Starting phenix.real_space_refine on Thu Aug 6 01:10:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25ij_80135/08_2026/25ij_80135.cif Found real_map, /net/cci-nas-00/data/ceres_data/25ij_80135/08_2026/25ij_80135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25ij_80135/08_2026/25ij_80135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25ij_80135/08_2026/25ij_80135.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25ij_80135/08_2026/25ij_80135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25ij_80135/08_2026/25ij_80135.map" } resolution = 3.1 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= 0.005 sd= 0.073 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 92 5.16 5 C 8102 2.51 5 N 1874 2.21 5 O 2156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12227 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 10168 Classifications: {'peptide': 1259} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 1217} Chain breaks: 4 Chain: "B" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 193 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 3, 'TRANS': 21} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'TRANS': 172} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Unusual residues: {'9Z9': 1, 'NAG': 4, 'PCW': 3, 'Y01': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N NH2 B 26 " occ=0.00 Time building chain proxies: 2.10, per 1000 atoms: 0.17 Number of scatterers: 12227 At special positions: 0 Unit cell: (113.084, 135.042, 137.238, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 3 15.00 O 2156 8.00 N 1874 7.00 C 8102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 906 " - pdb=" SG CYS A 912 " distance=2.03 Simple disulfide: pdb=" SG CYS A 944 " - pdb=" SG CYS A 953 " distance=2.03 Simple disulfide: pdb=" SG CYS A1356 " - pdb=" SG CYS A1376 " distance=2.03 Simple disulfide: pdb=" SG CYS A1721 " - pdb=" SG CYS A1736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 43 " distance=2.03 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 121 " distance=2.03 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=1, symmetry=0 Links applied ALPHA1-2 " MAN D 5 " - " MAN D 6 " " MAN D 8 " - " MAN D 9 " ALPHA1-3 " BMA D 3 " - " MAN D 8 " " MAN D 4 " - " MAN D 7 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 5 " BETA1-3 " NAG D 1 " - " NAG D 2 " BETA1-4 " NAG D 2 " - " BMA D 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2001 " - " ASN A1372 " " NAG A2002 " - " ASN A 295 " " NAG A2003 " - " ASN A1358 " " NAG A2004 " - " ASN A 308 " " NAG D 1 " - " ASN A 326 " " NAG F 1 " - " ASN C 135 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 451.3 milliseconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 5 sheets defined 71.1% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 18 through 33 removed outlier: 3.661A pdb=" N ILE A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.667A pdb=" N LYS A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 149 removed outlier: 3.585A pdb=" N SER A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 159 through 180 removed outlier: 4.206A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 191 removed outlier: 3.588A pdb=" N ARG A 191 " --> pdb=" O THR A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 192 through 211 removed outlier: 3.831A pdb=" N TRP A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.730A pdb=" N ARG A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 227 Processing helix chain 'A' and resid 228 through 234 removed outlier: 4.417A pdb=" N SER A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 removed outlier: 3.622A pdb=" N ILE A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 251 through 273 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 301 through 307 removed outlier: 3.502A pdb=" N TYR A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 355 through 369 removed outlier: 3.516A pdb=" N LEU A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 384 removed outlier: 4.052A pdb=" N LEU A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 400 removed outlier: 4.025A pdb=" N PHE A 391 " --> pdb=" O TYR A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 427 removed outlier: 3.743A pdb=" N ALA A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 751 removed outlier: 3.622A pdb=" N LEU A 748 " --> pdb=" O GLU A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 771 removed outlier: 3.590A pdb=" N ASP A 756 " --> pdb=" O ASP A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 806 Processing helix chain 'A' and resid 808 through 813 removed outlier: 3.699A pdb=" N TYR A 812 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 834 removed outlier: 3.848A pdb=" N GLY A 822 " --> pdb=" O ASN A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 838 Processing helix chain 'A' and resid 839 through 847 removed outlier: 4.049A pdb=" N LEU A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 857 Processing helix chain 'A' and resid 858 through 873 removed outlier: 3.542A pdb=" N MET A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 864 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 871 " --> pdb=" O ILE A 867 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 872 " --> pdb=" O ILE A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 898 Processing helix chain 'A' and resid 899 through 904 Processing helix chain 'A' and resid 904 through 909 removed outlier: 4.003A pdb=" N ILE A 908 " --> pdb=" O CYS A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 934 Processing helix chain 'A' and resid 937 through 949 removed outlier: 3.950A pdb=" N ASP A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 982 removed outlier: 3.607A pdb=" N CYS A 953 " --> pdb=" O GLY A 949 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 956 " --> pdb=" O MET A 952 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 958 " --> pdb=" O LEU A 954 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A 961 " --> pdb=" O PHE A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1006 Processing helix chain 'A' and resid 1178 through 1197 Processing helix chain 'A' and resid 1197 through 1214 removed outlier: 3.522A pdb=" N