Starting phenix.real_space_refine on Thu Sep 18 10:36:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7udu_26460/09_2025/7udu_26460.cif Found real_map, /net/cci-nas-00/data/ceres_data/7udu_26460/09_2025/7udu_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_26460/09_2025/7udu_26460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7udu_26460/09_2025/7udu_26460.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7udu_26460/09_2025/7udu_26460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7udu_26460/09_2025/7udu_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-2.0-5805/lib/python3.9/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: 3.90, per 1000 atoms: 0.25 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: 1.17 Conformation dependent library (CDL) restraints added in 718.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.65 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: 3.31 Time building geometry restraints manager: 1.62 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: 12.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.050 Find NCS groups from input model: 0.180 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 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 aren 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 covalent geometry : bond 0.00362 (16038) covalent geometry : angle 0.67406 (21720) hydrogen bonds : bond 0.17244 ( 751) hydrogen bonds : angle 6.76509 ( 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 : 0.687 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: 0.7715 (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: 0.8600 (pt0) REVERT: A 217 CYS cc_start: 0.8171 (m) cc_final: 0.7694 (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: 0.7852 (m110) REVERT: B 119 MET cc_start: 0.7695 (ttm) cc_final: 0.7357 (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: 0.5349 (mtt90) REVERT: B 299 MET cc_start: 0.7912 (mmm) cc_final: 0.7537 (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: 0.6959 (m-30) REVERT: C 80 ASP cc_start: 0.8755 (m-30) cc_final: 0.8523 (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: 0.5711 (t60) REVERT: C 355 MET cc_start: 0.7536 (mtt) cc_final: 0.7113 (mmp) REVERT: C 370 VAL cc_start: 0.7962 (p) cc_final: 0.7607 (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: 0.8743 (mmm160) REVERT: E 107 PHE cc_start: 0.9215 (m-10) cc_final: 0.8937 (m-10) 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: 0.1464 time to fit residues: 134.1678 Evaluate side-chains 374 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3713 r_free = 0.3713 target = 0.120652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.095859 restraints weight = 38906.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098230 restraints weight = 22231.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.099810 restraints weight = 14663.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.100764 restraints weight = 10880.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101567 restraints weight = 8937.491| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16038 Z= 0.150 Angle : 0.665 9.982 21720 Z= 0.330 Chirality : 0.045 0.183 2405 Planarity : 0.004 0.041 2800 Dihedral : 7.004 104.648 2194 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.12 % Allowed : 4.51 % Favored : 95.37 % 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 aren not related in a simple way. whole: -0.18 (0.20), residues: 1943 helix: 0.75 (0.18), residues: 915 sheet: -1.06 (0.29), residues: 294 loop : -0.69 (0.25), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1812 TYR 0.017 0.002 TYR D1376 PHE 0.019 0.002 PHE E 38 TRP 0.019 0.002 TRP D1619 HIS 0.004 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00338 (16038) covalent geometry : angle 0.66517 (21720) hydrogen bonds : bond 0.04413 ( 751) hydrogen bonds : angle 5.18249 ( 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 431 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 429 time to evaluate : 0.659 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: 0.7926 (t0) cc_final: 0.7240 (t0) REVERT: A 142 LEU cc_start: 0.8873 (mt) cc_final: 0.8638 (mt) REVERT: A 154 ASP cc_start: 0.6773 (t70) cc_final: 0.6553 (t70) REVERT: A 283 MET cc_start: 0.7339 (mmt) cc_final: 0.7015 (mmt) REVERT: A 296 ASN cc_start: 0.6707 (m-40) cc_final: 0.6355 (m-40) REVERT: A 364 GLU cc_start: 0.8306 (pt0) cc_final: 0.7881 (pt0) REVERT: B 95 ARG cc_start: 0.7157 (mtt180) cc_final: 0.6784 (tpm170) REVERT: B 191 LYS cc_start: 0.8901 (ttmm) cc_final: 0.8658 (mmtt) REVERT: B 214 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7606 (tm-30) REVERT: B 279 TYR cc_start: 0.8075 (t80) cc_final: 0.7872 (t80) REVERT: B 290 ARG cc_start: 0.7781 (mtt180) cc_final: 0.7489 (mtt90) REVERT: B 314 GLN cc_start: 0.7645 (tm-30) cc_final: 0.7295 (tm-30) REVERT: C 137 GLN cc_start: 0.7577 (mp10) cc_final: 0.7183 (mp10) REVERT: C 140 LEU cc_start: 0.8104 (mm) cc_final: 0.7728 (mm) REVERT: C 198 TYR cc_start: 0.8797 (m-80) cc_final: 0.8083 (m-80) REVERT: