Starting phenix.real_space_refine on Fri Jul 3 20:36:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7udu_26460/07_2026/7udu_26460.cif Found real_map, /net/cci-nas-00/data/ceres_data/7udu_26460/07_2026/7udu_26460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7udu_26460/07_2026/7udu_26460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7udu_26460/07_2026/7udu_26460.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7udu_26460/07_2026/7udu_26460.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7udu_26460/07_2026/7udu_26460.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7udu_26460/07_2026/7udu_26460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7udu_26460/07_2026/7udu_26460.map" } resolution = 4.15 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= 0.002 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 100 5.16 5 C 9944 2.51 5 N 2671 2.21 5 O 2984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15711 Number of models: 1 Model: "" Number of chains: 9 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: "B" 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: "C" 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: 5661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5661 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 23, 'TRANS': 677} Chain breaks: 2 Chain: "E" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1187 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} 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: "B" 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: "C" 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} Time building chain proxies: 2.82, per 1000 atoms: 0.18 Number of scatterers: 15711 At special positions: 0 Unit cell: (98.88, 174.07, 166.86, 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 100 16.00 P 8 15.00 Mg 4 11.99 O 2984 8.00 N 2671 7.00 C 9944 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: 1.20 Conformation dependent library (CDL) restraints added in 662.0 milliseconds 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3684 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 24 sheets defined 53.0% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 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: 3.516A 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: 4.022A 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: 3.614A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.777A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.556A 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: 3.607A 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: 4.041A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'B' and resid 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: 3.746A 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: 3.612A 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: 3.556A 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: 3.607A 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: 3.507A 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: 4.040A 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: 3.806A 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: 3.953A 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: 3.606A 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: 3.504A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.130A 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 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: 3.717A 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: 3.762A 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: 3.765A 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: 3.848A pdb=" N ARG D1810 " --> pdb=" O LEU D1806 " (cutoff:3.500A) Processing helix chain 'D' and resid 1822 through 1829 removed outlier: 3.865A pdb=" N TYR D1829 " --> pdb=" O PHE D1825 " (cutoff:3.500A) Processing helix chain 'D' and resid 1846 through 1855 Processing helix chain 'D' and resid 1871 through 1910 removed outlier: 3.703A pdb=" N ARG D1910 " --> pdb=" O PHE D1906 " (cutoff:3.500A) Processing helix chain 'D' and resid 1913 through 1922 Processing helix chain 'E' and resid 27 through 42 removed outlier: 3.918A pdb=" N GLN E 32 " --> pdb=" O GLN E 28 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU E 33 " --> pdb=" O SER E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 60 removed outlier: 3.913A pdb=" N LEU E 54 " --> pdb=" O ASP E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 93 Processing helix chain 'E' and resid 99 through 109 Processing helix chain 'E' and resid 120 through 130 removed outlier: 3.706A pdb=" N MET E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 Processing helix chain 'E' and resid 156 through 166 removed outlier: 3.842A pdb=" N GLY E 166 " --> pdb=" O ILE E 162 " (cutoff:3.500A) 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: 5.623A 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: 4.258A 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: 4.258A 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: 7.462A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.957A 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 '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=AB1, first strand: chain 'B' and resid 35 through 38 Processing sheet with id=AB2, 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=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 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: 3.618A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 38 Processing sheet with id=AB6, 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=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.631A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 1237 through 1239 removed outlier: 6.468A pdb=" N LEU D1243 " --> pdb=" O ARG D1778 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU D1780 " --> pdb=" O LEU D1243 " (cutoff:3.500A) removed outlier: 6.819A 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: 3.580A pdb=" N ALA D1569 " --> pdb=" O GLN D1293 " (cutoff:3.500A) removed outlier: 4.727A 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=AC2, first strand: chain 'D' and resid 1237 through 1239 removed outlier: 6.468A pdb=" N LEU D1243 " --> pdb=" O ARG D1778 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU D1780 " --> pdb=" O LEU D1243 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER D1245 " --> pdb=" O LEU D1780 " (cutoff:3.500A) Processing sheet with id=AC3, 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=AC4, first strand: chain 'D' and resid 1513 through 1517 Processing sheet with id=AC5, first strand: chain 'D' and resid 1673 through 1674 Processing sheet with id=AC6, first strand: chain 'E' and resid 118 through 119 765 hydrogen bonds defined for protein. 