints weight = 14828.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.083621 restraints weight = 9988.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.083830 restraints weight = 8658.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.083727 restraints weight = 7604.554| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14523 Z= 0.148 Angle : 0.586 7.050 19687 Z= 0.287 Chirality : 0.044 0.154 2194 Planarity : 0.004 0.038 2528 Dihedral : 6.408 92.985 1997 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.92 % Allowed : 9.68 % Favored : 89.40 % 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: 0.39 (0.21), residues: 1765 helix: 1.21 (0.19), residues: 802 sheet: -0.74 (0.28), residues: 306 loop : -0.28 (0.27), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 372 TYR 0.015 0.001 TYR D1255 PHE 0.013 0.001 PHE D1699 TRP 0.040 0.002 TRP D1550 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00354 (14523) covalent geometry : angle 0.58610 (19687) hydrogen bonds : bond 0.03522 ( 668) hydrogen bonds : angle 4.45613 ( 1875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.541 Fit side-chains REVERT: A 313 MET cc_start: 0.8570 (tpp) cc_final: 0.8239 (ttm) REVERT: D 1286 MET cc_start: 0.7860 (ptp) cc_final: 0.7569 (ptm) REVERT: D 1881 MET cc_start: 0.8660 (tmm) cc_final: 0.8381 (tmm) REVERT: B 95 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7257 (mmt180) REVERT: C 95 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7422 (mmt180) outliers start: 14 outliers final: 8 residues processed: 126 average time/residue: 0.1086 time to fit residues: 21.2935 Evaluate side-chains 109 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 180 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 71 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 88 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 32 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.119509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.084836 restraints weight = 27100.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.084174 restraints weight = 14810.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.085026 restraints weight = 10112.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.085426 restraints weight = 8799.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.085459 restraints weight = 7483.972| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14523 Z= 0.103 Angle : 0.567 7.909 19687 Z= 0.272 Chirality : 0.043 0.136 2194 Planarity : 0.004 0.038 2528 Dihedral : 6.195 88.118 1997 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.18 % Allowed : 10.14 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1765 helix: 1.33 (0.19), residues: 803 sheet: -0.66 (0.29), residues: 306 loop : -0.23 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 372 TYR 0.016 0.001 TYR D1255 PHE 0.009 0.001 PHE D1822 TRP 0.013 0.001 TRP B 340 HIS 0.004 0.001 HIS D1274 Details of bonding type rmsd covalent geometry : bond 0.00238 (14523) covalent geometry : angle 0.56694 (19687) hydrogen bonds : bond 0.03078 ( 668) hydrogen bonds : angle 4.33960 ( 1875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.578 Fit side-chains REVERT: A 192 ILE cc_start: 0.9407 (tp) cc_final: 0.9159 (tp) REVERT: A 313 MET cc_start: 0.8508 (tpp) cc_final: 0.8165 (ttm) REVERT: D 1286 MET cc_start: 0.7814 (ptp) cc_final: 0.7530 (ptm) REVERT: D 1550 TRP cc_start: 0.8628 (t60) cc_final: 0.8317 (t60) REVERT: D 1881 MET cc_start: 0.8625 (tmm) cc_final: 0.8365 (tmm) REVERT: B 95 ARG cc_start: 0.7750 (mtt180) cc_final: 0.7245 (mmt180) REVERT: B 207 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: C 95 ARG cc_start: 0.7927 (mtt180) cc_final: 0.7378 (mmt180) outliers start: 18 outliers final: 8 residues processed: 133 average time/residue: 0.1013 time to fit residues: 21.4815 Evaluate side-chains 114 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 180 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 103 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 175 optimal weight: 0.0000 chunk 5 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.119471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.085531 restraints weight = 26994.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083490 restraints weight = 18281.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.084870 restraints weight = 13218.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.085260 restraints weight = 9716.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.085377 restraints weight = 8168.072| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14523 Z= 0.108 Angle : 0.564 8.007 19687 Z= 0.272 Chirality : 0.043 0.132 2194 Planarity : 0.004 0.047 2528 Dihedral : 6.043 84.194 1997 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.37 % Allowed : 10.20 % Favored : 88.42 % 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: 0.57 (0.21), residues: 1765 helix: 1.36 (0.19), residues: 804 sheet: -0.61 (0.29), residues: 306 loop : -0.21 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 312 TYR 0.015 0.001 TYR D1255 PHE 0.009 0.001 PHE D1822 TRP 0.011 0.001 TRP B 340 HIS 0.003 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00254 (14523) covalent geometry : angle 0.56382 (19687) hydrogen bonds : bond 0.03045 ( 