D 1251 MET cc_start: 0.7810 (tpt) cc_final: 0.7595 (mmp) REVERT: D 1343 ASN cc_start: 0.7502 (m-40) cc_final: 0.7247 (m110) REVERT: D 1376 TYR cc_start: 0.8071 (m-80) cc_final: 0.7665 (m-80) REVERT: D 1397 TYR cc_start: 0.8233 (m-80) cc_final: 0.7924 (m-80) REVERT: D 1658 THR cc_start: 0.8847 (p) cc_final: 0.8385 (t) REVERT: D 1675 LYS cc_start: 0.9239 (tttt) cc_final: 0.8648 (ptpt) REVERT: D 1764 ASP cc_start: 0.8174 (t70) cc_final: 0.7497 (t0) REVERT: D 1870 LEU cc_start: 0.8466 (tp) cc_final: 0.8197 (tp) REVERT: D 1906 PHE cc_start: 0.9548 (m-80) cc_final: 0.9163 (m-80) REVERT: E 104 ARG cc_start: 0.9271 (mmm160) cc_final: 0.8758 (mpt180) REVERT: E 107 PHE cc_start: 0.8993 (m-10) cc_final: 0.8746 (m-10) outliers start: 2 outliers final: 0 residues processed: 431 average time/residue: 0.1295 time to fit residues: 83.7004 Evaluate side-chains 301 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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: 1.9990 chunk 184 optimal weight: 1.9990 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: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN D1389 ASN D1406 GLN D1703 ASN D1706 GLN ** 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 = 0.3622 r_free = 0.3622 target = 0.114138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088889 restraints weight = 40654.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091052 restraints weight = 23883.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092520 restraints weight = 16171.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.093534 restraints weight = 12248.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094192 restraints weight = 10044.289| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 16038 Z= 0.246 Angle : 0.764 8.433 21720 Z= 0.388 Chirality : 0.049 0.236 2405 Planarity : 0.005 0.058 2800 Dihedral : 7.155 101.926 2194 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.18 % Allowed : 5.10 % Favored : 94.72 % 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 aren not related in a simple way. whole: -0.41 (0.20), residues: 1943 helix: 0.32 (0.17), residues: 952 sheet: -0.76 (0.30), residues: 288 loop : -0.69 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1819 TYR 0.031 0.002 TYR C 294 PHE 0.025 0.002 PHE D1699 TRP 0.016 0.003 TRP B 86 HIS 0.012 0.002 HIS D1905 Details of bonding type rmsd covalent geometry : bond 0.00558 (16038) covalent geometry : angle 0.76410 (21720) hydrogen bonds : bond 0.04836 ( 751) hydrogen bonds : angle 5.08579 ( 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 381 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 378 time to evaluate : 0.637 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 44 MET cc_start: 0.8737 (mtt) cc_final: 0.8264 (mtt) REVERT: A 78 ASN cc_start: 0.8136 (t0) cc_final: 0.7734 (t0) REVERT: A 132 MET cc_start: 0.8290 (ppp) cc_final: 0.8058 (ppp) REVERT: A 154 ASP cc_start: 0.7184 (t70) cc_final: 0.6669 (t70) REVERT: A 269 MET cc_start: 0.7797 (mmm) cc_final: 0.7352 (mtp) REVERT: A 314 GLN cc_start: 0.9167 (pp30) cc_final: 0.8944 (pp30) REVERT: A 364 GLU cc_start: 0.8320 (pt0) cc_final: 0.8099 (pt0) REVERT: B 44 MET cc_start: 0.6445 (tpt) cc_final: 0.6223 (tpt) REVERT: B 95 ARG cc_start: 0.7340 (mtt180) cc_final: 0.6650 (tpm170) REVERT: B 214 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7962 (tm-30) REVERT: B 279 TYR cc_start: 0.8321 (t80) cc_final: 0.8059 (t80) REVERT: B 290 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7751 (mtt90) REVERT: C 88 HIS cc_start: 0.8426 (t70) cc_final: 0.8026 (t-90) REVERT: C 140 LEU cc_start: 0.8343 (mm) cc_final: 0.7969 (mm) REVERT: C 299 MET cc_start: 0.8417 (mmm) cc_final: 0.7987 (mmm) REVERT: C 313 MET cc_start: 0.8837 (ttp) cc_final: 0.8605 (ttp) REVERT: C 325 MET cc_start: 0.6205 (mpp) cc_final: 0.5977 (mmt) REVERT: D 1211 MET cc_start: 0.8260 (mpp) cc_final: 0.7976 (mpp) REVERT: D 1243 LEU cc_start: 0.9030 (tp) cc_final: 0.8651 (tt) REVERT: D 1251 MET cc_start: 0.7858 (tpt) cc_final: 0.7468 (mmp) REVERT: D 1343 ASN cc_start: 0.8162 (m-40) cc_final: 0.7825 (m110) REVERT: D 1349 ASN cc_start: 0.8366 (t0) cc_final: 0.7995 (t0) REVERT: D 1397 TYR cc_start: 0.8333 (m-80) cc_final: 0.6856 (m-80) REVERT: D 1408 ARG cc_start: 0.5534 (mmt180) cc_final: 0.3928 (mmm-85) REVERT: D 1428 CYS cc_start: 0.6979 (m) cc_final: 0.6363 (m) REVERT: D 1658 THR cc_start: 0.8874 (p) cc_final: 0.8473 (t) REVERT: D 1675 LYS cc_start: 0.9190 (tttt) cc_final: 0.8815 (ptpt) REVERT: D 1870 LEU cc_start: 0.8477 (tp) cc_final: 0.8244 (tp) REVERT: D 1906 PHE cc_start: 0.9607 (m-80) cc_final: 0.9266 (m-80) REVERT: E 104 ARG cc_start: 0.9326 (mmm160) cc_final: 0.8799 (mpt180) REVERT: E 107 PHE cc_start: 0.9046 (m-10) cc_final: 0.8374 (m-10) REVERT: E 122 TYR cc_start: 0.9331 (t80) cc_final: 0.9118 (t80) REVERT: E 124 ARG cc_start: 0.9223 (mpt-90) cc_final: 0.8911 (mmm-85) REVERT: E 139 VAL cc_start: 0.9620 (t) cc_final: 0.9356 (t) REVERT: E 143 TYR cc_start: 0.8239 (m-10) cc_final: 0.7801 (m-10) outliers start: 3 outliers final: 0 residues processed: 381 average time/residue: 0.1276 time to fit residues: 72.4856 Evaluate side-chains 266 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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: 4.9990 chunk 121 optimal weight: 0.0970 chunk 40 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 166 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 D1886 GLN ** 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 = 0.3678 r_free = 0.3678 target = 0.117759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092111 restraints weight = 39926.