Starting phenix.real_space_refine on Sat Aug 23 14:23:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j8j_9782/08_2025/6j8j_9782_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j8j_9782/08_2025/6j8j_9782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6j8j_9782/08_2025/6j8j_9782_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j8j_9782/08_2025/6j8j_9782_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6j8j_9782/08_2025/6j8j_9782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j8j_9782/08_2025/6j8j_9782.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 966 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 7725 2.51 5 N 1857 2.21 5 O 2085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11764 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 980 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "A" Number of atoms: 9192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9192 Classifications: {'peptide': 1140} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 1108} Chain breaks: 3 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "D" 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: "E" 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {'9SR': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.04, per 1000 atoms: 0.26 Number of scatterers: 11764 At special positions: 0 Unit cell: (134.193, 139.648, 114.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 2085 8.00 N 1857 7.00 C 7725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.57 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS A 895 " distance=2.24 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.04 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 315 " distance=1.98 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.02 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=1.91 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=1.98 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.12 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.00 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2005 " - " ASN A1375 " " NAG A2006 " - " ASN A 283 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG B 304 " - " ASN B 135 " " NAG C 301 " - " ASN C 66 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 580.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 7 sheets defined 69.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'A' and resid 115 through 124 Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.804A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 176 removed outlier: 4.130A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 186 removed outlier: 4.516A pdb=" N ASP A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 204 removed outlier: 4.376A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 removed outlier: 3.838A pdb=" N THR A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.864A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 268 removed outlier: 3.770A pdb=" N LYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 280 through 284 removed outlier: 4.038A pdb=" N ASN A 283 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 284 " --> pdb=" O GLU A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 285 through 293 removed outlier: 3.937A pdb=" N ASN A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.886A pdb=" N TYR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.698A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 removed outlier: 3.895A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 417 removed outlier: 3.533A pdb=" N GLU A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.515A pdb=" N PHE A 733 " --> pdb=" O TYR A 729 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 734 " --> pdb=" O TRP A 730 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 763 removed outlier: 3.717A pdb=" N MET A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 806 removed outlier: 3.624A pdb=" N LEU A 795 " --> pdb=" O MET A 791 " (cutoff:3.500A) Proline residue: A 800 - end of helix removed outlier: 4.197A pdb=" N VAL A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 822 removed outlier: 3.700A pdb=" N LEU A 814 " --> pdb=" O ILE A 810 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 836 Processing helix chain 'A' and resid 837 through 847 removed outlier: 3.709A pdb=" N ARG A 841 " --> pdb=" O ARG A 838 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 842 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 845 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 864 removed outlier: 3.595A pdb=" N SER A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 896 removed outlier: 5.242A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 900 removed outlier: 3.907A pdb=" N ASN A 900 " --> pdb=" O CYS A 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 900' Processing helix chain 'A' and resid 912 