2121 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: 2.83 Time building geometry restraints manager: 1.63 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: 3232 1.33 - 1.45: 3695 1.45 - 1.57: 8929 1.57 - 1.69: 12 1.69 - 1.82: 170 Bond restraints: 16038 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 8.54e+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 8.35e+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 8.33e+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 6.03e+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 4.91e+00 ... (remaining 16033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 21356 2.23 - 4.46: 318 4.46 - 6.69: 40 6.69 - 8.92: 4 8.92 - 11.15: 2 Bond angle restraints: 21720 Sorted by residual: angle pdb=" C VAL D1833 " pdb=" N ALA D1834 " pdb=" CA ALA D1834 " ideal model delta sigma weight residual 122.63 133.78 -11.15 1.44e+00 4.82e-01 6.00e+01 angle pdb=" C GLY D1256 " pdb=" N PRO D1257 " pdb=" CA PRO D1257 " ideal model delta sigma weight residual 119.56 113.02 6.54 1.01e+00 9.80e-01 4.19e+01 angle pdb=" N ASN D1320 " pdb=" CA ASN D1320 " pdb=" C ASN D1320 " ideal model delta sigma weight residual 109.76 101.14 8.62 1.64e+00 3.72e-01 2.76e+01 angle pdb=" N ILE D1242 " pdb=" CA ILE D1242 " pdb=" C ILE D1242 " ideal model delta sigma weight residual 109.55 116.57 -7.02 1.38e+00 5.25e-01 2.59e+01 angle pdb=" C ILE D1239 " pdb=" CA ILE D1239 " pdb=" CB ILE D1239 " ideal model delta sigma weight residual 113.22 108.29 4.93 1.12e+00 7.97e-01 1.94e+01 ... (remaining 21715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.36: 9084 23.36 - 46.71: 520 46.71 - 70.07: 54 70.07 - 93.42: 14 93.42 - 116.78: 4 Dihedral angle restraints: 9676 sinusoidal: 3954 harmonic: 5722 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 -176.78 116.78 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 -176.75 116.75 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 -176.74 116.74 1 2.00e+01 2.50e-03 3.48e+01 ... (remaining 9673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2147 0.072 - 0.143: 248 0.143 - 0.215: 6 0.215 - 0.287: 3 0.287 - 0.359: 1 Chirality restraints: 2405 Sorted by residual: chirality pdb=" CA LEU D1837 " pdb=" N LEU D1837 " pdb=" C LEU D1837 " pdb=" CB LEU D1837 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 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 0.25 2.00e-01 2.50e+01 1.54e+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 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2402 not shown) Planarity restraints: 2800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D1251 " 0.016 2.00e-02 2.50e+03 3.22e-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 2.83e-02 8.01e+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 4.09e-02 2.68e+00 pdb=" N PRO A 243 " -0.071 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 2797 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 894 2.73 - 3.27: 15954 3.27 - 3.81: 25342 3.81 - 4.36: 29794 4.36 - 4.90: 51316 Nonbonded interactions: 123300 Sorted by model distance: nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.186 2.170 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 2.187 2.170 nonbonded pdb=" N GLU D1872 " pdb=" OE1 GLU D1872 " model vdw 2.209 3.120 nonbonded pdb=" O THR D1808 " pdb=" CG1 ILE D1811 " model vdw 2.211 3.440 ... (remaining 123295 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: 10.920 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.310 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 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 16038 Z= 0.177 Angle : 0.674 11.152 21720 Z= 0.372 Chirality : 0.045 0.359 2405 Planarity : 0.004 0.041 2800 Dihedral : 14.256 116.776 5992 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1943 helix: 0.68 (0.18), residues: 926 sheet: -1.06 (0.30), residues: 288 loop : -0.81 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1491 TYR 0.010 0.001 TYR D1420 PHE 0.018 0.001 PHE E 34 TRP 0.026 0.002 TRP D1619 HIS 0.003 0.001 HIS D1905 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (16038) covalent geometry : angle 0.67406 / 0.37 (21720) hydrogen bonds : bond 0.17244 / 11.61 ( 751) hydrogen bonds : angle 6.76509 / 4.74 ( 2121) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 649 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8121 (t70) cc_final: 0.7196 (p0) REVERT: A 34 ILE cc_start: 0.8234 (mt) cc_final: 0.7758 (tp) REVERT: A 82 MET cc_start: 0.8065 (tpt) cc_final: 0.7714 (tpp) REVERT: A 111 ASN cc_start: 0.8162 (m-40) cc_final: 0.7944 (m110) REVERT: A 128 ASN cc_start: 0.8823 (t0) cc_final: 0.8587 (t0) REVERT: A 137 GLN cc_start: 0.7962 (mt0) cc_final: 0.7681 (mp10) REVERT: A 179 ASP cc_start: 0.8512 (m-30) cc_final: 0.8094 (p0) REVERT: A 195 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8601 (pt0) REVERT: A 217 CYS cc_start: 0.8171 (m) cc_final: 0.7695 (m) REVERT: A 246 GLN cc_start: 0.6084 (tt0) cc_final: 0.5678 (mt0) REVERT: A 253 GLU cc_start: 0.7320 (mp0) cc_final: 0.6828 (pm20) REVERT: A 283 MET cc_start: 0.7023 (mmt) cc_final: 0.6691 (mmt) REVERT: A 285 CYS cc_start: 0.8352 (m) cc_final: 0.8098 (p) REVERT: A 291 LYS cc_start: 0.8983 (tptp) cc_final: 0.8610 (mmtt) REVERT: A 299 MET cc_start: 0.9280 (mmm) cc_final: 0.8456 (mmp) REVERT: A 355 MET cc_start: 0.7652 (mtt) cc_final: 0.6945 (tpp) REVERT: A 360 GLN cc_start: 0.9358 (tp40) cc_final: 0.9051 (tp-100) REVERT: B 34 ILE cc_start: 0.8335 (mt) cc_final: 0.8004 (mt) REVERT: B 78 ASN cc_start: 0.7722 (t0) cc_final: 0.6752 (t0) REVERT: B 80 ASP cc_start: 0.8723 (m-30) cc_final: 0.8350 (p0) REVERT: B 95 ARG cc_start: 0.7514 (mtt180) cc_final: 0.6629 (tpm170) REVERT: B 96 VAL cc_start: 0.8787 (t) cc_final: 0.8582 (p) REVERT: B 107 