ALA A1214 " --> pdb=" O LEU A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1218 Processing helix chain 'A' and resid 1219 through 1224 removed outlier: 4.285A pdb=" N GLU A1223 " --> pdb=" O ILE A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1255 removed outlier: 4.084A pdb=" N ARG A1229 " --> pdb=" O ARG A1225 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A1237 " --> pdb=" O GLU A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1262 through 1285 removed outlier: 3.555A pdb=" N TRP A1266 " --> pdb=" O ASN A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1296 Processing helix chain 'A' and resid 1297 through 1308 removed outlier: 3.555A pdb=" N ARG A1302 " --> pdb=" O ARG A1299 " (cutoff:3.500A) Proline residue: A1303 - end of helix removed outlier: 3.792A pdb=" N SER A1308 " --> pdb=" O ARG A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1323 removed outlier: 3.552A pdb=" N VAL A1316 " --> pdb=" O GLY A1312 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A1321 " --> pdb=" O VAL A1317 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A1323 " --> pdb=" O ALA A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1350 removed outlier: 3.524A pdb=" N LEU A1332 " --> pdb=" O MET A1328 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A1333 " --> pdb=" O ASN A1329 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A1341 " --> pdb=" O PHE A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1381 Processing helix chain 'A' and resid 1398 through 1411 removed outlier: 3.913A pdb=" N LEU A1404 " --> pdb=" O GLY A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1424 removed outlier: 3.654A pdb=" N ILE A1418 " --> pdb=" O GLY A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1440 through 1451 removed outlier: 4.283A pdb=" N PHE A1444 " --> pdb=" O MET A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1475 removed outlier: 3.526A pdb=" N LEU A1456 " --> pdb=" O SER A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1498 removed outlier: 3.859A pdb=" N TYR A1488 " --> pdb=" O GLU A1484 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A1494 " --> pdb=" O ASN A1490 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU A1495 " --> pdb=" O ALA A1491 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLY A1496 " --> pdb=" O MET A1492 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A1497 " --> pdb=" O LYS A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1521 removed outlier: 3.718A pdb=" N VAL A1515 " --> pdb=" O ILE A1511 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN A1521 " --> pdb=" O ASP A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1541 removed outlier: 3.661A pdb=" N ASP A1525 " --> pdb=" O GLN A1521 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS A1533 " --> pdb=" O MET A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1547 through 1577 Processing helix chain 'A' and resid 1578 through 1583 removed outlier: 3.584A pdb=" N PHE A1581 " --> pdb=" O HIS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1603 Processing helix chain 'A' and resid 1604 through 1608 Processing helix chain 'A' and resid 1612 through 1620 Processing helix chain 'A' and resid 1621 through 1626 removed outlier: 3.971A pdb=" N GLY A1625 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG A1626 " --> pdb=" O ALA A1622 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1621 through 1626' Processing helix chain 'A' and resid 1627 through 1633 removed outlier: 3.520A pdb=" N GLY A1633 " --> pdb=" O LEU A1630 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1647 removed outlier: 3.575A pdb=" N LEU A1641 " --> pdb=" O ILE A1637 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A1645 " --> pdb=" O LEU A1641 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1673 removed outlier: 3.570A pdb=" N ASN A1653 " --> pdb=" O PRO A1649 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A1654 " --> pdb=" O ALA A1650 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A1672 " --> pdb=" O PHE A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1703 removed outlier: 3.625A pdb=" N GLN A1700 " --> pdb=" O ILE A1696 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A1703 " --> pdb=" O PHE A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1712 removed outlier: 3.620A pdb=" N LEU A1710 " --> pdb=" O GLY A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1713 through 1716 Processing helix chain 'A' and resid 1738 through 1772 removed outlier: 3.704A pdb=" N PHE A1744 " --> pdb=" O SER A1740 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A1759 " --> pdb=" O LEU A1755 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A1760 " --> pdb=" O ILE A1756 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A1761 " --> pdb=" O VAL A1757 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 removed outlier: 3.651A pdb=" N LEU B 7 " --> pdb=" O PRO B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 25 Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 153 through 192 removed outlier: 3.622A pdb=" N TYR C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS C 184 " --> pdb=" O TYR C 180 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 97 Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 283 Processing sheet with id=AA3, first strand: chain 'A' and resid 1363 through 1364 Processing sheet with id=AA4, first strand: chain 'C' and resid 29 through 31 removed outlier: 5.749A pdb=" N ALA C 30 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN C 50 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N THR C 53 " --> pdb=" O GLU C 74 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLU C 74 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR C 55 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG C 72 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TRP C 57 " --> pdb=" O ILE C 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 38 708 hydrogen bonds defined for protein. 