through 925 removed outlier: 3.536A pdb=" N CYS A 925 " --> pdb=" O PHE A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 removed outlier: 4.412A pdb=" N THR A 931 " --> pdb=" O GLU A 927 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 972 Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 4.205A pdb=" N ASN A1180 " --> pdb=" O LYS A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1211 removed outlier: 3.984A pdb=" N LEU A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A1211 " --> pdb=" O GLY A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 4.200A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1255 removed outlier: 3.534A pdb=" N LYS A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A1232 " --> pdb=" O TYR A1228 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR A1252 " --> pdb=" O TYR A1248 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A1255 " --> pdb=" O LYS A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1284 through 1291 removed outlier: 3.706A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1298 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1299 through 1304 removed outlier: 4.172A pdb=" N ARG A1303 " --> pdb=" O ARG A1299 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A1304 " --> pdb=" O ALA A1300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1299 through 1304' Processing helix chain 'A' and resid 1304 through 1344 removed outlier: 3.520A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix removed outlier: 3.537A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 removed outlier: 3.640A pdb=" N ALA A1372 " --> pdb=" O SER A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1405 Processing helix chain 'A' and resid 1407 through 1418 removed outlier: 4.118A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A1414 " --> pdb=" O ILE A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1445 removed outlier: 3.671A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1467 Processing helix chain 'A' and resid 1475 through 1488 removed outlier: 3.764A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1514 removed outlier: 3.538A pdb=" N VAL A1512 " --> pdb=" O ILE A1508 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A1514 " --> pdb=" O ASP A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1534 removed outlier: 3.887A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A1532 " --> pdb=" O ASN A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1570 Processing helix chain 'A' and resid 1570 through 1576 removed outlier: 4.127A pdb=" N PHE A1574 " --> pdb=" O ARG A1570 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A1575 " --> pdb=" O HIS A1571 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A1576 " --> pdb=" O TYR A1572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1570 through 1576' Processing helix chain 'A' and resid 1576 through 1603 Processing helix chain 'A' and resid 1605 through 1614 removed outlier: 3.555A pdb=" N VAL A1611 " --> pdb=" O THR A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 4.073A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A1621 " --> pdb=" O ILE A1617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1616 through 1621' Processing helix chain 'A' and resid 1622 through 1627 removed outlier: 4.191A pdb=" N GLY A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1622 through 1627' Processing helix chain 'A' and resid 1627 through 1640 removed outlier: 3.539A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A1637 " --> pdb=" O LEU A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1667 removed outlier: 3.584A pdb=" N ALA A1667 " --> pdb=" O MET A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.137A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1709 removed outlier: 3.591A pdb=" N LEU A1703 " --> pdb=" O GLY A1699 " (cutoff:3.500A) Proline residue: A1706 - end of helix removed outlier: 4.013A pdb=" N ASN A1709 " --> pdb=" O ALA A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1732 through 1768 removed outlier: 3.500A pdb=" N ASN A1753 " --> pdb=" O LEU A1749 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 192 removed outlier: 3.504A pdb=" N TYR B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.114A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.302A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA5, first strand: chain 'A' and resid 1357 through 1358 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 5.800A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 138 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 68 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 41 716 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 3621 1.36 - 1.52: 6832 1.52 - 1.69: 1431 1.69 - 1.85: 155 1.85 - 2.01: 1 Bond restraints: 12040 Sorted by residual: bond pdb=" C13 9SR A2007 " pdb=" N14 9SR A2007 " ideal model delta sigma