GLU cc_start: 0.6857 (tt0) cc_final: 0.6372 (tt0) REVERT: B 111 ASN cc_start: 0.8083 (m-40) cc_final: 0.7851 (m110) REVERT: B 119 MET cc_start: 0.7695 (ttm) cc_final: 0.7358 (ttm) REVERT: B 191 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8309 (mmtt) REVERT: B 196 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7656 (mtt180) REVERT: B 198 TYR cc_start: 0.8609 (m-80) cc_final: 0.8241 (m-80) REVERT: B 214 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7448 (tm-30) REVERT: B 246 GLN cc_start: 0.8674 (tt0) cc_final: 0.8180 (tm-30) REVERT: B 256 ARG cc_start: 0.7430 (ttp-110) cc_final: 0.7062 (mtp-110) REVERT: B 279 TYR cc_start: 0.6655 (t80) cc_final: 0.6300 (t80) REVERT: B 290 ARG cc_start: 0.5614 (mtt180) cc_final: 0.5350 (mtt90) REVERT: B 299 MET cc_start: 0.7912 (mmm) cc_final: 0.7538 (mtt) REVERT: B 316 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7699 (mm-30) REVERT: B 354 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8109 (pt0) REVERT: C 11 ASP cc_start: 0.7687 (t70) cc_final: 0.6960 (m-30) REVERT: C 80 ASP cc_start: 0.8755 (m-30) cc_final: 0.8524 (m-30) REVERT: C 82 MET cc_start: 0.7571 (tpt) cc_final: 0.7303 (tpt) REVERT: C 95 ARG cc_start: 0.8839 (mtt180) cc_final: 0.8259 (tpm170) REVERT: C 163 VAL cc_start: 0.7446 (t) cc_final: 0.7219 (t) REVERT: C 198 TYR cc_start: 0.8541 (m-80) cc_final: 0.7421 (m-80) REVERT: C 222 ASP cc_start: 0.7993 (t0) cc_final: 0.7229 (t0) REVERT: C 288 ASP cc_start: 0.6958 (m-30) cc_final: 0.6336 (p0) REVERT: C 340 TRP cc_start: 0.6248 (t60) cc_final: 0.5710 (t60) REVERT: C 355 MET cc_start: 0.7536 (mtt) cc_final: 0.7112 (mmp) REVERT: C 370 VAL cc_start: 0.7962 (p) cc_final: 0.7608 (m) REVERT: D 1251 MET cc_start: 0.8931 (tpt) cc_final: 0.8469 (mmp) REVERT: D 1274 HIS cc_start: 0.8595 (t70) cc_final: 0.7951 (t70) REVERT: D 1326 MET cc_start: 0.6889 (ptp) cc_final: 0.6430 (mmp) REVERT: D 1341 PHE cc_start: 0.7701 (m-10) cc_final: 0.7480 (m-80) REVERT: D 1349 ASN cc_start: 0.6904 (t0) cc_final: 0.6557 (t0) REVERT: D 1389 ASN cc_start: 0.8647 (m-40) cc_final: 0.8004 (t0) REVERT: D 1392 ASN cc_start: 0.8544 (t0) cc_final: 0.7246 (t0) REVERT: D 1428 CYS cc_start: 0.7638 (m) cc_final: 0.7049 (m) REVERT: D 1520 ARG cc_start: 0.8698 (mtt90) cc_final: 0.8290 (mtt-85) REVERT: D 1607 GLU cc_start: 0.8261 (tt0) cc_final: 0.7927 (tt0) REVERT: D 1609 GLN cc_start: 0.8630 (mt0) cc_final: 0.8245 (tp-100) REVERT: D 1658 THR cc_start: 0.8464 (p) cc_final: 0.7728 (t) REVERT: D 1675 LYS cc_start: 0.8794 (tttt) cc_final: 0.7976 (ptpt) REVERT: D 1688 TYR cc_start: 0.7972 (p90) cc_final: 0.7531 (p90) REVERT: D 1692 VAL cc_start: 0.8653 (t) cc_final: 0.8270 (p) REVERT: D 1752 HIS cc_start: 0.7541 (m170) cc_final: 0.7282 (m-70) REVERT: D 1823 GLN cc_start: 0.9196 (tp40) cc_final: 0.8908 (tp-100) REVERT: D 1900 PHE cc_start: 0.9663 (t80) cc_final: 0.9217 (m-80) REVERT: D 1906 PHE cc_start: 0.9833 (m-80) cc_final: 0.9430 (m-80) REVERT: E 104 ARG cc_start: 0.9048 (mmm160) cc_final: 0.8747 (mmm160) REVERT: E 110 PHE cc_start: 0.8214 (m-80) cc_final: 0.7410 (m-80) REVERT: E 143 TYR cc_start: 0.8934 (m-10) cc_final: 0.8182 (m-10) outliers start: 1 outliers final: 0 residues processed: 650 average time/residue: 0.1306 time to fit residues: 121.3284 Evaluate side-chains 375 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN B 40 HIS B 115 ASN C 40 HIS ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1320 ASN D1321 GLN D1471 ASN D1590 ASN D1703 ASN ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.120872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.095962 restraints weight = 38930.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098318 restraints weight = 22113.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099914 restraints weight = 14623.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101006 restraints weight = 10856.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101609 restraints weight = 8797.305| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16038 Z= 0.150 Angle : 0.668 9.749 21720 Z= 0.332 Chirality : 0.045 0.185 2405 Planarity : 0.004 0.041 2800 Dihedral : 7.006 104.672 2194 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.12 % Allowed : 4.63 % Favored : 95.26 % 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: -0.18 (0.20), residues: 1943 helix: 0.75 (0.18), residues: 916 sheet: -1.03 (0.29), residues: 294 loop : -0.69 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 124 TYR 0.018 0.002 TYR D1376 PHE 0.019 0.002 PHE E 38 TRP 0.019 0.002 TRP D1619 HIS 0.005 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (16038) covalent geometry : angle 0.66787 / 0.33 (21720) hydrogen bonds : bond 0.04309 / 2.99 ( 751) hydrogen bonds : angle 5.18342 / 3.59 ( 2121) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 428 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.7905 (t0) cc_final: 0.7209 (t0) REVERT: A 142 LEU cc_start: 0.8841 (mt) cc_final: 0.8630 (mt) REVERT: A 154 ASP cc_start: 0.6848 (t70) cc_final: 0.6584 (t70) REVERT: A 283 MET cc_start: 0.7328 (mmt) cc_final: 0.7045 (mmt) REVERT: A 364 GLU cc_start: 0.8314 (pt0) cc_final: 0.7874 (pt0) REVERT: B 95 ARG cc_start: 0.7159 (mtt180) cc_final: 0.6810 (tpm170) REVERT: B 191 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8642 (mmtt) REVERT: B 214 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7600 (tm-30) REVERT: B 290 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7498 (mtt90) REVERT: B 314 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7294 (tm-30) REVERT: C 137 GLN cc_start: 0.7494 (mp10) cc_final: 0.7155 (mp10) REVERT: C 140 LEU cc_start: 0.8061 (mm) cc_final: 0.7699 (mm) REVERT: C 198 TYR cc_start: 0.8783 (m-80) cc_final: 0.8079 (m-80) REVERT: D 1251 MET cc_start: 0.7803 (tpt) cc_final: 0.7595 (mmp) REVERT: D 1343 ASN cc_start: 0.7460 (m-40) cc_final: 0.7168 (m110) REVERT: D 1376 TYR cc_start: 0.8080 (m-80) cc_final: 0.7691 (m-80) REVERT: D 1397 TYR cc_start: 0.8210 (m-80) cc_final: 0.7900 (m-80) REVERT: D 1647 ASP cc_start: 0.7703 (m-30) cc_final: 0.7489 (m-30) REVERT: D 1658 THR cc_start: 0.8832 (p) cc_final: 0.8360 (t) REVERT: D 1675 LYS cc_start: 0.9234 (tttt) cc_final: 0.8653 (ptpt) REVERT: D 1764 ASP cc_start: 0.8149 (t70) cc_final: 0.7467 (t0) REVERT: D 1906 PHE cc_start: 0.9545 (m-80) cc_final: 0.9160 (m-80) REVERT: E 104 ARG cc_start: 0.9280 (mmm160) cc_final: 0.8744 (mmm160) REVERT: E 107 PHE cc_start: 0.9005 (m-10) cc_final: 0.8543 (m-10) outliers start: 2 outliers final: 0 residues processed: 430 average time/residue: 0.1132 time to fit residues: 73.2820 Evaluate side-chains 305 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 165 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 184 optimal weight: 8.9990 chunk 176 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 187 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 HIS A 296 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1213 GLN D1389 ASN ** D1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1703 ASN D1706 GLN D1886 GLN ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.115961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091026 restraints weight = 40154.