668) hydrogen bonds : angle 4.27116 ( 1875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.558 Fit side-chains REVERT: A 192 ILE cc_start: 0.9408 (tp) cc_final: 0.9129 (tp) REVERT: A 313 MET cc_start: 0.8561 (tpp) cc_final: 0.8045 (ttm) REVERT: D 1286 MET cc_start: 0.7969 (ptp) cc_final: 0.7598 (ptm) REVERT: D 1881 MET cc_start: 0.8707 (tmm) cc_final: 0.8462 (tmm) REVERT: B 95 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7247 (mmt180) REVERT: B 207 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: C 95 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7350 (mmt180) outliers start: 21 outliers final: 11 residues processed: 129 average time/residue: 0.0975 time to fit residues: 20.1657 Evaluate side-chains 117 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 298 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 42 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.111715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.076649 restraints weight = 27485.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.075065 restraints weight = 18135.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.075977 restraints weight = 13320.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.077000 restraints weight = 10698.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.076947 restraints weight = 9428.292| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.086 14523 Z= 0.399 Angle : 0.801 9.688 19687 Z= 0.402 Chirality : 0.053 0.240 2194 Planarity : 0.005 0.048 2528 Dihedral : 7.032 101.114 1997 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.05 % Allowed : 11.71 % Favored : 87.25 % 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: 0.06 (0.21), residues: 1765 helix: 0.84 (0.18), residues: 826 sheet: -0.65 (0.30), residues: 289 loop : -0.51 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 183 TYR 0.025 0.002 TYR B 294 PHE 0.027 0.002 PHE C 255 TRP 0.013 0.002 TRP D1619 HIS 0.005 0.001 HIS D1666 Details of bonding type rmsd covalent geometry : bond 0.00955 (14523) covalent geometry : angle 0.80078 (19687) hydrogen bonds : bond 0.05089 ( 668) hydrogen bonds : angle 4.78449 ( 1875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 192 ILE cc_start: 0.9401 (tp) cc_final: 0.9080 (tp) REVERT: A 313 MET cc_start: 0.8830 (tpp) cc_final: 0.8449 (tpt) REVERT: D 1286 MET cc_start: 0.8026 (ptp) cc_final: 0.7500 (ptm) REVERT: D 1550 TRP cc_start: 0.8734 (t60) cc_final: 0.8447 (t60) REVERT: D 1797 MET cc_start: 0.9342 (mmm) cc_final: 0.9128 (mmt) REVERT: D 1881 MET cc_start: 0.8705 (tmm) cc_final: 0.8451 (tmm) REVERT: B 95 ARG cc_start: 0.8225 (mtt180) cc_final: 0.7344 (mmt180) REVERT: C 47 MET cc_start: 0.7874 (mtt) cc_final: 0.6824 (ptt) REVERT: C 95 ARG cc_start: 0.8355 (mtt180) cc_final: 0.7601 (mmt180) outliers start: 16 outliers final: 10 residues processed: 116 average time/residue: 0.0978 time to fit residues: 18.0082 Evaluate side-chains 106 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 288 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 3 optimal weight: 0.4980 chunk 98 optimal weight: 20.0000 chunk 151 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.116862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.082076 restraints weight = 27076.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.081095 restraints weight = 14744.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.082002 restraints weight = 12030.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.082740 restraints weight = 8735.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.082550 restraints weight = 7575.545| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 14523 Z= 0.121 Angle : 0.610 8.926 19687 Z= 0.297 Chirality : 0.044 0.153 2194 Planarity : 0.004 0.039 2528 Dihedral : 6.533 95.055 1997 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.92 % Allowed : 11.97 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1765 helix: 1.16 (0.19), residues: 826 sheet: -0.52 (0.30), residues: 289 loop : -0.29 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.016 0.001 TYR B 166 PHE 0.013 0.001 PHE D1341 TRP 0.017 0.002 TRP B 340 HIS 0.003 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00286 (14523) covalent geometry : angle 0.61000 (19687) hydrogen bonds : bond 0.03381 ( 668) hydrogen bonds : angle 4.40402 ( 1875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.426 Fit side-chains REVERT: A 192 ILE cc_start: 0.9393 (tp) cc_final: 0.9080 (tp) REVERT: A 313 MET cc_start: 0.8608 (tpp) cc_final: 0.8081 (ttm) REVERT: D 1286 MET cc_start: 0.7930 (ptp) cc_final: 0.7422 (ptm) REVERT: D 1881 MET cc_start: 0.8690 (tmm) cc_final: 0.8358 (ppp) REVERT: B 95 ARG cc_start: 0.8120 (mtt180) cc_final: 0.7311 (mmt180) REVERT: C 47 MET cc_start: 0.7779 (mtt) cc_final: 0.6747 (ptt) REVERT: C 95 ARG cc_start: 0.8264 (mtt180) cc_final: 0.7581 (mmt180) outliers start: 14 outliers final: 8 residues processed: 118 average time/residue: 0.1004 time to fit residues: 18.8175 Evaluate side-chains 109 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 127 optimal weight: 0.0670 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.117940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.083642 restraints weight = 27211.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081923 restraints weight = 17608.