weight residual 1.281 1.499 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " ideal model delta sigma weight residual 1.808 2.008 -0.200 3.30e-02 9.18e+02 3.66e+01 bond pdb=" C CYS A 324 " pdb=" N PRO A 325 " ideal model delta sigma weight residual 1.332 1.404 -0.073 1.26e-02 6.30e+03 3.31e+01 bond pdb=" C GLN A1424 " pdb=" N PRO A1425 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.11e-02 8.12e+03 2.46e+01 bond pdb=" C03 9SR A2007 " pdb=" C21 9SR A2007 " ideal model delta sigma weight residual 1.528 1.626 -0.098 2.00e-02 2.50e+03 2.42e+01 ... (remaining 12035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 16007 4.61 - 9.22: 271 9.22 - 13.83: 34 13.83 - 18.43: 4 18.43 - 23.04: 1 Bond angle restraints: 16317 Sorted by residual: angle pdb=" N CYS A 925 " pdb=" CA CYS A 925 " pdb=" C CYS A 925 " ideal model delta sigma weight residual 110.55 94.30 16.25 1.35e+00 5.49e-01 1.45e+02 angle pdb=" N GLN A1378 " pdb=" CA GLN A1378 " pdb=" C GLN A1378 " ideal model delta sigma weight residual 111.36 124.11 -12.75 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N TRP A 928 " pdb=" CA TRP A 928 " pdb=" C TRP A 928 " ideal model delta sigma weight residual 111.28 122.43 -11.15 1.09e+00 8.42e-01 1.05e+02 angle pdb=" N LEU B 101 " pdb=" CA LEU B 101 " pdb=" C LEU B 101 " ideal model delta sigma weight residual 111.07 121.97 -10.90 1.07e+00 8.73e-01 1.04e+02 angle pdb=" N TYR A 304 " pdb=" CA TYR A 304 " pdb=" C TYR A 304 " ideal model delta sigma weight residual 111.07 120.56 -9.49 1.07e+00 8.73e-01 7.86e+01 ... (remaining 16312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5872 17.79 - 35.57: 806 35.57 - 53.36: 437 53.36 - 71.15: 169 71.15 - 88.94: 17 Dihedral angle restraints: 7301 sinusoidal: 3099 harmonic: 4202 Sorted by residual: dihedral pdb=" CB CYS B 21 " pdb=" SG CYS B 21 " pdb=" SG CYS B 43 " pdb=" CB CYS B 43 " ideal model delta sinusoidal sigma weight residual 93.00 -179.52 -87.48 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 935 " pdb=" SG CYS A 935 " pdb=" SG CYS A 944 " pdb=" CB CYS A 944 " ideal model delta sinusoidal sigma weight residual 93.00 179.51 -86.51 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CB CYS A1350 " pdb=" SG CYS A1350 " pdb=" SG CYS A1370 " pdb=" CB CYS A1370 " ideal model delta sinusoidal sigma weight residual -86.00 -150.21 64.21 1 1.00e+01 1.00e-02 5.42e+01 ... (remaining 7298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1693 0.152 - 0.303: 191 0.303 - 0.455: 17 0.455 - 0.606: 4 0.606 - 0.758: 2 Chirality restraints: 1907 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-02 2.50e+03 1.44e+03 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.91e+01 chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 110 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 1904 not shown) Planarity restraints: 1993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 110 " 0.212 2.00e-02 2.50e+03 2.52e-01 7.92e+02 pdb=" CG ASN B 110 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN B 110 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 110 " -0.418 2.00e-02 2.50e+03 pdb=" C1 NAG B 302 " 0.300 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 283 " 0.085 2.00e-02 2.50e+03 1.95e-01 4.75e+02 pdb=" CG ASN A 283 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 283 " 0.105 2.00e-02 2.50e+03 pdb=" ND2 ASN A 283 " -0.350 2.00e-02 2.50e+03 pdb=" C1 NAG A2006 " 0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 135 " -0.116 2.00e-02 2.50e+03 1.71e-01 3.64e+02 pdb=" CG ASN B 135 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN B 135 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN B 135 " 0.300 2.00e-02 2.50e+03 pdb=" C1 NAG B 304 " -0.192 2.00e-02 2.50e+03 ... (remaining 1990 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 148 2.44 - 3.06: 8878 3.06 - 3.67: 17026 3.67 - 4.29: 25840 4.29 - 4.90: 42266 Nonbonded interactions: 94158 Sorted by model distance: nonbonded pdb=" O ASP A1677 " pdb=" OD1 ASP A1677 " model vdw 1.829 3.040 nonbonded pdb=" O ILE A 899 " pdb=" ND2 ASN A 900 " model vdw 1.878 3.120 nonbonded pdb=" N GLN A1541 " pdb=" OE1 GLN A1541 " model vdw 1.886 3.120 nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 1.980 3.040 nonbonded pdb=" OE1 GLU B 87 " pdb=" N GLY B 88 " model vdw 2.013 3.120 ... (remaining 94153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } 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=0.41 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.810 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.012 0.540 12061 Z= 0.756 Angle : 1.876 55.391 16370 Z= 1.158 Chirality : 0.103 0.758 1907 Planarity : 0.009 0.185 1984 Dihedral : 21.778 88.937 4557 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 70.92 Ramachandran Plot: Outliers : 1.34 % Allowed : 2.46 % Favored : 96.20 % Rotamer: Outliers : 28.80 % Allowed : 19.25 % Favored : 51.