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.093220 restraints weight = 23332.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094745 restraints weight = 15651.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.095735 restraints weight = 11748.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.096494 restraints weight = 9586.092| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 16038 Z= 0.223 Angle : 0.717 7.855 21720 Z= 0.363 Chirality : 0.048 0.232 2405 Planarity : 0.005 0.064 2800 Dihedral : 7.029 102.204 2194 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.18 % Allowed : 4.03 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1943 helix: 0.58 (0.17), residues: 928 sheet: -0.77 (0.30), residues: 290 loop : -0.67 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1819 TYR 0.029 0.002 TYR C 294 PHE 0.021 0.002 PHE E 110 TRP 0.032 0.003 TRP C 86 HIS 0.011 0.001 HIS D1905 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (16038) covalent geometry : angle 0.71693 / 0.36 (21720) hydrogen bonds : bond 0.04532 / 3.13 ( 751) hydrogen bonds : angle 5.02513 / 3.48 ( 2121) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 385 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8700 (mtt) cc_final: 0.8268 (mtt) REVERT: A 78 ASN cc_start: 0.8097 (t0) cc_final: 0.7645 (t0) REVERT: A 132 MET cc_start: 0.8310 (ppp) cc_final: 0.8068 (ppp) REVERT: A 154 ASP cc_start: 0.7041 (t70) cc_final: 0.6503 (t70) REVERT: A 269 MET cc_start: 0.7832 (mmm) cc_final: 0.7209 (mtp) REVERT: A 364 GLU cc_start: 0.8362 (pt0) cc_final: 0.8111 (pt0) REVERT: B 44 MET cc_start: 0.6466 (tpt) cc_final: 0.6199 (tpt) REVERT: B 78 ASN cc_start: 0.8289 (t0) cc_final: 0.7987 (t0) REVERT: B 95 ARG cc_start: 0.7350 (mtt180) cc_final: 0.6703 (tpm170) REVERT: B 214 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7894 (tm-30) REVERT: B 279 TYR cc_start: 0.8258 (t80) cc_final: 0.8018 (t80) REVERT: C 86 TRP cc_start: 0.7700 (m-10) cc_final: 0.7329 (m-10) REVERT: C 140 LEU cc_start: 0.8290 (mm) cc_final: 0.7937 (mm) REVERT: C 198 TYR cc_start: 0.8888 (m-80) cc_final: 0.8322 (m-80) REVERT: C 299 MET cc_start: 0.8355 (mmm) cc_final: 0.7953 (mmm) REVERT: D 1211 MET cc_start: 0.8200 (mpp) cc_final: 0.7939 (mpp) REVERT: D 1243 LEU cc_start: 0.8985 (tp) cc_final: 0.8602 (tt) REVERT: D 1251 MET cc_start: 0.7827 (tpt) cc_final: 0.7497 (mmp) REVERT: D 1343 ASN cc_start: 0.7989 (m-40) cc_final: 0.7592 (m110) REVERT: D 1349 ASN cc_start: 0.8292 (t0) cc_final: 0.7965 (t0) REVERT: D 1397 TYR cc_start: 0.8252 (m-80) cc_final: 0.6848 (m-80) REVERT: D 1408 ARG cc_start: 0.5504 (mmt180) cc_final: 0.4051 (mmm-85) REVERT: D 1428 CYS cc_start: 0.6941 (m) cc_final: 0.6410 (m) REVERT: D 1658 THR cc_start: 0.8896 (p) cc_final: 0.8424 (t) REVERT: D 1675 LYS cc_start: 0.9200 (tttt) cc_final: 0.8781 (ptpt) REVERT: D 1906 PHE cc_start: 0.9589 (m-80) cc_final: 0.9251 (m-80) REVERT: E 104 ARG cc_start: 0.9321 (mmm160) cc_final: 0.8802 (mpt180) REVERT: E 107 PHE cc_start: 0.9056 (m-10) cc_final: 0.8388 (m-10) REVERT: E 122 TYR cc_start: 0.9362 (t80) cc_final: 0.9098 (t80) REVERT: E 124 ARG cc_start: 0.9230 (mpt-90) cc_final: 0.8980 (mtp85) REVERT: E 139 VAL cc_start: 0.9613 (t) cc_final: 0.9298 (t) REVERT: E 143 TYR cc_start: 0.8213 (m-10) cc_final: 0.7665 (m-10) outliers start: 3 outliers final: 0 residues processed: 388 average time/residue: 0.1246 time to fit residues: 72.7292 Evaluate side-chains 271 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 139 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 40 optimal weight: 0.0670 chunk 31 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 59 GLN A 128 ASN B 121 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1389 ASN ** D1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.117210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092593 restraints weight = 39506.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.094844 restraints weight = 22834.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.096412 restraints weight = 15217.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.097480 restraints weight = 11329.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098001 restraints weight = 9161.544| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16038 Z= 0.136 Angle : 0.647 7.312 21720 Z= 0.321 Chirality : 0.044 0.197 2405 Planarity : 0.004 0.072 2800 Dihedral : 6.813 95.983 2194 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.18 % Allowed : 3.02 % Favored : 96.80 % 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: -0.09 (0.20), residues: 1943 helix: 0.60 (0.17), residues: 941 sheet: -0.63 (0.30), residues: 294 loop : -0.51 (0.26), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 372 TYR 0.020 0.001 TYR C 306 PHE 0.022 0.001 PHE E 110 TRP 0.014 0.001 TRP A 340 HIS 0.011 0.001 HIS D1664 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (16038) covalent geometry : angle 0.64737 / 0.32 (21720) hydrogen bonds : bond 0.03843 / 2.63 ( 751) hydrogen bonds : angle 4.77084 / 3.32 ( 2121) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 378 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8694 (mtt) cc_final: 0.8298 (mtt) REVERT: A 78 ASN cc_start: 0.8328 (t0) cc_final: 0.7592 (t0) REVERT: A 132 MET cc_start: 0.8182 (ppp) cc_final: 0.7910 (ppp) REVERT: A 154 ASP cc_start: 0.6955 (t70) cc_final: 0.6486 (t70) REVERT: A 166 TYR