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.094407 restraints weight = 23084.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.095981 restraints weight = 15469.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.097080 restraints weight = 11633.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.097686 restraints weight = 9447.224| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4482 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= 0.125 Angle : 0.646 7.336 21720 Z= 0.319 Chirality : 0.044 0.200 2405 Planarity : 0.004 0.071 2800 Dihedral : 6.844 94.110 2194 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % 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 aren not related in a simple way. whole: -0.12 (0.20), residues: 1943 helix: 0.55 (0.17), residues: 941 sheet: -0.62 (0.30), residues: 296 loop : -0.52 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 124 TYR 0.019 0.001 TYR C 69 PHE 0.021 0.001 PHE E 34 TRP 0.014 0.001 TRP A 340 HIS 0.014 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00280 (16038) covalent geometry : angle 0.64604 (21720) hydrogen bonds : bond 0.03719 ( 751) hydrogen bonds : angle 4.74789 ( 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 378 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 375 time to evaluate : 0.611 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: A 78 ASN cc_start: 0.8322 (t0) cc_final: 0.7631 (t0) REVERT: A 132 MET cc_start: 0.8157 (ppp) cc_final: 0.7909 (ppp) REVERT: A 154 ASP cc_start: 0.7042 (t70) cc_final: 0.6525 (t70) REVERT: A 166 TYR cc_start: 0.7801 (t80) cc_final: 0.7408 (t80) REVERT: A 269 MET cc_start: 0.7748 (mmm) cc_final: 0.7233 (mtp) REVERT: A 270 GLU cc_start: 0.6218 (mm-30) cc_final: 0.5535 (mm-30) REVERT: A 285 CYS cc_start: 0.7836 (p) cc_final: 0.7357 (p) REVERT: A 314 GLN cc_start: 0.9223 (pp30) cc_final: 0.8894 (pp30) REVERT: B 44 MET cc_start: 0.6373 (tpt) cc_final: 0.6134 (tpt) REVERT: B 95 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6579 (tpm170) REVERT: B 196 ARG cc_start: 0.7245 (mtt180) cc_final: 0.6803 (mtt90) REVERT: B 214 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7804 (tm-30) REVERT: B 279 TYR cc_start: 0.8238 (t80) cc_final: 0.7934 (t80) REVERT: B 290 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7382 (mtt90) REVERT: B 314 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7501 (tm-30) REVERT: C 11 ASP cc_start: 0.7865 (t0) cc_final: 0.7459 (m-30) REVERT: C 69 TYR cc_start: 0.8536 (m-80) cc_final: 0.8305 (m-10) REVERT: C 88 HIS cc_start: 0.8458 (t70) cc_final: 0.8103 (t70) REVERT: C 140 LEU cc_start: 0.8022 (mm) cc_final: 0.7585 (mm) REVERT: C 198 TYR cc_start: 0.8921 (m-80) cc_final: 0.8392 (m-80) REVERT: C 280 ASN cc_start: 0.8349 (m-40) cc_final: 0.7966 (t0) REVERT: C 299 MET cc_start: 0.8286 (mmm) cc_final: 0.7981 (mmm) REVERT: D 1211 MET cc_start: 0.8235 (mpp) cc_final: 0.7966 (mpp) REVERT: D 1343 ASN cc_start: 0.8129 (m-40) cc_final: 0.7819 (m110) REVERT: D 1349 ASN cc_start: 0.8122 (t0) cc_final: 0.7764 (t0) REVERT: D 1376 TYR cc_start: 0.8079 (m-80) cc_final: 0.7796 (m-80) REVERT: D 1397 TYR cc_start: 0.8234 (m-80) cc_final: 0.6796 (m-80) REVERT: D 1408 ARG cc_start: 0.5484 (mmt180) cc_final: 0.3985 (mmm-85) REVERT: D 1428 CYS cc_start: 0.6816 (m) cc_final: 0.6377 (m) REVERT: D 1572 ASP cc_start: 0.7084 (t0) cc_final: 0.6772 (t0) REVERT: D 1658 THR cc_start: 0.8821 (p) cc_final: 0.8448 (t) REVERT: D 1675 LYS cc_start: 0.9256 (tttt) cc_final: 0.8744 (ptpt) REVERT: D 1870 LEU cc_start: 0.8525 (tp) cc_final: 0.8226 (tp) REVERT: D 1906 PHE cc_start: 0.9574 (m-80) cc_final: 0.9230 (m-80) REVERT: E 93 LYS cc_start: 0.8810 (tppt) cc_final: 0.8578 (mmmm) REVERT: E 101 ASP cc_start: 0.9271 (m-30) cc_final: 0.9011 (p0) REVERT: E 104 ARG cc_start: 0.9359 (mmm160) cc_final: 0.8948 (mmm160) REVERT: E 107 PHE cc_start: 0.9012 (m-10) cc_final: 0.8647 (m-10) outliers start: 3 outliers final: 0 residues processed: 378 average time/residue: 0.1263 time to fit residues: 71.1539 Evaluate side-chains 266 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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: 3.9990 chunk 177 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 158 optimal weight: 0.0040 chunk 130 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1389 ASN D1666 HIS D1905 HIS ** 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 = 0.3670 r_free = 0.3670 target = 0.117006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.091466 restraints weight = 40016.