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.21), residues: 1421 helix: 3.02 (0.16), residues: 797 sheet: 1.66 (0.45), residues: 126 loop : -0.11 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.022 0.002 TYR A 367 PHE 0.022 0.002 PHE B 54 TRP 0.016 0.002 TRP B 92 HIS 0.013 0.002 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.01020 (12040) covalent geometry : angle 1.51373 (16317) SS BOND : bond 0.19107 ( 10) SS BOND : angle 27.59347 ( 20) hydrogen bonds : bond 0.28061 ( 716) hydrogen bonds : angle 7.74120 ( 2079) link_BETA1-4 : bond 0.00154 ( 2) link_BETA1-4 : angle 5.52087 ( 6) link_NAG-ASN : bond 0.06477 ( 9) link_NAG-ASN : angle 13.35589 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 371 poor density : 319 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7414 (mp) REVERT: A 122 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7642 (mt) REVERT: A 166 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6482 (pt0) REVERT: A 206 ASN cc_start: 0.5210 (OUTLIER) cc_final: 0.4997 (p0) REVERT: A 220 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6950 (mtt90) REVERT: A 231 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7445 (mp) REVERT: A 243 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7724 (mptt) REVERT: A 255 CYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7408 (m) REVERT: A 293 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7417 (pt) REVERT: A 296 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6911 (tp30) REVERT: A 300 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7404 (mtt90) REVERT: A 356 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8094 (ttt180) REVERT: A 371 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8705 (mp) REVERT: A 379 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7779 (ttt) REVERT: A 415 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.4286 (mm-30) REVERT: A 761 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7173 (mtm) REVERT: A 765 HIS cc_start: 0.8414 (OUTLIER) cc_final: 0.7887 (m-70) REVERT: A 766 HIS cc_start: 0.6854 (OUTLIER) cc_final: 0.6111 (t-170) REVERT: A 839 LEU cc_start: 0.8632 (mm) cc_final: 0.8408 (mm) REVERT: A 857 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7069 (tttt) REVERT: A 1209 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8995 (mt) REVERT: A 1223 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8425 (ttpt) REVERT: A 1246 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7948 (mm) REVERT: A 1267 ASP cc_start: 0.8090 (m-30) cc_final: 0.7881 (m-30) REVERT: A 1278 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7321 (tp) REVERT: A 1322 MET cc_start: 0.8834 (mmm) cc_final: 0.8558 (mmt) REVERT: A 1358 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.5968 (mtm-85) REVERT: A 1423 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7628 (mmtp) REVERT: A 1449 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7999 (tp) REVERT: A 1504 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7530 (pt) REVERT: A 1537 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: A 1602 TYR cc_start: 0.7055 (m-10) cc_final: 0.6033 (t80) REVERT: A 1603 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7150 (m-80) REVERT: A 1670 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7806 (ttpp) REVERT: A 1711 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7208 (pttt) REVERT: A 1749 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8611 (mm) REVERT: A 1755 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.7188 (t80) REVERT: B 81 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6779 (tp30) REVERT: B 131 ASN cc_start: 0.6971 (OUTLIER) cc_final: 0.6705 (t0) REVERT: B 141 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8300 (mtpp) REVERT: B 190 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6591 (tp30) REVERT: B 191 THR cc_start: 0.4610 (OUTLIER) cc_final: 0.4112 (m) outliers start: 371 outliers final: 144 residues processed: 577 average time/residue: 0.1282 time to fit residues: 102.4183 Evaluate side-chains 406 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 225 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1217 GLU Chi-restraints excluded: chain A residue 1223 LYS Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1293 ARG Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1307 MET Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1409 THR Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1422 ASP Chi-restraints excluded: chain A residue 1423 LYS Chi-restraints excluded: chain A residue 1426 LYS Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1499 ARG Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1505 GLN Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1532 MET Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1550 ILE Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1601 THR Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1670 