cc_start: 0.7838 (t80) cc_final: 0.7466 (t80) REVERT: A 269 MET cc_start: 0.7735 (mmm) cc_final: 0.7199 (mtp) REVERT: A 314 GLN cc_start: 0.9068 (pp30) cc_final: 0.8842 (pp30) REVERT: B 44 MET cc_start: 0.6374 (tpt) cc_final: 0.6173 (tpt) REVERT: B 95 ARG cc_start: 0.7364 (mtt180) cc_final: 0.6655 (tpm170) REVERT: B 214 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7822 (tm-30) REVERT: B 279 TYR cc_start: 0.8213 (t80) cc_final: 0.7906 (t80) REVERT: B 314 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 69 TYR cc_start: 0.8506 (m-80) cc_final: 0.8261 (m-10) REVERT: C 140 LEU cc_start: 0.8184 (mm) cc_final: 0.7722 (mm) REVERT: C 198 TYR cc_start: 0.8916 (m-80) cc_final: 0.8328 (m-80) REVERT: C 280 ASN cc_start: 0.8380 (m-40) cc_final: 0.7996 (t0) REVERT: C 299 MET cc_start: 0.8213 (mmm) cc_final: 0.7820 (mmm) REVERT: D 1211 MET cc_start: 0.8207 (mpp) cc_final: 0.7911 (mpp) REVERT: D 1343 ASN cc_start: 0.8112 (m-40) cc_final: 0.7756 (m110) REVERT: D 1349 ASN cc_start: 0.8071 (t0) cc_final: 0.7681 (t0) REVERT: D 1397 TYR cc_start: 0.8203 (m-80) cc_final: 0.6743 (m-80) REVERT: D 1403 LEU cc_start: 0.6528 (tp) cc_final: 0.5192 (tp) REVERT: D 1408 ARG cc_start: 0.5508 (mmt180) cc_final: 0.3924 (mmm-85) REVERT: D 1428 CYS cc_start: 0.6871 (m) cc_final: 0.6394 (m) REVERT: D 1658 THR cc_start: 0.8813 (p) cc_final: 0.8452 (t) REVERT: D 1675 LYS cc_start: 0.9281 (tttt) cc_final: 0.8782 (ptpt) REVERT: D 1906 PHE cc_start: 0.9536 (m-80) cc_final: 0.9203 (m-80) REVERT: E 104 ARG cc_start: 0.9350 (mmm160) cc_final: 0.8848 (mmm160) REVERT: E 107 PHE cc_start: 0.9008 (m-10) cc_final: 0.8628 (m-10) REVERT: E 122 TYR cc_start: 0.9370 (t80) cc_final: 0.9072 (t80) REVERT: E 124 ARG cc_start: 0.9279 (mpt-90) cc_final: 0.8823 (mmm-85) REVERT: E 139 VAL cc_start: 0.9612 (t) cc_final: 0.9310 (t) REVERT: E 143 TYR cc_start: 0.8216 (m-10) cc_final: 0.7505 (m-10) outliers start: 3 outliers final: 0 residues processed: 380 average time/residue: 0.1254 time to fit residues: 71.3561 Evaluate side-chains 273 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 43 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 158 optimal weight: 0.0970 chunk 130 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 2 optimal weight: 0.3980 chunk 175 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN B 121 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1389 ASN ** D1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1609 GLN D1905 HIS ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.117421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.092627 restraints weight = 39715.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.094935 restraints weight = 22850.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.096498 restraints weight = 15178.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.097569 restraints weight = 11251.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.098187 restraints weight = 9095.514| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16038 Z= 0.130 Angle : 0.649 8.265 21720 Z= 0.320 Chirality : 0.045 0.196 2405 Planarity : 0.004 0.062 2800 Dihedral : 6.641 91.243 2194 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.24 % Allowed : 2.31 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1943 helix: 0.57 (0.17), residues: 947 sheet: -0.52 (0.30), residues: 294 loop : -0.44 (0.26), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 124 TYR 0.020 0.001 TYR D1236 PHE 0.021 0.001 PHE E 34 TRP 0.013 0.001 TRP D1619 HIS 0.013 0.001 HIS D1905 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16038) covalent geometry : angle 0.64871 / 0.32 (21720) hydrogen bonds : bond 0.03661 / 2.51 ( 751) hydrogen bonds : angle 4.70312 / 3.28 ( 2121) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 362 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8333 (t0) cc_final: 0.8095 (t0) REVERT: A 132 MET cc_start: 0.8156 (ppp) cc_final: 0.7839 (ppp) REVERT: A 154 ASP cc_start: 0.7009 (t70) cc_final: 0.6505 (t70) REVERT: A 246 GLN cc_start: 0.7884 (mt0) cc_final: 0.7660 (mt0) REVERT: A 269 MET cc_start: 0.7613 (mmm) cc_final: 0.7312 (mtp) REVERT: A 314 GLN cc_start: 0.9120 (pp30) cc_final: 0.8903 (pp30) REVERT: B 82 MET cc_start: 0.8190 (tpt) cc_final: 0.7918 (tpt) REVERT: B 95 ARG cc_start: 0.7311 (mtt180) cc_final: 0.6567 (tpm170) REVERT: B 214 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7832 (tm-30) REVERT: B 290 ARG cc_start: 0.7789 (mtt180) cc_final: 0.7447 (mtt90) REVERT: B 314 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7478 (tm-30) REVERT: C 72 GLU cc_start: 0.7929 (tp30) cc_final: 0.7678 (mm-30) REVERT: C 132 MET cc_start: 0.7784 (ppp) cc_final: 0.7514 (ppp) REVERT: C 140 LEU cc_start: 0.8227 (mm) cc_final: 0.7797 (mm) REVERT: C 190 MET cc_start: 0.7945 (ttp) cc_final: 0.7671 (ttm) REVERT: C 198 TYR cc_start: 0.8911 (m-80) cc_final: 0.8372 (m-80) REVERT: C 280 ASN cc_start: 0.8348 (m-40) cc_final: 0.7973 (t0) REVERT: C 299 MET cc_start: 0.8274 (mmm) cc_final: 0.7908 (mmm) REVERT: D 1343 ASN cc_start: 0.8101 (m-40) cc_final: 0.7717 (m110) REVERT: D 1349 ASN cc_start: 0.8219 (t0) cc_final: 0.7850 (t0) REVERT: D 1397 TYR cc_start: 0.8255 (m-80) cc_final: 0.6794 (m-80) REVERT: D 1408 ARG cc_start: 0.5612 (mmt180) cc_final: 0.4178 (mmm-85) REVERT: D 1428 CYS cc_start: 0.6859 (m) cc_final: 0.6282 (m) REVERT: D 1658 THR cc_start: 0.8768 (p) cc_final: 0.8401 (t) REVERT: D 1675 LYS cc_start: 0.9240 (tttt) cc_final: 0.8730 (ptpt) REVERT: D 1900 PHE cc_start: 0.8688 (m-80) cc_final: 0.8438 (m-80) REVERT: D 1906 PHE cc_start: 0.9520 (m-80) cc_final: 0.9236 (m-80) REVERT: E 101 ASP cc_start: 0.9223 (m-30) cc_final: 0.8974 (p0) REVERT: E 104 ARG cc_start: 0.9360 (mmm160) cc_final: 0.9028 (mmm160) REVERT: E 107 PHE cc_start: 0.8999 (m-10) cc_final: 0.8423 (m-10) outliers start: 4 outliers final: 0 residues processed: 365 average time/residue: 0.1193 time to fit residues: 66.1523 Evaluate side-chains 269 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 168 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 59 GLN A 128 ASN B 121 GLN B 371 HIS ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 111 ASN D1262 GLN D1389 ASN ** D1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.112836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088547 restraints weight = 39884.