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.093754 restraints weight = 23166.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095330 restraints weight = 15486.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096419 restraints weight = 11586.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097023 restraints weight = 9395.384| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4784 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= 0.135 Angle : 0.657 10.963 21720 Z= 0.322 Chirality : 0.045 0.200 2405 Planarity : 0.004 0.060 2800 Dihedral : 6.619 91.032 2194 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.24 % Allowed : 2.19 % Favored : 97.57 % 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 aren not related in a simple way. whole: -0.08 (0.20), residues: 1943 helix: 0.51 (0.17), residues: 944 sheet: -0.52 (0.30), residues: 294 loop : -0.42 (0.26), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 161 TYR 0.019 0.001 TYR C 279 PHE 0.023 0.001 PHE D1901 TRP 0.013 0.001 TRP A 340 HIS 0.013 0.001 HIS D1905 Details of bonding type rmsd covalent geometry : bond 0.00308 (16038) covalent geometry : angle 0.65692 (21720) hydrogen bonds : bond 0.03635 ( 751) hydrogen bonds : angle 4.68060 ( 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 355 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 351 time to evaluate : 0.816 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: 0.8339 (t0) cc_final: 0.8127 (t0) REVERT: A 132 MET cc_start: 0.8098 (ppp) cc_final: 0.7797 (ppp) REVERT: A 154 ASP cc_start: 0.6994 (t70) cc_final: 0.6460 (t70) REVERT: A 166 TYR cc_start: 0.7837 (t80) cc_final: 0.7441 (t80) REVERT: A 246 GLN cc_start: 0.7936 (mt0) cc_final: 0.7722 (mt0) REVERT: A 269 MET cc_start: 0.7742 (mmm) cc_final: 0.7460 (mtp) REVERT: A 314 GLN cc_start: 0.9222 (pp30) cc_final: 0.8955 (pp30) REVERT: B 44 MET cc_start: 0.6356 (tpt) cc_final: 0.6072 (tpt) REVERT: B 95 ARG cc_start: 0.7399 (mtt180) cc_final: 0.6551 (tpm170) REVERT: B 214 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7818 (tm-30) REVERT: B 290 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7520 (mtt90) REVERT: B 314 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7456 (tm-30) REVERT: C 11 ASP cc_start: 0.7801 (t0) cc_final: 0.7422 (m-30) REVERT: C 72 GLU cc_start: 0.8172 (tp30) cc_final: 0.7510 (mm-30) REVERT: C 77 THR cc_start: 0.8232 (m) cc_final: 0.7819 (t) REVERT: C 140 LEU cc_start: 0.8127 (mm) cc_final: 0.7770 (mm) REVERT: C 198 TYR cc_start: 0.8929 (m-80) cc_final: 0.8429 (m-80) REVERT: C 280 ASN cc_start: 0.8368 (m-40) cc_final: 0.8010 (t0) REVERT: C 299 MET cc_start: 0.8278 (mmm) cc_final: 0.7887 (mmm) REVERT: D 1343 ASN cc_start: 0.8161 (m-40) cc_final: 0.7791 (m110) REVERT: D 1349 ASN cc_start: 0.8236 (t0) cc_final: 0.7849 (t0) REVERT: D 1376 TYR cc_start: 0.8037 (m-80) cc_final: 0.7781 (m-80) REVERT: D 1397 TYR cc_start: 0.8284 (m-80) cc_final: 0.6824 (m-80) REVERT: D 1428 CYS cc_start: 0.6881 (m) cc_final: 0.6309 (m) REVERT: D 1658 THR cc_start: 0.8831 (p) cc_final: 0.8433 (t) REVERT: D 1675 LYS cc_start: 0.9236 (tttt) cc_final: 0.8732 (ptpt) REVERT: D 1870 LEU cc_start: 0.8545 (tp) cc_final: 0.8250 (tp) REVERT: D 1900 PHE cc_start: 0.8831 (m-10) cc_final: 0.8585 (m-80) REVERT: D 1906 PHE cc_start: 0.9563 (m-80) cc_final: 0.9259 (m-80) REVERT: E 101 ASP cc_start: 0.9259 (m-30) cc_final: 0.9000 (p0) REVERT: E 104 ARG cc_start: 0.9435 (mmm160) cc_final: 0.9051 (mmm160) REVERT: E 107 PHE cc_start: 0.9025 (m-10) cc_final: 0.8661 (m-10) outliers start: 4 outliers final: 0 residues processed: 354 average time/residue: 0.1228 time to fit residues: 66.1890 Evaluate side-chains 277 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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: 0.5980 chunk 19 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 111 ASN A 128 ASN B 371 HIS ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1262 GLN D1389 ASN D1703 ASN ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.115881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090596 restraints weight = 39785.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.092842 restraints weight = 22833.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094373 restraints weight = 15219.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095402 restraints weight = 11345.