1995 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: 1.49 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1867 1.32 - 1.44: 3439 1.44 - 1.57: 7056 1.57 - 1.69: 6 1.69 - 1.82: 152 Bond restraints: 12520 Sorted by residual: bond pdb=" C4 PCW A2006 " pdb=" O4P PCW A2006 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C2 MAN D 5 " pdb=" O2 MAN D 5 " ideal model delta sigma weight residual 1.407 1.458 -0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" N ASN A 295 " pdb=" CA ASN A 295 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.18e-02 7.18e+03 6.24e+00 bond pdb=" C4 PCW A2010 " pdb=" O4P PCW A2010 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" N GLY C 20 " pdb=" CA GLY C 20 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.98e+00 ... (remaining 12515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 16642 1.90 - 3.80: 262 3.80 - 5.70: 34 5.70 - 7.60: 9 7.60 - 9.50: 3 Bond angle restraints: 16950 Sorted by residual: angle pdb=" N ASN A 295 " pdb=" CA ASN A 295 " pdb=" C ASN A 295 " ideal model delta sigma weight residual 112.72 108.22 4.50 1.14e+00 7.69e-01 1.56e+01 angle pdb=" CB MET A 204 " pdb=" CG MET A 204 " pdb=" SD MET A 204 " ideal model delta sigma weight residual 112.70 122.20 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" O ILE A1340 " pdb=" C ILE A1340 " pdb=" N PHE A1341 " ideal model delta sigma weight residual 121.91 124.71 -2.80 9.80e-01 1.04e+00 8.18e+00 angle pdb=" N GLY A1382 " pdb=" CA GLY A1382 " pdb=" C GLY A1382 " ideal model delta sigma weight residual 111.21 114.12 -2.91 1.04e+00 9.25e-01 7.83e+00 angle pdb=" CA ILE A1340 " pdb=" C ILE A1340 " pdb=" O ILE A1340 " ideal model delta sigma weight residual 121.17 118.41 2.76 1.06e+00 8.90e-01 6.77e+00 ... (remaining 16945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 7506 35.73 - 71.45: 233 71.45 - 107.18: 23 107.18 - 142.90: 6 142.90 - 178.63: 2 Dihedral angle restraints: 7770 sinusoidal: 3512 harmonic: 4258 Sorted by residual: dihedral pdb=" CB CYS A 324 " pdb=" SG CYS A 324 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual -86.00 -153.05 67.05 1 1.00e+01 1.00e-02 5.86e+01 dihedral pdb=" CB CYS A 944 " pdb=" SG CYS A 944 " pdb=" SG CYS A 953 " pdb=" CB CYS A 953 " ideal model delta sinusoidal sigma weight residual 93.00 140.60 -47.60 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" C22 9Z9 A2005 " pdb=" C23 9Z9 A2005 " pdb=" C48 9Z9 A2005 " pdb=" O49 9Z9 A2005 " ideal model delta sinusoidal sigma weight residual 177.15 -1.48 178.63 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 7767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1912 0.096 - 0.192: 57 0.192 - 0.288: 0 0.288 - 0.384: 2 0.384 - 0.479: 1 Chirality restraints: 1972 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 326 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" C1 NAG A2002 " pdb=" ND2 ASN A 295 " pdb=" C2 NAG A2002 " pdb=" O5 NAG A2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1969 not shown) Planarity restraints: 2043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 295 " 0.062 2.00e-02 2.50e+03 2.77e-01 9.59e+02 pdb=" CG ASN A 295 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN A 295 " 0.185 2.00e-02 2.50e+03 pdb=" ND2 ASN A 295 " -0.487 2.00e-02 2.50e+03 pdb=" C1 NAG A2002 " 0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PCW A2010 " 0.100 2.00e-02 2.50e+03 2.48e-01 6.14e+02 pdb=" C39 PCW A2010 " -0.333 2.00e-02 2.50e+03 pdb=" C40 PCW A2010 " 0.338 2.00e-02 2.50e+03 pdb=" C41 PCW A2010 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW A2010 " -0.096 2.00e-02 2.50e+03 2.38e-01 5.67e+02 pdb=" C19 PCW A2010 " 0.316 2.00e-02 2.50e+03 pdb=" C20 PCW A2010 " -0.326 2.00e-02 2.50e+03 pdb=" C21 PCW A2010 " 0.106 2.00e-02 2.50e+03 ... (remaining 2040 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3018 2.79 - 3.32: 12173 3.32 - 3.85: 19079 3.85 - 4.37: 23352 4.37 - 4.90: 39510 Nonbonded interactions: 97132 Sorted by model distance: nonbonded pdb=" O TYR A 88 " pdb=" OG1 THR A 93 " model vdw 2.264 3.040 nonbonded pdb=" O ILE A1186 " pdb=" OG1 THR A1190 " model vdw 2.267 3.040 nonbonded pdb=" OD1 ASP C 153 " pdb=" N MET C 154 " model vdw 2.287 3.120 nonbonded pdb=" N GLU C 65 " pdb=" OE1 GLU C 65 " model vdw 2.301 3.120 nonbonded pdb=" O LEU A1335 " pdb=" OH TYR A1403 " model vdw 2.315 3.040 ... (remaining 97127 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.400 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 0.100 12544 Z= 0.212 Angle : 0.609 9.503 17011 Z= 0.288 Chirality : 0.041 0.479 1972 Planarity : 0.009 0.248 2037 Dihedral : 17.003 178.626 4992 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.46 % Allowed : 12.50 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.23), residues: 1443 helix: 0.36 (0.18), residues: 870 sheet: -0.69 (0.59), residues: 74 loop : -0.04 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 344 TYR 0.010 0.001 TYR A1580 PHE 0.032 0.001 PHE A 104 TRP 0.006 0.001 TRP A1415 HIS 0.003 0.001 HIS A1197 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (12520) covalent geometry : angle 0.58736 / 0.28 (16950) SS BOND : bond 0.00257 / 0.15 ( 8) SS BOND : angle 0.67458 / 0.38 ( 16) hydrogen bonds : bond 0.23532 / 15.37 ( 708) hydrogen bonds : angle 8.14462 / 5.71 ( 1995) Misc. bond : bond 0.10040 / 6.69 ( 1) link_ALPHA1-2 : bond 0.01077 / 0.74 ( 2) link_ALPHA1-2 : angle 3.98978 / 2.36 ( 6) link_ALPHA1-3 : bond 0.00985 / 0.69 ( 2) link_ALPHA1-3 : angle 2.33099 / 1.68 ( 6) link_ALPHA1-6 : bond 0.00787 / 0.55 ( 2) link_ALPHA1-6 : angle 1.89278 / 1.46 ( 6) link_BETA1-3 : bond 0.01589 / 1.06 ( 1) link_BETA1-3 : angle 1.94176 / 1.46 ( 3) link_BETA1-4 : bond 0.00701 / 0.47 ( 2) link_BETA1-4 : angle 3.67501 / 2.20 ( 6) link_NAG-ASN : bond 0.00548 / 0.29 ( 6) link_NAG-ASN : angle 3.35909 / 2.43 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 212 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 127 LYS cc_start: 0.8437 (pttt) cc_final: 0.8112 (pttm) REVERT: A 196 TRP cc_start: 0.7926 (m100) cc_final: 0.7057 (m100) REVERT: A 255 MET cc_start: 0.8268 (mmt) cc_final: 0.7720 (mtm) REVERT: A 400 PHE cc_start: 0.6978 (m-10) cc_final: 0.6766 (m-80) REVERT: A 765 LEU cc_start: 0.8865 (mt) cc_final: 0.8622 (tt) REVERT: A 820 PHE cc_start: 0.8077 (t80) cc_final: 0.7723 (t80) REVERT: A 919 MET cc_start: 0.9272 (mtp) cc_final: 0.9032 (mtt) REVERT: C 89 ARG cc_start: 0.8794 (ptp90) cc_final: 0.8443 (ptp90) REVERT: C 178 MET cc_start: 0.8134 (ttm) cc_final: 0.7859 (mtm) outliers start: 6 outliers final: 1 residues processed: 215 average time/residue: 0.0865 time to fit residues: 27.3131 Evaluate side-chains 195 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN A 419 GLN A1384 ASN A1398 ASN A1437 ASN A1535 ASN B 18 GLN C 50 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101855 restraints weight = 16999.901| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.08 r_work: 0.3057 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12544 Z= 0.173 Angle : 0.649 13.421 17011 Z= 0.330 Chirality : 0.045 0.423 1972 Planarity : 0.004 0.035 2037 Dihedral : 13.502 179.740 2219 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.70 % Allowed : 14.35 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1443 helix: 0.74 (0.17), residues: 900 sheet: -0.75 (0.57), residues: 77 loop : -0.00 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1299 TYR 0.020 0.002 TYR A 376 PHE 0.024 0.002 PHE A 980 TRP 0.009 0.001 TRP A1707 HIS 0.006 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (12520) covalent geometry : angle 0.62194 / 0.32 (16950) SS BOND : bond 0.00359 / 0.21 ( 8) SS BOND : angle 0.91113 / 0.52 ( 16) hydrogen bonds : bond 0.05516 / 3.51 ( 708) hydrogen bonds : angle 4.89195 / 3.42 ( 1995) Misc. bond : bond 0.00121 / 0.08 ( 1) link_ALPHA1-2 : bond 0.00496 / 0.34 ( 2) link_ALPHA1-2 : angle 3.08559 / 1.73 ( 6) link_ALPHA1-3 : bond 0.01065 / 0.73 ( 2) link_ALPHA1-3 : angle 1.13946 / 0.68 ( 6) link_ALPHA1-6 : bond 0.00282 / 0.20 ( 2) link_ALPHA1-6 : angle 1.66443 / 1.13 ( 6) link_BETA1-3 : bond 0.01504 / 1.00 ( 1) link_BETA1-3 : angle 3.07523 / 2.37 ( 3) link_BETA1-4 : bond 0.00980 / 0.65 ( 2) link_BETA1-4 : angle 2.49839 / 1.46 ( 6) link_NAG-ASN : bond 0.00440 / 0.24 ( 6) link_NAG-ASN : angle 4.97772 / 3.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LYS cc_start: 0.8599 (pttt) cc_final: 0.8143 (pttm) REVERT: A 137 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8715 (pt) REVERT: A 196 TRP cc_start: 0.8041 (m100) cc_final: 0.7713 (m100) REVERT: A 220 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7637 (mmm160) REVERT: A 222 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.8078 (t80) REVERT: A 223 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7949 (ptp-110) REVERT: A 255 MET cc_start: 0.8533 (mmt) cc_final: 0.7698 (mtm) REVERT: A 830 MET cc_start: 0.7224 (mmm) cc_final: 0.6914 (mmm) REVERT: A 919 MET cc_start: 0.9314 (mtp) cc_final: 0.9074 (mtt) REVERT: A 1379 LEU cc_start: 0.8952 (mm) cc_final: 0.8740 (tp) REVERT: A 1440 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.9017 (tpp) REVERT: C 32 TYR cc_start: 0.8724 (t80) cc_final: 0.8420 (t80) REVERT: C 83 ASP cc_start: 0.8683 (t0) cc_final: 0.8449 (t0) REVERT: C 144 ILE cc_start: 0.9169 (mt) cc_final: 0.8866 (tt) outliers start: 22 outliers final: 6 residues processed: 229 average time/residue: 0.0851 time to fit residues: 29.2140 Evaluate side-chains 205 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 196 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1482 THR Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 53 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 126 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 30.0000 chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 418 ASN A 965 ASN A1384 ASN A1457 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103977 restraints weight = 17047.463| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.08 r_work: 0.3101 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12544 Z= 0.118 Angle : 0.548 12.583 17011 Z= 0.277 Chirality : 0.041 0.415 1972 Planarity : 0.004 0.040 2037 Dihedral : 12.677 166.098 2218 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.62 % Allowed : 16.51 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.23), residues: 1443 helix: 1.10 (0.18), residues: 894 sheet: -0.66 (0.58), residues: 77 loop : -0.12 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 180 TYR 0.023 0.001 TYR C 180 PHE 0.020 0.001 PHE A 189 TRP 0.009 0.001 TRP A 157 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (12520) covalent geometry : angle 0.52577 / 0.27 (16950) SS BOND : bond 0.00252 / 0.15 ( 8) SS BOND : angle 0.70009 / 0.39 ( 16) hydrogen bonds : bond 0.04272 / 2.73 ( 708) hydrogen bonds : angle 4.36099 / 3.05 ( 1995) Misc. bond : bond 0.00010 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00519 / 0.35 ( 2) link_ALPHA1-2 : angle 2.79184 / 1.52 ( 6) link_ALPHA1-3 : bond 0.01037 / 0.71 ( 2) link_ALPHA1-3 : angle 1.07852 / 0.73 ( 6) link_ALPHA1-6 : bond 0.00452 / 0.31 ( 2) link_ALPHA1-6 : angle 1.67276 / 1.15 ( 6) link_BETA1-3 : bond 0.01343 / 0.90 ( 1) link_BETA1-3 : angle 2.59194 / 1.92 ( 3) link_BETA1-4 : bond 0.00638 / 0.43 ( 2) link_BETA1-4 : angle 1.91042 / 1.11 ( 6) link_NAG-ASN : bond 0.00793 / 0.45 ( 6) link_NAG-ASN : angle 4.15956 / 3.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LYS cc_start: 0.8567 (pttt) cc_final: 0.8109 (pttm) REVERT: A 172 GLU cc_start: 0.8772 (tt0) cc_final: 0.8258 (tt0) REVERT: A 196 TRP cc_start: 0.8017 (m100) cc_final: 0.7701 (m100) REVERT: A 220 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7602 (mmm160) REVERT: A 222 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.8034 (t80) REVERT: A 223 ARG cc_start: 0.8260 (mtm110) cc_final: 0.7883 (ptp-110) REVERT: A 255 MET cc_start: 0.8521 (mmt) cc_final: 0.7744 (mtm) REVERT: A 919 MET cc_start: 0.9309 (mtp) cc_final: 0.9074 (mtt) REVERT: A 1646 MET cc_start: 0.8452 (tpp) cc_final: 0.8249 (mmp) REVERT: C 53 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8449 (t) REVERT: C 144 ILE cc_start: 0.9141 (mt) cc_final: 0.8825 (tt) REVERT: C 184 LYS cc_start: 0.8595 (mmtm) cc_final: 0.8330 (mppt) outliers start: 21 outliers final: 11 residues processed: 214 average time/residue: 0.0832 time to fit residues: 26.8388 Evaluate side-chains 204 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1427 LYS Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1670 MET Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 53 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 31 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 