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.090670 restraints weight = 23305.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092092 restraints weight = 15646.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.093066 restraints weight = 11776.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.093645 restraints weight = 9631.353| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16038 Z= 0.230 Angle : 0.749 14.891 21720 Z= 0.370 Chirality : 0.048 0.228 2405 Planarity : 0.005 0.050 2800 Dihedral : 6.792 90.693 2194 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.18 % Allowed : 2.31 % Favored : 97.51 % 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: -0.25 (0.20), residues: 1943 helix: 0.42 (0.17), residues: 960 sheet: -0.69 (0.30), residues: 296 loop : -0.54 (0.26), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 206 TYR 0.027 0.002 TYR E 122 PHE 0.026 0.002 PHE D1341 TRP 0.011 0.002 TRP B 340 HIS 0.009 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (16038) covalent geometry : angle 0.74858 / 0.37 (21720) hydrogen bonds : bond 0.04300 / 3.00 ( 751) hydrogen bonds : angle 4.93788 / 3.45 ( 2121) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 343 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8579 (t0) cc_final: 0.8064 (t0) REVERT: A 132 MET cc_start: 0.8203 (ppp) cc_final: 0.7829 (ppp) REVERT: A 154 ASP cc_start: 0.7225 (t70) cc_final: 0.6783 (t70) REVERT: A 314 GLN cc_start: 0.9276 (pp30) cc_final: 0.8897 (pp30) REVERT: B 95 ARG cc_start: 0.7549 (mtt180) cc_final: 0.6618 (tpm170) REVERT: B 123 MET cc_start: 0.7845 (ttm) cc_final: 0.7598 (ttm) REVERT: B 214 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8046 (tm-30) REVERT: B 290 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7786 (mtt90) REVERT: B 314 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7851 (tm-30) REVERT: C 132 MET cc_start: 0.8223 (ppp) cc_final: 0.7940 (ppp) REVERT: C 280 ASN cc_start: 0.8382 (m-40) cc_final: 0.8040 (t0) REVERT: C 299 MET cc_start: 0.8406 (mmm) cc_final: 0.8061 (mmm) REVERT: D 1343 ASN cc_start: 0.8271 (m-40) cc_final: 0.7948 (m110) REVERT: D 1349 ASN cc_start: 0.8491 (t0) cc_final: 0.8011 (t0) REVERT: D 1397 TYR cc_start: 0.8382 (m-80) cc_final: 0.6816 (m-80) REVERT: D 1408 ARG cc_start: 0.5611 (mmt180) cc_final: 0.3828 (mmm-85) REVERT: D 1428 CYS cc_start: 0.6843 (m) cc_final: 0.6298 (m) REVERT: D 1565 THR cc_start: 0.6987 (p) cc_final: 0.6718 (p) REVERT: D 1658 THR cc_start: 0.8818 (p) cc_final: 0.8476 (t) REVERT: D 1675 LYS cc_start: 0.9184 (tttt) cc_final: 0.8746 (ptpt) REVERT: D 1900 PHE cc_start: 0.8684 (m-80) cc_final: 0.8470 (m-80) REVERT: D 1906 PHE cc_start: 0.9545 (m-80) cc_final: 0.9282 (m-80) REVERT: E 104 ARG cc_start: 0.9352 (mmm160) cc_final: 0.8871 (mpt180) REVERT: E 107 PHE cc_start: 0.9012 (m-10) cc_final: 0.8382 (m-10) outliers start: 3 outliers final: 0 residues processed: 345 average time/residue: 0.1239 time to fit residues: 64.6172 Evaluate side-chains 254 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 191 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 184 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 59 GLN B 121 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1389 ASN ** D1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1703 ASN ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.115223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.091328 restraints weight = 39124.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.093463 restraints weight = 22713.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094952 restraints weight = 15141.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095826 restraints weight = 11217.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096533 restraints weight = 9230.107| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16038 Z= 0.146 Angle : 0.681 12.233 21720 Z= 0.334 Chirality : 0.045 0.164 2405 Planarity : 0.004 0.053 2800 Dihedral : 6.720 84.992 2194 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.18 % Allowed : 1.66 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1943 helix: 0.55 (0.17), residues: 952 sheet: -0.69 (0.30), residues: 296 loop : -0.46 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D1898 TYR 0.027 0.002 TYR D1421 PHE 0.022 0.002 PHE E 34 TRP 0.034 0.002 TRP D1550 HIS 0.007 0.001 HIS D1664 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16038) covalent geometry : angle 0.68101 / 0.33 (21720) hydrogen bonds : bond 0.03830 / 2.63 ( 751) hydrogen bonds : angle 4.75967 / 3.31 ( 2121) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 351 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8432 (t0) cc_final: 0.7956 (t0) REVERT: A 154 ASP cc_start: 0.7129 (t70) cc_final: 0.6689 (t70) REVERT: A 270 GLU cc_start: 0.6524 (mm-30) cc_final: 0.6178 (mm-30) REVERT: A 314 GLN cc_start: 0.9268 (pp30) cc_final: 0.8888 (pp30) REVERT: B 82 MET cc_start: 0.8156 (tpt) cc_final: 0.7842 (tpt) REVERT: B 95 ARG cc_start: 0.7489 (mtt180) cc_final: 0.6593 (tpm170) REVERT: B 214 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7872 (tm-30) REVERT: B 279 TYR cc_start: 0.8308 (t80) cc_final: 0.7999 (t80) REVERT: B 290 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7724 (mtt90) REVERT: B 314 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7773 (tm-30) REVERT: C 34 ILE cc_start: 0.8830 (mt) cc_final: 0.8603 (tp) REVERT: C 88 HIS cc_start: 0.8161 (t-170) cc_final: 0.7732 (t-170) REVERT: C 280 ASN cc_start: 0.8349 (m-40) cc_final: 0.8070 (t0) REVERT: C 299 MET cc_start: 0.8358 (mmm) cc_final: 0.8074 (mmm) REVERT: D 1343 ASN cc_start: 0.8297 (m-40) cc_final: 0.7984 (m110) REVERT: D 1349 ASN cc_start: 0.8434 (t0) cc_final: 0.7955 (t0) REVERT: D 1397 TYR cc_start: 0.8368 (m-80) cc_final: 0.7948 (m-80) REVERT: D 1572 ASP cc_start: 0.7535 (t0) cc_final: 0.7204 (t0) REVERT: D 1651 PHE cc_start: 0.7129 (t80) cc_final: 0.6868 (t80) REVERT: D 1658 THR cc_start: 0.8767 (p) cc_final: 0.8449 (t) REVERT: D 1675 LYS cc_start: 0.9195 (tttt) cc_final: 0.8696 (ptpt) REVERT: D 1769 MET cc_start: 0.8086 (mmp) cc_final: 0.7849 (mmp) REVERT: D 1900 PHE cc_start: 0.8612 (m-80) cc_final: 0.8409 (m-80) REVERT: D 1906 PHE cc_start: 0.9545 (m-80) cc_final: 0.9278 (m-80) REVERT: E 104 ARG cc_start: 0.9361 (mmm160) cc_final: 0.8891 (mmm160) REVERT: E 107 PHE cc_start: 0.9021 (m-10) cc_final: 0.8449 (m-10) outliers start: 3 outliers final: 0 residues processed: 353 average time/residue: 0.1178 time to fit residues: 64.0543 Evaluate side-chains 258 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 50 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 138 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 26 optimal weight: 0.0670 chunk 118 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 128 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1389 ASN ** D1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1703 ASN ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.113956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.090409 restraints weight = 39569.