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096102 restraints weight = 9263.212| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16038 Z= 0.147 Angle : 0.668 11.835 21720 Z= 0.328 Chirality : 0.045 0.203 2405 Planarity : 0.004 0.055 2800 Dihedral : 6.510 87.777 2194 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.24 % Allowed : 1.54 % Favored : 98.22 % 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 aren not related in a simple way. whole: -0.13 (0.20), residues: 1943 helix: 0.45 (0.17), residues: 958 sheet: -0.53 (0.30), residues: 294 loop : -0.43 (0.26), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 183 TYR 0.018 0.001 TYR D1236 PHE 0.029 0.002 PHE E 110 TRP 0.012 0.001 TRP A 340 HIS 0.008 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00339 (16038) covalent geometry : angle 0.66846 (21720) hydrogen bonds : bond 0.03691 ( 751) hydrogen bonds : angle 4.67704 ( 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 357 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 353 time to evaluate : 0.573 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: A 78 ASN cc_start: 0.8387 (t0) cc_final: 0.7840 (t0) REVERT: A 314 GLN cc_start: 0.9263 (pp30) cc_final: 0.8920 (pp30) REVERT: A 364 GLU cc_start: 0.8369 (pt0) cc_final: 0.7504 (pt0) REVERT: B 44 MET cc_start: 0.6197 (tpt) cc_final: 0.5964 (tpt) REVERT: B 82 MET cc_start: 0.8126 (tpt) cc_final: 0.7835 (tpt) REVERT: B 95 ARG cc_start: 0.7407 (mtt180) cc_final: 0.6548 (tpm170) REVERT: B 196 ARG cc_start: 0.7229 (mtt180) cc_final: 0.6995 (mtt90) REVERT: B 214 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7854 (tm-30) REVERT: B 279 TYR cc_start: 0.8229 (t80) cc_final: 0.8007 (t80) REVERT: B 290 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7564 (mtt90) REVERT: B 314 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7471 (tm-30) REVERT: C 11 ASP cc_start: 0.7886 (t0) cc_final: 0.7388 (m-30) REVERT: C 72 GLU cc_start: 0.7973 (tp30) cc_final: 0.7535 (mm-30) REVERT: C 198 TYR cc_start: 0.8902 (m-80) cc_final: 0.8288 (m-80) REVERT: C 280 ASN cc_start: 0.8387 (m-40) cc_final: 0.8038 (t0) REVERT: C 346 LEU cc_start: 0.9353 (tt) cc_final: 0.9151 (tt) REVERT: D 1343 ASN cc_start: 0.8222 (m-40) cc_final: 0.7864 (m110) REVERT: D 1349 ASN cc_start: 0.8330 (t0) cc_final: 0.7883 (t0) REVERT: D 1376 TYR cc_start: 0.8142 (m-80) cc_final: 0.7855 (m-80) REVERT: D 1397 TYR cc_start: 0.8259 (m-80) cc_final: 0.6864 (m-80) REVERT: D 1408 ARG cc_start: 0.5571 (mmt180) cc_final: 0.3931 (mmm-85) REVERT: D 1428 CYS cc_start: 0.6897 (m) cc_final: 0.6458 (m) REVERT: D 1565 THR cc_start: 0.6782 (p) cc_final: 0.6520 (p) REVERT: D 1658 THR cc_start: 0.8789 (p) cc_final: 0.8438 (t) REVERT: D 1675 LYS cc_start: 0.9223 (tttt) cc_final: 0.8665 (ptpt) REVERT: D 1769 MET cc_start: 0.8046 (mmp) cc_final: 0.7793 (mmp) REVERT: D 1870 LEU cc_start: 0.8514 (tp) cc_final: 0.8197 (tp) REVERT: D 1906 PHE cc_start: 0.9567 (m-80) cc_final: 0.9270 (m-80) REVERT: E 104 ARG cc_start: 0.9443 (mmm160) cc_final: 0.9036 (mmm160) REVERT: E 107 PHE cc_start: 0.9024 (m-10) cc_final: 0.8529 (m-10) outliers start: 4 outliers final: 0 residues processed: 356 average time/residue: 0.1325 time to fit residues: 71.1290 Evaluate side-chains 263 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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: 3.9990 chunk 40 optimal weight: 0.7980 chunk 184 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN A 128 ASN C 371 HIS D1389 ASN D1703 ASN ** 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 = 0.3650 r_free = 0.3650 target = 0.115722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090625 restraints weight = 39577.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092803 restraints weight = 22960.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.094266 restraints weight = 15403.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.095261 restraints weight = 11626.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095854 restraints weight = 9538.600| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5175 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= 0.140 Angle : 0.663 8.934 21720 Z= 0.324 Chirality : 0.045 0.175 2405 Planarity : 0.004 0.050 2800 Dihedral : 6.404 83.081 2194 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.30 % Allowed : 1.25 % 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 aren not related in a simple way. whole: -0.05 (0.20), residues: 1943 helix: 0.55 (0.17), residues: 953 sheet: -0.59 (0.31), residues: 293 loop : -0.40 (0.26), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D1898 TYR 0.017 0.001 TYR D1421 PHE 0.033 0.002 PHE D1900 TRP 0.011 0.001 TRP A 340 HIS 0.008 0.001 HIS D1730 Details of bonding type rmsd covalent geometry : bond 0.00320 (16038) covalent geometry : angle 0.66313 (21720) hydrogen bonds : bond 0.03639 ( 751) hydrogen bonds : angle 4.66660 ( 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 350 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 345 time to evaluate : 0.478 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: A 78 ASN cc_start: 0.8357 (t0) cc_final: 0.7802 (t0) REVERT: A 132 MET cc_start: 0.8262 (ppp) cc_final: 0.7851 (ppp) REVERT: A 202 THR cc_start: 0.9208 (m) cc_final: 0.8965 (p) REVERT: A 314 GLN cc_start: 0.9274 (pp30) cc_final: 0.8906 (pp30) REVERT: B 44 MET cc_start: 0.6196 (tpt) cc_final: 0.5973 (tpt) REVERT: B 95 ARG cc_start: 0.7469 (mtt180) cc_final: 0.6598 (tpm170) REVERT: B 214 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7830 (tm-30) REVERT: B 290 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7639 (mtt90) REVERT: B 314 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 363 ASP cc_start: 