LYS Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 191 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 118 GLN C 126 ASN A 146 ASN A 154 ASN A 278 ASN A 282 ASN A 291 ASN A 360 GLN A 365 ASN A 395 ASN A 410 GLN A 757 ASN A 774 ASN A 909 HIS A 941 GLN A1191 HIS A1462 GLN A1505 GLN A1514 ASN ** A1528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1732 ASN A1762 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.161934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127461 restraints weight = 17589.117| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.26 r_work: 0.3376 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 12061 Z= 0.200 Angle : 0.850 12.078 16370 Z= 0.434 Chirality : 0.050 0.630 1907 Planarity : 0.005 0.081 1984 Dihedral : 15.214 99.551 2229 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.03 % Favored : 96.69 % Rotamer: Outliers : 12.89 % Allowed : 22.36 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.21), residues: 1421 helix: 2.34 (0.16), residues: 830 sheet: 1.10 (0.47), residues: 123 loop : -0.47 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 115 TYR 0.028 0.002 TYR A1755 PHE 0.052 0.002 PHE A 843 TRP 0.020 0.002 TRP A 363 HIS 0.007 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00429 (12040) covalent geometry : angle 0.81007 (16317) SS BOND : bond 0.00887 ( 10) SS BOND : angle 2.84752 ( 20) hydrogen bonds : bond 0.06964 ( 716) hydrogen bonds : angle 5.51042 ( 2079) link_BETA1-4 : bond 0.02616 ( 2) link_BETA1-4 : angle 4.42904 ( 6) link_NAG-ASN : bond 0.00767 ( 9) link_NAG-ASN : angle 5.55958 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 252 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 47 ARG cc_start: 0.5251 (ttt90) cc_final: 0.4727 (ttt90) REVERT: C 113 MET cc_start: 0.5704 (ppp) cc_final: 0.5257 (ttt) REVERT: C 148 MET cc_start: 0.3442 (mmm) cc_final: 0.2714 (tmm) REVERT: A 115 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7590 (mp) REVERT: A 192 ASP cc_start: 0.8688 (t0) cc_final: 0.8066 (m-30) REVERT: A 231 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7768 (mp) REVERT: A 243 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7666 (mptt) REVERT: A 290 MET cc_start: 0.7663 (mmp) cc_final: 0.7311 (mmp) REVERT: A 293 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7472 (pt) REVERT: A 294 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5696 (mt-10) REVERT: A 299 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7402 (t80) REVERT: A 300 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7457 (ttm-80) REVERT: A 318 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8130 (t) REVERT: A 766 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6836 (t-170) REVERT: A 791 MET cc_start: 0.8267 (ttp) cc_final: 0.7588 (tmm) REVERT: A 805 GLN cc_start: 0.6514 (tm130) cc_final: 0.5584 (mt0) REVERT: A 857 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6364 (ttpt) REVERT: A 900 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7596 (m-40) REVERT: A 1177 ILE cc_start: 0.8497 (mm) cc_final: 0.8056 (tp) REVERT: A 1182 ARG cc_start: 0.8441 (mtp85) cc_final: 0.5950 (tmt170) REVERT: A 1190 GLU cc_start: 0.7610 (pp20) cc_final: 0.7353 (pp20) REVERT: A 1209 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9010 (mt) REVERT: A 1267 ASP cc_start: 0.8732 (m-30) cc_final: 0.8488 (m-30) REVERT: A 1399 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8579 (mt) REVERT: A 1433 MET cc_start: 0.8456 (mmt) cc_final: 0.8241 (mmm) REVERT: A 1482 TYR cc_start: 0.8003 (t80) cc_final: 0.7792 (t80) REVERT: A 1504 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7769 (tp) REVERT: A 1505 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7740 (mm-40) REVERT: A 1522 MET cc_start: 0.8071 (tpp) cc_final: 0.7813 (tpp) REVERT: A 1602 TYR cc_start: 0.7098 (m-10) cc_final: 0.6170 (t80) REVERT: A 1603 PHE cc_start: 0.8038 (m-80) cc_final: 0.7257 (t80) REVERT: A 1711 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7367 (pttt) REVERT: A 1749 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8505 (mm) REVERT: B 65 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: B 131 ASN cc_start: 0.7204 (OUTLIER) cc_final: 0.6999 (t0) REVERT: B 178 MET cc_start: 0.7710 (mtm) cc_final: 0.7402 (ttt) REVERT: B 190 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6484 (tp30) REVERT: B 191 THR cc_start: 0.5901 (OUTLIER) cc_final: 0.5405 (m) outliers start: 166 outliers final: 86 residues processed: 373 average time/residue: 0.0920 time to fit residues: 50.0157 Evaluate side-chains 315 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 210 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1422 ASP Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1505 GLN Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1562 CYS Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 191 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 