16 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN A1384 ASN C 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.159025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102969 restraints weight = 16888.811| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.06 r_work: 0.3090 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12544 Z= 0.129 Angle : 0.548 12.174 17011 Z= 0.277 Chirality : 0.042 0.408 1972 Planarity : 0.004 0.042 2037 Dihedral : 12.326 159.292 2218 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.16 % Allowed : 17.36 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.23), residues: 1443 helix: 1.18 (0.18), residues: 894 sheet: -0.56 (0.58), residues: 77 loop : -0.18 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1299 TYR 0.021 0.001 TYR C 180 PHE 0.018 0.001 PHE A 189 TRP 0.009 0.001 TRP A 157 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (12520) covalent geometry : angle 0.52684 / 0.27 (16950) SS BOND : bond 0.00295 / 0.17 ( 8) SS BOND : angle 0.77987 / 0.45 ( 16) hydrogen bonds : bond 0.04002 / 2.58 ( 708) hydrogen bonds : angle 4.23139 / 2.96 ( 1995) Misc. bond : bond 0.00005 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00464 / 0.31 ( 2) link_ALPHA1-2 : angle 2.51378 / 1.37 ( 6) link_ALPHA1-3 : bond 0.00958 / 0.66 ( 2) link_ALPHA1-3 : angle 1.07806 / 0.69 ( 6) link_ALPHA1-6 : bond 0.00349 / 0.24 ( 2) link_ALPHA1-6 : angle 1.76448 / 1.21 ( 6) link_BETA1-3 : bond 0.01244 / 0.83 ( 1) link_BETA1-3 : angle 2.77854 / 2.08 ( 3) link_BETA1-4 : bond 0.00574 / 0.39 ( 2) link_BETA1-4 : angle 2.23260 / 1.32 ( 6) link_NAG-ASN : bond 0.00611 / 0.39 ( 6) link_NAG-ASN : angle 3.93496 / 2.93 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LYS cc_start: 0.8558 (pttt) cc_final: 0.8106 (pttm) REVERT: A 136 MET cc_start: 0.6817 (mmt) cc_final: 0.6579 (mmm) REVERT: A 172 GLU cc_start: 0.8714 (tt0) cc_final: 0.8248 (tt0) REVERT: A 196 TRP cc_start: 0.8005 (m100) cc_final: 0.7711 (m100) REVERT: A 220 ARG cc_start: 0.8342 (mmm160) cc_final: 0.7481 (mmm160) REVERT: A 222 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8030 (t80) REVERT: A 223 ARG cc_start: 0.8246 (mtm110) cc_final: 0.7851 (ptp-110) REVERT: A 255 MET cc_start: 0.8471 (mmt) cc_final: 0.7674 (mtm) REVERT: A 751 MET cc_start: 0.8716 (tpp) cc_final: 0.8316 (tpp) REVERT: A 807 MET cc_start: 0.5681 (pp-130) cc_final: 0.5248 (pp-130) REVERT: A 830 MET cc_start: 0.7331 (mmm) cc_final: 0.7017 (mmm) REVERT: A 919 MET cc_start: 0.9318 (mtp) cc_final: 0.9087 (mtt) REVERT: A 969 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 1440 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8941 (tpp) REVERT: A 1529 MET cc_start: 0.7464 (ttm) cc_final: 0.7218 (ttp) REVERT: A 1530 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6814 (mmp) REVERT: C 53 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8487 (t) REVERT: C 83 ASP cc_start: 0.8654 (t0) cc_final: 0.8443 (t0) REVERT: C 144 ILE cc_start: 0.9147 (mt) cc_final: 0.8829 (tt) outliers start: 28 outliers final: 14 residues processed: 214 average time/residue: 0.0805 time to fit residues: 25.8435 Evaluate side-chains 207 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1427 LYS Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1482 THR Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1548 LYS Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 53 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 ASN A1384 ASN C 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.157819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101303 restraints weight = 17048.680| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.14 r_work: 0.3053 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12544 Z= 0.161 Angle : 0.563 11.733 17011 Z= 0.284 Chirality : 0.042 0.387 1972 Planarity : 0.004 0.042 2037 Dihedral : 11.961 148.446 2218 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.09 % Allowed : 16.98 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.22), residues: 1443 helix: 1.19 (0.18), residues: 890 sheet: -0.59 (0.57), residues: 77 loop : -0.23 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 180 TYR 0.020 0.002 TYR C 180 PHE 0.024 0.001 PHE A 94 TRP 0.009 0.001 TRP A 157 HIS 0.003 0.001 HIS A 918 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (12520) covalent geometry : angle 0.54231 / 0.28 (16950) SS BOND : bond 0.00342 / 0.20 ( 8) SS BOND : angle 0.88825 / 0.52 ( 16) hydrogen bonds : bond 0.04049 / 2.61 ( 708) hydrogen bonds : angle 4.22268 / 2.96 ( 1995) Misc. bond : bond 0.00010 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00453 / 0.31 ( 2) link_ALPHA1-2 : angle 2.42272 / 1.33 ( 6) link_ALPHA1-3 : bond 0.00938 / 0.65 ( 2) link_ALPHA1-3 : angle 1.13624 / 0.73 ( 6) link_ALPHA1-6 : bond 0.00382 / 0.27 ( 2) link_ALPHA1-6 : angle 1.84824 / 1.26 ( 6) link_BETA1-3 : bond 0.01016 / 0.68 ( 1) link_BETA1-3 : angle 2.92859 / 2.20 ( 3) link_BETA1-4 : bond 0.00571 / 0.39 ( 2) link_BETA1-4 : angle 2.21565 / 1.31 ( 6) link_NAG-ASN : bond 0.00967 / 0.57 ( 6) link_NAG-ASN : angle 3.94321 / 2.94 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8783 (tt0) cc_final: 0.8343 (tt0) REVERT: A 182 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.6077 (m-80) REVERT: A 196 TRP cc_start: 0.8005 (m100) cc_final: 0.7728 (m100) REVERT: A 222 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.8052 (t80) REVERT: A 329 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8524 (m-30) REVERT: A 751 MET cc_start: 0.8739 (tpp) cc_final: 0.8336 (tpp) REVERT: A 807 MET cc_start: 0.5490 (pp-130) cc_final: 0.5092 (pp-130) REVERT: A 830 MET cc_start: 0.7219 (mmm) cc_final: 0.6903 (mmm) REVERT: A 919 MET cc_start: 0.9327 (mtp) cc_final: 0.9095 (mtt) REVERT: A 961 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8257 (ttm) REVERT: A 1440 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8966 (tpp) REVERT: B 24 GLN cc_start: 0.8322 (tt0) cc_final: 0.8017 (tt0) REVERT: C 53 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8521 (t) REVERT: C 72 ARG cc_start: 0.8156 (ttt180) cc_final: 0.7751 (ttt90) REVERT: C 131 ASN cc_start: 0.8782 (m-40) cc_final: 0.8304 (t0) REVERT: C 144 ILE cc_start: 0.9168 (mt) cc_final: 0.8862 (tt) outliers start: 40 outliers final: 22 residues processed: 214 average time/residue: 0.0847 time to fit residues: 26.9865 Evaluate side-chains 216 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1372 ASN Chi-restraints excluded: chain A residue 1427 LYS Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1482 THR Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1548 LYS Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1670 MET Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 53 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 965 ASN C 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.158923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103797 restraints weight = 16862.577| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.60 r_work: 0.3047 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12544 Z= 0.120 Angle : 0.546 11.191 17011 Z= 0.271 Chirality : 0.041 0.380 1972 Planarity : 0.004 0.044 2037 Dihedral : 11.430 136.784 2218 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.01 % Allowed : 17.44 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1443 helix: 1.31 (0.18), residues: 890 sheet: -0.41 (0.59), residues: 77 loop : -0.20 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.021 0.001 TYR C 180 PHE 0.022 0.001 PHE A 94 TRP 0.008 0.001 TRP A 157 HIS 0.002 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (12520) covalent geometry : angle 0.52616 / 0.27 (16950) SS BOND : bond 0.00286 / 0.16 ( 8) SS BOND : angle 0.77151 / 0.44 ( 16) hydrogen bonds : bond 0.03749 / 2.42 ( 708) hydrogen bonds : angle 4.07906 / 2.86 ( 1995) Misc. bond : bond 0.00004 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00464 / 0.31 ( 2) link_ALPHA1-2 : angle 2.28100 / 1.26 ( 6) link_ALPHA1-3 : bond 0.00939 / 0.64 ( 2) link_ALPHA1-3 : angle 1.10137 / 0.72 ( 6) link_ALPHA1-6 : bond 0.00349 / 0.24 ( 2) link_ALPHA1-6 : angle 1.75291 / 1.20 ( 6) link_BETA1-3 : bond 0.01236 / 0.82 ( 1) link_BETA1-3 : angle 2.66358 / 2.00 ( 3) link_BETA1-4 : bond 0.00524 / 0.36 ( 2) link_BETA1-4 : angle 2.10858 / 1.23 ( 6) link_NAG-ASN : bond 0.00953 / 0.55 ( 6) link_NAG-ASN : angle 3.77059 / 2.79 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8788 (tt0) cc_final: 0.8367 (tt0) REVERT: A 182 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.6075 (m-80) REVERT: A 196 TRP cc_start: 0.7928 (m100) cc_final: 0.7695 (m100) REVERT: A 222 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8048 (t80) REVERT: A 255 MET cc_start: 0.8646 (tpp) cc_final: 0.8146 (mtm) REVERT: A 751 MET cc_start: 0.8686 (tpp) cc_final: 0.8295 (tpp) REVERT: A 807 MET cc_start: 0.5399 (pp-130) cc_final: 0.5043 (pp-130) REVERT: A 830 MET cc_start: 0.7121 (mmm) cc_final: 0.6492 (mmm) REVERT: A 919 MET cc_start: 0.9365 (mtp) cc_final: 0.9135 (mtt) REVERT: A 969 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8172 (tt) REVERT: A 1530 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6949 (mmp) REVERT: B 24 GLN cc_start: 0.8299 (tt0) cc_final: 0.7983 (tt0) REVERT: C 53 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8492 (t) REVERT: C 131 ASN cc_start: 0.8815 (m-40) cc_final: 0.8317 (t0) REVERT: C 144 ILE cc_start: 0.9145 (mt) cc_final: 0.8825 (tt) outliers start: 39 outliers final: 22 residues processed: 214 average time/residue: 0.0858 time to fit residues: 27.4903 Evaluate side-chains 216 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 PHE Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1372 ASN Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1482 THR Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1548 LYS Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 53 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1768 ASN C 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.157713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.102578 restraints weight = 16972.976| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.49 r_work: 0.3035 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12544 Z= 0.152 Angle : 0.561 11.049 17011 Z= 0.281 Chirality : 0.042 0.376 1972 Planarity : 0.004 0.043 2037 Dihedral : 11.156 128.580 2218 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.40 % Allowed : 17.28 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1443 helix: 1.26 (0.18), residues: 890 sheet: -0.39 (0.59), residues: 72 loop : -0.25 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.022 0.002 TYR A 414 PHE 0.020 0.001 PHE A 189 TRP 0.009 0.001 TRP A 157 HIS 0.003 0.001 HIS A 918 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (12520) covalent geometry : angle 0.54157 / 0.28 (16950) SS BOND : bond 0.00343 / 0.20 ( 8) SS BOND : angle 0.88718 / 0.52 ( 16) hydrogen bonds : bond 0.03864 / 2.49 ( 708) hydrogen bonds : angle 4.11338 / 2.88 ( 1995) Misc. bond : bond 0.00006 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00390 / 0.26 ( 2) link_ALPHA1-2 : angle 2.23206 / 1.25 ( 6) link_ALPHA1-3 : bond 0.00896 / 0.61 ( 2) link_ALPHA1-3 : angle 1.10408 / 0.71 ( 6) link_ALPHA1-6 : bond 0.00192 / 0.13 ( 2) link_ALPHA1-6 : angle 1.78177 / 1.17 ( 6) link_BETA1-3 : bond 0.01209 / 0.81 ( 1) link_BETA1-3 : angle 2.80179 / 2.09 ( 3) link_BETA1-4 : bond 0.00514 / 0.35 ( 2) link_BETA1-4 : angle 2.30694 / 1.35 ( 6) link_NAG-ASN : bond 0.00930 / 0.53 ( 6) link_NAG-ASN : angle 3.73836 / 2.