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.083340 restraints weight = 12585.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083713 restraints weight = 9504.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.083838 restraints weight = 7899.331| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14523 Z= 0.110 Angle : 0.595 9.634 19687 Z= 0.288 Chirality : 0.044 0.331 2194 Planarity : 0.004 0.038 2528 Dihedral : 6.145 88.266 1997 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.59 % Allowed : 12.95 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1765 helix: 1.37 (0.19), residues: 807 sheet: -0.63 (0.29), residues: 306 loop : -0.22 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.012 0.001 TYR D1255 PHE 0.009 0.001 PHE D1451 TRP 0.015 0.002 TRP B 340 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00262 (14523) covalent geometry : angle 0.59521 (19687) hydrogen bonds : bond 0.03130 ( 668) hydrogen bonds : angle 4.25575 ( 1875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.639 Fit side-chains REVERT: A 192 ILE cc_start: 0.9401 (tp) cc_final: 0.9107 (tp) REVERT: A 313 MET cc_start: 0.8609 (tpp) cc_final: 0.8155 (tpt) REVERT: D 1881 MET cc_start: 0.8636 (tmm) cc_final: 0.8373 (ppp) REVERT: B 95 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7312 (mmt180) REVERT: C 47 MET cc_start: 0.7826 (mtt) cc_final: 0.6779 (ptt) REVERT: C 95 ARG cc_start: 0.8210 (mtt180) cc_final: 0.7552 (mmt180) outliers start: 9 outliers final: 7 residues processed: 115 average time/residue: 0.1032 time to fit residues: 19.1061 Evaluate side-chains 112 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1341 PHE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 143 optimal weight: 0.9980 chunk 173 optimal weight: 0.0570 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.117100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.082581 restraints weight = 27018.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.081012 restraints weight = 18040.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.082231 restraints weight = 12315.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.082663 restraints weight = 9673.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.082795 restraints weight = 8007.397| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14523 Z= 0.140 Angle : 0.615 10.391 19687 Z= 0.295 Chirality : 0.045 0.268 2194 Planarity : 0.004 0.035 2528 Dihedral : 6.064 87.083 1997 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.59 % Allowed : 13.15 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1765 helix: 1.39 (0.19), residues: 807 sheet: -0.61 (0.29), residues: 306 loop : -0.23 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.012 0.001 TYR D1255 PHE 0.010 0.001 PHE D1451 TRP 0.013 0.001 TRP B 340 HIS 0.003 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00341 (14523) covalent geometry : angle 0.61498 (19687) hydrogen bonds : bond 0.03264 ( 668) hydrogen bonds : angle 4.25451 ( 1875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.412 Fit side-chains REVERT: A 192 ILE cc_start: 0.9389 (tp) cc_final: 0.9120 (tp) REVERT: A 313 MET cc_start: 0.8586 (tpp) cc_final: 0.8148 (tpt) REVERT: D 1286 MET cc_start: 0.8206 (ptm) cc_final: 0.7905 (ptt) REVERT: D 1881 MET cc_start: 0.8630 (tmm) cc_final: 0.8425 (tmm) REVERT: B 95 ARG cc_start: 0.8047 (mtt180) cc_final: 0.7301 (mmt180) REVERT: C 47 MET cc_start: 0.7796 (mtt) cc_final: 0.6781 (ptt) REVERT: C 95 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7590 (mmt180) outliers start: 9 outliers final: 9 residues processed: 109 average time/residue: 0.1039 time to fit residues: 18.2207 Evaluate side-chains 110 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1341 PHE Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 107 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1590 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.114435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.079626 restraints weight = 27236.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.078573 restraints weight = 15884.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.079527 restraints weight = 11619.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079743 restraints weight = 10122.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.079834 restraints weight = 9073.617| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 14523 Z= 0.229 Angle : 0.675 9.830 19687 Z= 0.330 Chirality : 0.047 0.259 2194 Planarity : 0.004 0.037 2528 Dihedral : 6.379 93.124 1997 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.65 % Allowed : 13.08 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.21), residues: 1765 helix: 1.27 (0.19), residues: 814 sheet: -0.47 (0.30), residues: 289 loop : -0.43 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 210 TYR 0.015 0.001 TYR B 294 PHE 0.016 0.001 PHE C 255 TRP 0.011 0.002 TRP B 340 HIS 0.004 0.001 HIS D1666 Details of bonding type rmsd covalent geometry : bond 0.00557 (14523) covalent geometry : angle 0.67465 (19687) hydrogen bonds : bond 0.03946 ( 668) hydrogen bonds : angle 4.40356 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2196.66 seconds wall clock time: 38 minutes 57.45 seconds (2337.45 seconds total)