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092447 restraints weight = 23100.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.093839 restraints weight = 15622.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094719 restraints weight = 11785.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095405 restraints weight = 9700.592| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16038 Z= 0.170 Angle : 0.698 7.845 21720 Z= 0.346 Chirality : 0.046 0.156 2405 Planarity : 0.005 0.051 2800 Dihedral : 6.715 83.200 2194 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.24 % Allowed : 1.30 % Favored : 98.46 % 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: -0.12 (0.20), residues: 1943 helix: 0.60 (0.17), residues: 932 sheet: -0.76 (0.30), residues: 296 loop : -0.51 (0.26), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 161 TYR 0.027 0.002 TYR E 122 PHE 0.027 0.002 PHE E 110 TRP 0.014 0.002 TRP C 340 HIS 0.007 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (16038) covalent geometry : angle 0.69804 / 0.35 (21720) hydrogen bonds : bond 0.04031 / 2.82 ( 751) hydrogen bonds : angle 4.78484 / 3.34 ( 2121) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 336 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7656 (tt0) REVERT: A 78 ASN cc_start: 0.8439 (t0) cc_final: 0.7860 (t0) REVERT: A 132 MET cc_start: 0.8279 (ppp) cc_final: 0.7875 (ppp) REVERT: A 314 GLN cc_start: 0.9227 (pp30) cc_final: 0.8944 (pp30) REVERT: B 95 ARG cc_start: 0.7688 (mtt180) cc_final: 0.6622 (tpm170) REVERT: B 214 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7962 (tm-30) REVERT: B 290 ARG cc_start: 0.8065 (mtt180) cc_final: 0.7729 (mtt90) REVERT: B 314 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7787 (tm-30) REVERT: C 34 ILE cc_start: 0.8937 (mt) cc_final: 0.8711 (tp) REVERT: C 88 HIS cc_start: 0.8151 (t-170) cc_final: 0.7834 (t-170) REVERT: C 183 ARG cc_start: 0.8002 (tpp80) cc_final: 0.7548 (ttm-80) REVERT: C 280 ASN cc_start: 0.8338 (m-40) cc_final: 0.8034 (t0) REVERT: C 299 MET cc_start: 0.8294 (mmm) cc_final: 0.8024 (mmm) REVERT: D 1343 ASN cc_start: 0.8274 (m-40) cc_final: 0.7892 (m110) REVERT: D 1349 ASN cc_start: 0.8564 (t0) cc_final: 0.8031 (t0) REVERT: D 1397 TYR cc_start: 0.8423 (m-80) cc_final: 0.7979 (m-80) REVERT: D 1572 ASP cc_start: 0.7568 (t0) cc_final: 0.7257 (t0) REVERT: D 1658 THR cc_start: 0.8754 (p) cc_final: 0.8447 (t) REVERT: D 1675 LYS cc_start: 0.9175 (tttt) cc_final: 0.8709 (ptpt) REVERT: D 1769 MET cc_start: 0.8086 (mmp) cc_final: 0.7854 (mmp) REVERT: D 1900 PHE cc_start: 0.8617 (m-80) cc_final: 0.8376 (m-80) REVERT: D 1906 PHE cc_start: 0.9555 (m-80) cc_final: 0.9290 (m-80) REVERT: E 104 ARG cc_start: 0.9356 (mmm160) cc_final: 0.8910 (mmm160) REVERT: E 107 PHE cc_start: 0.8976 (m-10) cc_final: 0.8493 (m-80) outliers start: 4 outliers final: 0 residues processed: 339 average time/residue: 0.1082 time to fit residues: 55.8232 Evaluate side-chains 255 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 165 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 181 optimal weight: 50.0000 chunk 75 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 130 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 128 ASN B 12 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1291 GLN D1389 ASN ** D1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.115065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.091150 restraints weight = 39549.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.093271 restraints weight = 22863.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094709 restraints weight = 15364.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095703 restraints weight = 11512.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096363 restraints weight = 9394.616| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16038 Z= 0.139 Angle : 0.685 7.713 21720 Z= 0.337 Chirality : 0.045 0.166 2405 Planarity : 0.004 0.090 2800 Dihedral : 6.586 77.609 2194 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.30 % Allowed : 0.89 % Favored : 98.81 % 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: -0.03 (0.20), residues: 1943 helix: 0.69 (0.17), residues: 931 sheet: -0.70 (0.30), residues: 298 loop : -0.49 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 161 TYR 0.020 0.001 TYR D1421 PHE 0.020 0.002 PHE D1548 TRP 0.015 0.002 TRP C 340 HIS 0.006 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16038) covalent geometry : angle 0.68519 / 0.34 (21720) hydrogen bonds : bond 0.03772 / 2.61 ( 751) hydrogen bonds : angle 4.74287 / 3.31 ( 2121) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 337 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7677 (tt0) REVERT: A 78 ASN cc_start: 0.8398 (t0) cc_final: 0.7858 (t0) REVERT: A 132 MET cc_start: 0.8206 (ppp) cc_final: 0.7912 (ppp) REVERT: A 202 THR cc_start: 0.9217 (m) cc_final: 0.8956 (p) REVERT: A 314 GLN cc_start: 0.9253 (pp30) cc_final: 0.8859 (pp30) REVERT: B 95 ARG cc_start: 0.7577 (mtt180) cc_final: 0.6527 (tpm170) REVERT: B 214 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7878 (tm-30) REVERT: B 290 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7737 (mtt90) REVERT: B 314 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7718 (tm-30) REVERT: C 88 HIS cc_start: 0.8161 (t-170) cc_final: 0.7686 (t-170) REVERT: C 183 ARG cc_start: 0.7942 (tpp80) cc_final: 0.7524 (ttm-80) REVERT: C 280 ASN cc_start: 0.8293 (m-40) cc_final: 