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8778 (tt0) cc_final: 0.8367 (tt0) REVERT: A 182 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.6163 (m-80) REVERT: A 196 TRP cc_start: 0.7996 (m100) cc_final: 0.7709 (m100) REVERT: A 222 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.8054 (t80) REVERT: A 255 MET cc_start: 0.8591 (tpp) cc_final: 0.8096 (mtm) REVERT: A 329 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8630 (m-30) REVERT: A 751 MET cc_start: 0.8684 (tpp) cc_final: 0.8304 (tpp) REVERT: A 807 MET cc_start: 0.5361 (pp-130) cc_final: 0.4978 (pp-130) REVERT: A 919 MET cc_start: 0.9357 (mtp) cc_final: 0.9122 (mtt) REVERT: A 969 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8206 (tt) REVERT: A 1440 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8961 (tpp) REVERT: B 24 GLN cc_start: 0.8406 (tt0) cc_final: 0.8089 (tt0) REVERT: C 53 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8532 (t) REVERT: C 72 ARG cc_start: 0.8177 (ttt180) cc_final: 0.7806 (ttt90) REVERT: C 131 ASN cc_start: 0.8833 (m-40) cc_final: 0.8319 (t0) REVERT: C 144 ILE cc_start: 0.9167 (mt) cc_final: 0.8858 (tt) REVERT: C 178 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8091 (mtm) outliers start: 44 outliers final: 28 residues processed: 215 average time/residue: 0.0865 time to fit residues: 27.8979 Evaluate side-chains 224 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 PHE Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1337 PHE Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1482 THR Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1548 LYS Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1645 MET Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 178 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 109 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.159044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103155 restraints weight = 16858.749| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.06 r_work: 0.3085 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12544 Z= 0.117 Angle : 0.544 10.703 17011 Z= 0.271 Chirality : 0.041 0.372 1972 Planarity : 0.003 0.044 2037 Dihedral : 10.616 128.962 2218 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.09 % Allowed : 17.36 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1443 helix: 1.39 (0.18), residues: 891 sheet: -0.25 (0.60), residues: 72 loop : -0.21 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.024 0.001 TYR C 32 PHE 0.020 0.001 PHE A 189 TRP 0.008 0.001 TRP A 157 HIS 0.002 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12520) covalent geometry : angle 0.52579 / 0.27 (16950) SS BOND : bond 0.00288 / 0.16 ( 8) SS BOND : angle 0.73670 / 0.41 ( 16) hydrogen bonds : bond 0.03615 / 2.33 ( 708) hydrogen bonds : angle 4.01250 / 2.81 ( 1995) Misc. bond : bond 0.00006 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00437 / 0.30 ( 2) link_ALPHA1-2 : angle 2.10480 / 1.18 ( 6) link_ALPHA1-3 : bond 0.00877 / 0.60 ( 2) link_ALPHA1-3 : angle 1.12928 / 0.71 ( 6) link_ALPHA1-6 : bond 0.00127 / 0.09 ( 2) link_ALPHA1-6 : angle 1.89208 / 1.17 ( 6) link_BETA1-3 : bond 0.01190 / 0.79 ( 1) link_BETA1-3 : angle 2.58729 / 1.95 ( 3) link_BETA1-4 : bond 0.00582 / 0.39 ( 2) link_BETA1-4 : angle 2.42649 / 1.45 ( 6) link_NAG-ASN : bond 0.01065 / 0.59 ( 6) link_NAG-ASN : angle 3.56024 / 2.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8772 (tt0) cc_final: 0.8352 (tt0) REVERT: A 182 PHE cc_start: 0.6397 (OUTLIER) cc_final: 0.6027 (m-80) REVERT: A 196 TRP cc_start: 0.7951 (m100) cc_final: 0.7718 (m100) REVERT: A 222 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7943 (t80) REVERT: A 255 MET cc_start: 0.8568 (tpp) cc_final: 0.8144 (mtm) REVERT: A 751 MET cc_start: 0.8689 (tpp) cc_final: 0.8301 (tpp) REVERT: A 807 MET cc_start: 0.5600 (pp-130) cc_final: 0.5176 (pp-130) REVERT: A 830 MET cc_start: 0.7241 (mmm) cc_final: 0.6584 (mmm) REVERT: A 919 MET cc_start: 0.9316 (mtp) cc_final: 0.9080 (mtt) REVERT: A 969 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8237 (tt) REVERT: B 24 GLN cc_start: 0.8439 (tt0) cc_final: 0.8131 (tt0) REVERT: C 53 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8461 (t) REVERT: C 131 ASN cc_start: 0.8760 (m-40) cc_final: 0.8295 (t0) REVERT: C 144 ILE cc_start: 0.9127 (mt) cc_final: 0.8831 (tt) REVERT: C 178 MET cc_start: 0.8290 (mtm) cc_final: 0.8016 (mtm) outliers start: 40 outliers final: 26 residues processed: 217 average time/residue: 0.0816 time to fit residues: 26.8354 Evaluate side-chains 216 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 PHE Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1337 PHE Chi-restraints excluded: chain A residue 1372 ASN Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1482 THR Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1548 LYS Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1645 MET Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN C 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.160162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103368 restraints weight = 16930.575| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.13 r_work: 0.3091 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12544 Z= 0.116 Angle : 0.552 11.610 17011 Z= 0.275 Chirality : 0.041 0.371 1972 Planarity : 0.004 0.044 2037 Dihedral : 10.387 127.892 2218 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.55 % Allowed : 18.13 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.23), residues: 1443 helix: 1.42 (0.18), residues: 892 sheet: -0.19 (0.59), residues: 72 loop : -0.18 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.023 0.001 TYR C 32 PHE 0.022 0.001 PHE A 189 TRP 0.008 0.001 TRP A 157 HIS 0.002 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12520) covalent geometry : angle 0.53380 / 0.27 (16950) SS BOND : bond 0.00283 / 0.16 ( 8) SS BOND : angle 0.76624 / 0.43 ( 16) hydrogen bonds : bond 0.03524 / 2.28 ( 708) hydrogen bonds : angle 3.97833 / 2.78 ( 1995) Misc. bond : bond 0.00006 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00429 / 0.29 ( 2) link_ALPHA1-2 : angle 2.03940 / 1.14 ( 6) link_ALPHA1-3 : bond 0.00776 / 0.54 ( 2) link_ALPHA1-3 : angle 1.21247 / 0.81 ( 6) link_ALPHA1-6 : bond 0.00110 / 0.08 ( 2) link_ALPHA1-6 : angle 1.95111 / 1.20 ( 6) link_BETA1-3 : bond 0.01154 / 0.77 ( 1) link_BETA1-3 : angle 2.58378 / 1.94 ( 3) link_BETA1-4 : bond 0.00523 / 0.36 ( 2) link_BETA1-4 : angle 2.52777 / 1.52 ( 6) link_NAG-ASN : bond 0.00953 / 0.54 ( 6) link_NAG-ASN : angle 3.52483 / 2.