0.8631 (m-30) cc_final: 0.8391 (m-30) REVERT: C 11 ASP cc_start: 0.7942 (t0) cc_final: 0.7317 (m-30) REVERT: C 12 ASN cc_start: 0.9175 (t0) cc_final: 0.8950 (t0) REVERT: C 190 MET cc_start: 0.8130 (ttp) cc_final: 0.7802 (ttm) REVERT: C 198 TYR cc_start: 0.8901 (m-80) cc_final: 0.8357 (m-80) REVERT: C 280 ASN cc_start: 0.8332 (m-40) cc_final: 0.8017 (t0) REVERT: D 1343 ASN cc_start: 0.8254 (m-40) cc_final: 0.7888 (m110) REVERT: D 1349 ASN cc_start: 0.8393 (t0) cc_final: 0.7920 (t0) REVERT: D 1376 TYR cc_start: 0.8108 (m-80) cc_final: 0.7883 (m-80) REVERT: D 1397 TYR cc_start: 0.8360 (m-80) cc_final: 0.7988 (m-80) REVERT: D 1408 ARG cc_start: 0.5595 (mmt180) cc_final: 0.3868 (mmm-85) REVERT: D 1658 THR cc_start: 0.8742 (p) cc_final: 0.8428 (t) REVERT: D 1675 LYS cc_start: 0.9193 (tttt) cc_final: 0.8650 (ptpt) REVERT: D 1769 MET cc_start: 0.8031 (mmp) cc_final: 0.7793 (mmp) REVERT: D 1870 LEU cc_start: 0.8467 (tp) cc_final: 0.8167 (tp) REVERT: D 1906 PHE cc_start: 0.9552 (m-80) cc_final: 0.9265 (m-80) REVERT: E 104 ARG cc_start: 0.9462 (mmm160) cc_final: 0.9125 (mmm160) REVERT: E 107 PHE cc_start: 0.9019 (m-10) cc_final: 0.8682 (m-10) outliers start: 5 outliers final: 0 residues processed: 348 average time/residue: 0.1076 time to fit residues: 56.5794 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 : 0.447 ------------------------------------------------------------------------------- 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: 3.9990 chunk 163 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 153 optimal weight: 0.4980 chunk 189 optimal weight: 0.7980 chunk 26 optimal weight: 0.0370 chunk 118 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 59 GLN A 128 ASN C 162 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1274 HIS D1389 ASN D1703 ASN ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.116005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090556 restraints weight = 39847.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.092844 restraints weight = 22724.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.094376 restraints weight = 15167.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095442 restraints weight = 11313.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096067 restraints weight = 9212.055| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5339 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= 0.129 Angle : 0.663 7.694 21720 Z= 0.323 Chirality : 0.044 0.163 2405 Planarity : 0.004 0.049 2800 Dihedral : 6.301 79.465 2194 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.18 % Allowed : 1.72 % Favored : 98.10 % 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 aren not related in a simple way. whole: -0.03 (0.20), residues: 1943 helix: 0.57 (0.17), residues: 953 sheet: -0.62 (0.31), residues: 295 loop : -0.37 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 161 TYR 0.018 0.001 TYR B 279 PHE 0.021 0.001 PHE D1548 TRP 0.015 0.001 TRP C 340 HIS 0.007 0.001 HIS D1730 Details of bonding type rmsd covalent geometry : bond 0.00297 (16038) covalent geometry : angle 0.66277 (21720) hydrogen bonds : bond 0.03498 ( 751) hydrogen bonds : angle 4.58743 ( 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 344 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 341 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: A 78 ASN cc_start: 0.8388 (t0) cc_final: 0.7812 (t0) REVERT: A 132 MET cc_start: 0.8253 (ppp) cc_final: 0.7915 (ppp) REVERT: A 202 THR cc_start: 0.9229 (m) cc_final: 0.8927 (p) REVERT: A 314 GLN cc_start: 0.9305 (pp30) cc_final: 0.8906 (pp30) REVERT: A 364 GLU cc_start: 0.8442 (pt0) cc_final: 0.7666 (pt0) REVERT: B 44 MET cc_start: 0.6212 (tpt) cc_final: 0.5942 (tpt) REVERT: B 95 ARG cc_start: 0.7578 (mtt180) cc_final: 0.6589 (tpm170) REVERT: B 214 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7823 (tm-30) REVERT: B 290 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7619 (mtt90) REVERT: B 314 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7304 (tm-30) REVERT: C 11 ASP cc_start: 0.7910 (t0) cc_final: 0.7371 (m-30) REVERT: C 72 GLU cc_start: 0.8060 (tp30) cc_final: 0.7515 (mm-30) REVERT: C 132 MET cc_start: 0.7890 (ppp) cc_final: 0.7647 (ppp) REVERT: C 140 LEU cc_start: 0.8195 (mm) cc_final: 0.7851 (mm) REVERT: C 190 MET cc_start: 0.8094 (ttp) cc_final: 0.7819 (ttm) REVERT: C 198 TYR cc_start: 0.8886 (m-80) cc_final: 0.8344 (m-80) REVERT: C 280 ASN cc_start: 0.8352 (m-40) cc_final: 0.8091 (t0) REVERT: D 1343 ASN cc_start: 0.8192 (m-40) cc_final: 0.7802 (m110) REVERT: D 1349 ASN cc_start: 0.8479 (t0) cc_final: 0.7956 (t0) REVERT: D 1376 TYR cc_start: 0.8121 (m-80) cc_final: 0.7916 (m-80) REVERT: D 1397 TYR cc_start: 0.8368 (m-80) cc_final: 0.8080 (m-80) REVERT: D 1658 THR cc_start: 0.8744 (p) cc_final: 0.8442 (t) REVERT: D 1675 LYS cc_start: 0.9181 (tttt) cc_final: 0.8676 (ptpt) REVERT: D 1769 MET cc_start: 0.8095 (mmp) cc_final: 0.7862 (mmp) REVERT: D 1792 GLU cc_start: 0.7974 (mp0) cc_final: 0.7730 (mp0) REVERT: D 1870 LEU cc_start: 0.8486 (tp) cc_final: 