0.7995 (t0) REVERT: D 1349 ASN cc_start: 0.8576 (t0) cc_final: 0.8071 (t0) REVERT: D 1397 TYR cc_start: 0.8362 (m-80) cc_final: 0.7967 (m-80) REVERT: D 1658 THR cc_start: 0.8717 (p) cc_final: 0.8402 (t) REVERT: D 1675 LYS cc_start: 0.9165 (tttt) cc_final: 0.8723 (tttp) REVERT: D 1769 MET cc_start: 0.8013 (mmp) cc_final: 0.7784 (mmp) REVERT: D 1792 GLU cc_start: 0.7935 (mp0) cc_final: 0.7700 (mp0) REVERT: D 1900 PHE cc_start: 0.8586 (m-80) cc_final: 0.8354 (m-80) REVERT: D 1906 PHE cc_start: 0.9574 (m-80) cc_final: 0.9296 (m-80) REVERT: E 40 MET cc_start: 0.5855 (tpt) cc_final: 0.5625 (tpt) REVERT: E 103 ILE cc_start: 0.9131 (mt) cc_final: 0.7960 (mt) REVERT: E 104 ARG cc_start: 0.9425 (mmm160) cc_final: 0.9024 (mmm160) REVERT: E 107 PHE cc_start: 0.8952 (m-10) cc_final: 0.8524 (m-80) outliers start: 5 outliers final: 0 residues processed: 341 average time/residue: 0.1083 time to fit residues: 56.7802 Evaluate side-chains 261 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 150 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 176 optimal weight: 0.2980 chunk 118 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 0.0170 chunk 37 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 128 ASN B 121 GLN D1389 ASN ** D1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1597 GLN ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.116130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.092287 restraints weight = 39081.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.094454 restraints weight = 22588.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095901 restraints weight = 15039.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.096818 restraints weight = 11224.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097556 restraints weight = 9200.335| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16038 Z= 0.128 Angle : 0.683 8.423 21720 Z= 0.334 Chirality : 0.045 0.165 2405 Planarity : 0.004 0.085 2800 Dihedral : 6.473 75.799 2194 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.24 % Allowed : 0.18 % Favored : 99.58 % 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: -0.04 (0.20), residues: 1943 helix: 0.66 (0.17), residues: 928 sheet: -0.72 (0.30), residues: 298 loop : -0.45 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 161 TYR 0.023 0.001 TYR E 122 PHE 0.023 0.001 PHE A 352 TRP 0.017 0.002 TRP C 340 HIS 0.006 0.001 HIS D1730 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (16038) covalent geometry : angle 0.68297 / 0.33 (21720) hydrogen bonds : bond 0.03654 / 2.51 ( 751) hydrogen bonds : angle 4.70960 / 3.29 ( 2121) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 341 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7659 (tt0) REVERT: A 78 ASN cc_start: 0.8393 (t0) cc_final: 0.7834 (t0) REVERT: A 132 MET cc_start: 0.8194 (ppp) cc_final: 0.7834 (ppp) REVERT: A 202 THR cc_start: 0.9231 (m) cc_final: 0.8952 (p) REVERT: A 314 GLN cc_start: 0.9204 (pp30) cc_final: 0.8857 (pp30) REVERT: B 95 ARG cc_start: 0.7515 (mtt180) cc_final: 0.6476 (tpm170) REVERT: B 214 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7816 (tm-30) REVERT: B 290 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7695 (mtt90) REVERT: B 314 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 325 MET cc_start: 0.8074 (tpp) cc_final: 0.7725 (mmt) REVERT: C 82 MET cc_start: 0.8842 (tpt) cc_final: 0.8322 (tpt) REVERT: C 88 HIS cc_start: 0.8149 (t-170) cc_final: 0.7859 (t-170) REVERT: C 280 ASN cc_start: 0.8273 (m-40) cc_final: 0.8047 (t0) REVERT: C 355 MET cc_start: 0.8125 (mmm) cc_final: 0.7802 (mmp) REVERT: D 1349 ASN cc_start: 0.8615 (t0) cc_final: 0.8086 (t0) REVERT: D 1397 TYR cc_start: 0.8369 (m-80) cc_final: 0.7930 (m-80) REVERT: D 1594 GLU cc_start: 0.8293 (tp30) cc_final: 0.7994 (tp30) REVERT: D 1658 THR cc_start: 0.8703 (p) cc_final: 0.8375 (t) REVERT: D 1675 LYS cc_start: 0.9138 (tttt) cc_final: 0.8693 (tttp) REVERT: D 1769 MET cc_start: 0.7997 (mmp) cc_final: 0.7758 (mmp) REVERT: D 1900 PHE cc_start: 0.8604 (m-80) cc_final: 0.8379 (m-80) REVERT: D 1906 PHE cc_start: 0.9592 (m-80) cc_final: 0.9315 (m-80) REVERT: E 103 ILE cc_start: 0.9158 (mt) cc_final: 0.7942 (mt) REVERT: E 104 ARG cc_start: 0.9436 (mmm160) cc_final: 0.9018 (mmm160) REVERT: E 107 PHE cc_start: 0.8978 (m-10) cc_final: 0.8546 (m-80) REVERT: E 124 ARG cc_start: 0.9292 (mpt-90) cc_final: 0.8757 (mtt-85) outliers start: 4 outliers final: 0 residues processed: 343 average time/residue: 0.1075 time to fit residues: 56.5464 Evaluate side-chains 261 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 56 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 180 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 86 optimal weight: 0.0670 chunk 40 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 128 ASN B 121 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1389 ASN ** D1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.116024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.092471 restraints weight = 38891.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094525 restraints weight = 23012.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.095926 restraints weight = 15568.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.096775 restraints weight = 11767.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.097469 restraints weight = 9738.224| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16038 Z= 0.131 Angle : 0.680 8.389 21720 Z= 0.332 Chirality : 0.045 0.158 2405 Planarity : 0.004 0.079 2800 Dihedral : 6.372 72.748 2194 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.18 % Allowed : 0.30 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1943 helix: 0.49 (0.17), residues: 967 sheet: -0.74 (0.30), residues: 298 loop : -0.54 (0.26), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 183 TYR 0.018 0.001 TYR D1421 PHE 0.025 0.002 PHE A 352 TRP 0.017 0.002 TRP C 340 HIS 0.007 0.001 HIS D1274 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (16038) covalent geometry : angle 0.68044 / 0.33 (21720) hydrogen bonds : bond 0.03609 / 2.47 ( 751) hydrogen bonds : angle 4.69329 / 3.27 ( 2121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2805.43 seconds wall clock time: 49 minutes 24.39 seconds (2964.39 seconds total)