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8777 (tt0) cc_final: 0.8347 (tt0) REVERT: A 182 PHE cc_start: 0.6310 (OUTLIER) cc_final: 0.5959 (m-80) REVERT: A 196 TRP cc_start: 0.7939 (m100) cc_final: 0.7714 (m100) REVERT: A 220 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7705 (mmm160) REVERT: A 222 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7948 (t80) REVERT: A 751 MET cc_start: 0.8661 (tpp) cc_final: 0.8282 (tpp) REVERT: A 807 MET cc_start: 0.5586 (pp-130) cc_final: 0.5204 (pp-130) REVERT: A 830 MET cc_start: 0.6889 (mmm) cc_final: 0.6639 (mmm) REVERT: A 919 MET cc_start: 0.9331 (mtp) cc_final: 0.9084 (mtt) REVERT: B 24 GLN cc_start: 0.8310 (tt0) cc_final: 0.7990 (tt0) REVERT: C 53 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8500 (t) REVERT: C 131 ASN cc_start: 0.8782 (m-40) cc_final: 0.8295 (t0) REVERT: C 144 ILE cc_start: 0.9117 (mt) cc_final: 0.8809 (tt) REVERT: C 178 MET cc_start: 0.8361 (mtm) cc_final: 0.8100 (mtm) outliers start: 33 outliers final: 26 residues processed: 214 average time/residue: 0.0771 time to fit residues: 24.8988 Evaluate side-chains 215 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 980 PHE Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1337 PHE Chi-restraints excluded: chain A residue 1372 ASN Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1482 THR Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1548 LYS Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1645 MET Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 92 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 129 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN C 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.159306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103426 restraints weight = 16972.939| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.06 r_work: 0.3089 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12544 Z= 0.123 Angle : 0.558 12.160 17011 Z= 0.278 Chirality : 0.042 0.368 1972 Planarity : 0.004 0.043 2037 Dihedral : 10.331 127.393 2218 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.55 % Allowed : 18.29 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.23), residues: 1443 helix: 1.41 (0.18), residues: 892 sheet: -0.31 (0.58), residues: 77 loop : -0.18 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.024 0.001 TYR C 32 PHE 0.022 0.001 PHE A 189 TRP 0.008 0.001 TRP A 157 HIS 0.002 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (12520) covalent geometry : angle 0.54124 / 0.27 (16950) SS BOND : bond 0.00293 / 0.17 ( 8) SS BOND : angle 0.78295 / 0.44 ( 16) hydrogen bonds : bond 0.03567 / 2.30 ( 708) hydrogen bonds : angle 3.96893 / 2.78 ( 1995) Misc. bond : bond 0.00007 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00416 / 0.28 ( 2) link_ALPHA1-2 : angle 2.00493 / 1.12 ( 6) link_ALPHA1-3 : bond 0.00808 / 0.56 ( 2) link_ALPHA1-3 : angle 1.17837 / 0.77 ( 6) link_ALPHA1-6 : bond 0.00137 / 0.10 ( 2) link_ALPHA1-6 : angle 1.84743 / 1.13 ( 6) link_BETA1-3 : bond 0.01103 / 0.74 ( 1) link_BETA1-3 : angle 2.62906 / 1.97 ( 3) link_BETA1-4 : bond 0.00522 / 0.36 ( 2) link_BETA1-4 : angle 2.54122 / 1.53 ( 6) link_NAG-ASN : bond 0.00910 / 0.52 ( 6) link_NAG-ASN : angle 3.44235 / 2.52 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LYS cc_start: 0.8380 (pttp) cc_final: 0.7885 (pttm) REVERT: A 172 GLU cc_start: 0.8793 (tt0) cc_final: 0.8367 (tt0) REVERT: A 182 PHE cc_start: 0.6326 (OUTLIER) cc_final: 0.5984 (m-80) REVERT: A 196 TRP cc_start: 0.7966 (m100) cc_final: 0.7755 (m100) REVERT: A 220 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7693 (mmm160) REVERT: A 222 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7842 (t80) REVERT: A 255 MET cc_start: 0.8585 (tpp) cc_final: 0.8146 (mtm) REVERT: A 751 MET cc_start: 0.8545 (tpp) cc_final: 0.8175 (tpp) REVERT: A 807 MET cc_start: 0.5638 (pp-130) cc_final: 0.5239 (pp-130) REVERT: A 830 MET cc_start: 0.6917 (mmm) cc_final: 0.6642 (mmm) REVERT: A 919 MET cc_start: 0.9317 (mtp) cc_final: 0.9089 (mtt) REVERT: A 1332 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8758 (mm) REVERT: B 24 GLN cc_start: 0.8360 (tt0) cc_final: 0.8047 (tt0) REVERT: C 53 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8522 (t) REVERT: C 131 ASN cc_start: 0.8753 (m-40) cc_final: 0.8300 (t0) REVERT: C 144 ILE cc_start: 0.9137 (mt) cc_final: 0.8840 (tt) REVERT: C 178 MET cc_start: 0.8338 (mtm) cc_final: 0.8082 (mtm) outliers start: 33 outliers final: 26 residues processed: 215 average time/residue: 0.0844 time to fit residues: 27.3983 Evaluate side-chains 220 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 980 PHE Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1337 PHE Chi-restraints excluded: chain A residue 1372 ASN Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1482 THR Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1548 LYS Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1645 MET Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 129 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.159666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103906 restraints weight = 16832.280| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.05 r_work: 0.3097 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12544 Z= 0.117 Angle : 0.554 10.987 17011 Z= 0.276 Chirality : 0.042 0.365 1972 Planarity : 0.004 0.043 2037 Dihedral : 10.249 126.662 2218 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.24 % Allowed : 18.83 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.23), residues: 1443 helix: 1.45 (0.18), residues: 893 sheet: -0.11 (0.60), residues: 72 loop : -0.13 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 223 TYR 0.023 0.001 TYR C 32 PHE 0.021 0.001 PHE A 189 TRP 0.007 0.001 TRP A 157 HIS 0.002 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12520) covalent geometry : angle 0.53749 / 0.27 (16950) SS BOND : bond 0.00281 / 0.16 ( 8) SS BOND : angle 0.75680 / 0.42 ( 16) hydrogen bonds : bond 0.03496 / 2.26 ( 708) hydrogen bonds : angle 3.94937 / 2.76 ( 1995) Misc. bond : bond 0.00003 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00432 / 0.29 ( 2) link_ALPHA1-2 : angle 1.93840 / 1.09 ( 6) link_ALPHA1-3 : bond 0.00773 / 0.53 ( 2) link_ALPHA1-3 : angle 1.20674 / 0.80 ( 6) link_ALPHA1-6 : bond 0.00158 / 0.11 ( 2) link_ALPHA1-6 : angle 1.84922 / 1.13 ( 6) link_BETA1-3 : bond 0.01165 / 0.78 ( 1) link_BETA1-3 : angle 2.56532 / 1.92 ( 3) link_BETA1-4 : bond 0.00495 / 0.34 ( 2) link_BETA1-4 : angle 2.52918 / 1.52 ( 6) link_NAG-ASN : bond 0.00855 / 0.50 ( 6) link_NAG-ASN : angle 3.39181 / 2.49 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3460.04 seconds wall clock time: 59 minutes 29.35 seconds (3569.35 seconds total)