0.8171 (tp) REVERT: D 1906 PHE cc_start: 0.9600 (m-80) cc_final: 0.9307 (m-80) REVERT: E 40 MET cc_start: 0.5844 (tpt) cc_final: 0.5632 (tpt) REVERT: E 104 ARG cc_start: 0.9452 (mmm160) cc_final: 0.9083 (mmm160) REVERT: E 107 PHE cc_start: 0.9031 (m-10) cc_final: 0.8586 (m-10) REVERT: E 124 ARG cc_start: 0.9299 (mpt-90) cc_final: 0.8894 (mmm-85) REVERT: E 139 VAL cc_start: 0.9597 (t) cc_final: 0.9350 (t) REVERT: E 143 TYR cc_start: 0.8232 (m-10) cc_final: 0.7621 (m-80) outliers start: 3 outliers final: 0 residues processed: 343 average time/residue: 0.1241 time to fit residues: 64.3560 Evaluate side-chains 262 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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: 1.9990 chunk 71 optimal weight: 0.9990 chunk 181 optimal weight: 30.0000 chunk 75 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 19 optimal weight: 0.0060 chunk 48 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 59 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1291 GLN D1389 ASN 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 = 0.3655 r_free = 0.3655 target = 0.115967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090763 restraints weight = 39764.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092954 restraints weight = 23076.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094437 restraints weight = 15493.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.095459 restraints weight = 11687.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096029 restraints weight = 9556.704| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16038 Z= 0.131 Angle : 0.666 7.609 21720 Z= 0.326 Chirality : 0.044 0.163 2405 Planarity : 0.004 0.049 2800 Dihedral : 6.242 76.982 2194 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.18 % Allowed : 0.47 % Favored : 99.35 % 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 aren not related in a simple way. whole: -0.00 (0.20), residues: 1943 helix: 0.59 (0.17), residues: 953 sheet: -0.62 (0.31), residues: 295 loop : -0.34 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 183 TYR 0.016 0.001 TYR C 279 PHE 0.025 0.001 PHE E 34 TRP 0.012 0.001 TRP A 340 HIS 0.007 0.001 HIS D1730 Details of bonding type rmsd covalent geometry : bond 0.00301 (16038) covalent geometry : angle 0.66587 (21720) hydrogen bonds : bond 0.03556 ( 751) hydrogen bonds : angle 4.69348 ( 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 344 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 341 time to evaluate : 0.673 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 78 ASN cc_start: 0.8338 (t0) cc_final: 0.7793 (t0) REVERT: A 132 MET cc_start: 0.8294 (ppp) cc_final: 0.7935 (ppp) REVERT: A 202 THR cc_start: 0.9165 (m) cc_final: 0.8890 (p) REVERT: A 269 MET cc_start: 0.7123 (mtp) cc_final: 0.6873 (mtp) REVERT: A 314 GLN cc_start: 0.9230 (pp30) cc_final: 0.8888 (pp30) REVERT: B 44 MET cc_start: 0.6156 (tpt) cc_final: 0.5929 (tpt) REVERT: B 95 ARG cc_start: 0.7582 (mtt180) cc_final: 0.6596 (tpm170) REVERT: B 214 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7820 (tm-30) REVERT: B 290 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7657 (mtt90) REVERT: B 314 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7350 (tm-30) REVERT: C 11 ASP cc_start: 0.7843 (t0) cc_final: 0.7371 (m-30) REVERT: C 72 GLU cc_start: 0.8043 (tp30) cc_final: 0.7493 (mm-30) REVERT: C 190 MET cc_start: 0.8227 (ttp) cc_final: 0.8007 (ttm) REVERT: C 198 TYR cc_start: 0.8874 (m-80) cc_final: 0.8338 (m-80) REVERT: C 280 ASN cc_start: 0.8430 (m-40) cc_final: 0.8055 (t0) REVERT: D 1349 ASN cc_start: 0.8528 (t0) cc_final: 0.8022 (t0) REVERT: D 1397 TYR cc_start: 0.8334 (m-80) cc_final: 0.7989 (m-80) REVERT: D 1658 THR cc_start: 0.8708 (p) cc_final: 0.8425 (t) REVERT: D 1675 LYS cc_start: 0.9159 (tttt) cc_final: 0.8668 (ptpt) REVERT: D 1769 MET cc_start: 0.8017 (mmp) cc_final: 0.7790 (mmp) REVERT: D 1792 GLU cc_start: 0.7931 (mp0) cc_final: 0.7679 (mp0) REVERT: D 1870 LEU cc_start: 0.8448 (tp) cc_final: 0.8178 (tp) REVERT: D 1906 PHE cc_start: 0.9594 (m-80) cc_final: 0.9287 (m-80) REVERT: E 85 MET cc_start: 0.7105 (mmp) cc_final: 0.6805 (mmm) REVERT: E 89 MET cc_start: 0.8894 (tmm) cc_final: 0.8526 (mmp) REVERT: E 104 ARG cc_start: 0.9471 (mmm160) cc_final: 0.9087 (mmm160) REVERT: E 107 PHE cc_start: 0.9013 (m-10) cc_final: 0.8620 (m-80) outliers start: 3 outliers final: 0 residues processed: 343 average time/residue: 0.1259 time to fit residues: 65.5855 Evaluate side-chains 265 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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: 2.9990 chunk 121 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 77 optimal weight: 0.0060 chunk 138 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 59 GLN A 128 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1389 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 = 0.3651 r_free = 0.3651 target = 0.115635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090569 restraints weight = 39451.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092769 restraints weight = 22489.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.094334 restraints weight = 15022.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095376 restraints weight = 11186.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.096003 restraints weight = 9088.214| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5603 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= 0.136 Angle : 0.687 9.026 21720 Z= 0.336 Chirality : 0.045 0.158 2405 Planarity : 0.004 0.050 2800 Dihedral : 6.221 75.061 2194 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.24 % Allowed : 0.42 % Favored : 99.35 % 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 aren not related in a simple way. whole: -0.06 (0.20), residues: 1943 helix: 0.56 (0.17), residues: 952 sheet: -0.64 (0.31), residues: 295 loop : -0.40 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 161 TYR 0.017 0.001 TYR C 279 PHE 0.026 0.001 PHE E 34 TRP 0.038 0.002 TRP D1550 HIS 0.007 0.001 HIS D1725 Details of bonding type rmsd covalent geometry : bond 0.00315 (16038) covalent geometry : angle 0.68679 (21720) hydrogen bonds : bond 0.03620 ( 751) hydrogen bonds : angle 4.71697 ( 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 342 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 338 time to evaluate : 0.647 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: 0.8349 (t0) cc_final: 0.7778 (t0) REVERT: A 132 MET cc_start: 0.8216 (ppp) cc_final: 0.7895 (ppp) REVERT: A 202 THR cc_start: 0.9189 (m) cc_final: 0.8894 (p) REVERT: A 269 MET cc_start: 0.7229 (mtp) cc_final: 0.6980 (mtp) REVERT: A 314 GLN cc_start: 0.9251 (pp30) cc_final: 0.8900 (pp30) REVERT: B 95 ARG cc_start: 0.7689 (mtt180) cc_final: 0.6600 (tpm170) REVERT: B 214 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7829 (tm-30) REVERT: B 290 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7657 (mtt90) REVERT: B 314 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7344 (tm-30) REVERT: C 11 ASP cc_start: 0.7994 (t0) cc_final: 0.7529 (m-30) REVERT: C 72 GLU cc_start: 0.8104 (tp30) cc_final: 0.7446 (mm-30) REVERT: C 280 ASN cc_start: 0.8431 (m-40) cc_final: 0.8046 (t0) REVERT: D 1343 ASN cc_start: 0.8207 (m-40) cc_final: 0.7832 (m110) REVERT: D 1349 ASN cc_start: 0.8585 (t0) cc_final: 0.8014 (t0) REVERT: D 1397 TYR cc_start: 0.8361 (m-80) cc_final: 0.7988 (m-80) REVERT: D 1658 THR cc_start: 0.8726 (p) cc_final: 0.8443 (t) REVERT: D 1675 LYS cc_start: 0.9139 (tttt) cc_final: 0.8703 (tttp) REVERT: D 1769 MET cc_start: 0.8055 (mmp) cc_final: 0.7825 (mmp) REVERT: D 1870 LEU cc_start: 0.8455 (tp) cc_final: 0.8230 (tp) REVERT: D 1900 PHE cc_start: 0.8648 (m-80) cc_final: 0.8382 (m-80) REVERT: D 1906 PHE cc_start: 0.9590 (m-80) cc_final: 0.9280 (m-80) REVERT: E 85 MET cc_start: 0.7120 (mmp) cc_final: 0.6815 (mmm) REVERT: E 89 MET cc_start: 0.8873 (tmm) cc_final: 0.8524 (mmp) REVERT: E 103 ILE cc_start: 0.9119 (mt) cc_final: 0.8016 (mm) REVERT: E 104 ARG cc_start: 0.9467 (mmm160) cc_final: 0.9118 (mmm160) REVERT: E 107 PHE cc_start: 0.8987 (m-10) cc_final: 0.8721 (m-80) outliers start: 4 outliers final: 0 residues processed: 340 average time/residue: 0.1214 time to fit residues: 63.1284 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 : 0.667 ------------------------------------------------------------------------------- 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: 0.5980 chunk 110 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 59 GLN A 128 ASN B 121 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1389 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 = 0.3652 r_free = 0.3652 target = 0.115731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.091699 restraints weight = 39078.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.093883 restraints weight = 22589.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095405 restraints weight = 15030.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.096397 restraints weight = 11187.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096983 restraints weight = 9117.918| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16038 Z= 0.138 Angle : 0.680 7.820 21720 Z= 0.333 Chirality : 0.045 0.152 2405 Planarity : 0.004 0.051 2800 Dihedral : 6.187 73.320 2194 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % 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 aren not related in a simple way. whole: -0.11 (0.20), residues: 1943 helix: 0.54 (0.17), residues: 952 sheet: -0.75 (0.30), residues: 298 loop : -0.41 (0.26), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 161 TYR 0.020 0.001 TYR C 306 PHE 0.024 0.001 PHE E 34 TRP 0.015 0.002 TRP D1550 HIS 0.006 0.001 HIS D1730 Details of bonding type rmsd covalent geometry : bond 0.00320 (16038) covalent geometry : angle 0.68037 (21720) hydrogen bonds : bond 0.03617 ( 751) hydrogen bonds : angle 4.68710 ( 2121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3008.94 seconds wall clock time: 52 minutes 50.34 seconds (3170.34 seconds total)