36 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 15 optimal weight: 0.0000 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1341 ASN A1378 GLN A1462 GLN ** A1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1528 ASN ** A1721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 143 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.158076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123413 restraints weight = 17626.458| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.33 r_work: 0.3318 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12061 Z= 0.197 Angle : 0.738 12.802 16370 Z= 0.378 Chirality : 0.046 0.539 1907 Planarity : 0.005 0.065 1984 Dihedral : 11.599 59.846 1996 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.31 % Favored : 96.48 % Rotamer: Outliers : 10.25 % Allowed : 23.45 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.22), residues: 1421 helix: 1.93 (0.17), residues: 839 sheet: 0.62 (0.47), residues: 124 loop : -0.63 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 46 TYR 0.028 0.002 TYR A 157 PHE 0.022 0.002 PHE B 54 TRP 0.019 0.002 TRP C 67 HIS 0.005 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00446 (12040) covalent geometry : angle 0.70852 (16317) SS BOND : bond 0.01219 ( 10) SS BOND : angle 2.11050 ( 20) hydrogen bonds : bond 0.05595 ( 716) hydrogen bonds : angle 5.12230 ( 2079) link_BETA1-4 : bond 0.01415 ( 2) link_BETA1-4 : angle 4.53051 ( 6) link_NAG-ASN : bond 0.00600 ( 9) link_NAG-ASN : angle 4.39196 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 228 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 47 ARG cc_start: 0.5473 (ttt90) cc_final: 0.5222 (ttt90) REVERT: C 70 GLN cc_start: 0.6237 (mt0) cc_final: 0.4929 (tt0) REVERT: C 148 MET cc_start: 0.3362 (mmm) cc_final: 0.2663 (tmm) REVERT: A 115 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7457 (mt) REVERT: A 122 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8093 (tp) REVERT: A 164 THR cc_start: 0.8424 (p) cc_final: 0.8206 (p) REVERT: A 192 ASP cc_start: 0.8804 (t0) cc_final: 0.8083 (m-30) REVERT: A 217 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7914 (ptp90) REVERT: A 243 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7778 (mptt) REVERT: A 249 MET cc_start: 0.7345 (mtm) cc_final: 0.7144 (mtm) REVERT: A 294 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5697 (mt-10) REVERT: A 300 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7606 (ttm-80) REVERT: A 318 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8051 (t) REVERT: A 354 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8753 (mm) REVERT: A 738 TYR cc_start: 0.6535 (OUTLIER) cc_final: 0.6175 (m-80) REVERT: A 742 MET cc_start: 0.4165 (mtt) cc_final: 0.3834 (ttm) REVERT: A 766 HIS cc_start: 0.7553 (OUTLIER) cc_final: 0.7326 (t-170) REVERT: A 791 MET cc_start: 0.8216 (ttp) cc_final: 0.7584 (tmm) REVERT: A 823 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6639 (tp) REVERT: A 845 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7622 (mp) REVERT: A 900 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7626 (m-40) REVERT: A 1177 ILE cc_start: 0.8550 (mm) cc_final: 0.8075 (tp) REVERT: A 1183 LYS cc_start: 0.8294 (ptpt) cc_final: 0.7909 (ptpt) REVERT: A 1399 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8427 (mt) REVERT: A 1505 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7742 (mm-40) REVERT: A 1522 MET cc_start: 0.8088 (tpp) cc_final: 0.7693 (mmp) REVERT: A 1602 TYR cc_start: 0.7105 (m-10) cc_final: 0.6248 (t80) REVERT: A 1603 PHE cc_start: 0.8069 (m-80) cc_final: 0.7403 (t80) REVERT: A 1634 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8819 (mm) REVERT: A 1711 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7576 (pttt) REVERT: B 65 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: B 131 ASN cc_start: 0.7374 (OUTLIER) cc_final: 0.7156 (t0) REVERT: B 190 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6459 (tp30) REVERT: B 191 THR cc_start: 0.5673 (OUTLIER) cc_final: 0.5224 (m) outliers start: 132 outliers final: 72 residues processed: 317 average time/residue: 0.0960 time to fit residues: 44.2591 Evaluate side-chains 299 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 208 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1505 GLN Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 191 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 13 optimal weight: 0.0270 chunk 45 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 30.0000 chunk 85 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.154772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119134 restraints weight = 17528.770| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.62 r_work: 0.3211 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12061 Z= 0.179 Angle : 0.685 11.382 16370 Z= 0.347 Chirality : 0.045 0.491 1907 Planarity : 0.004 0.052 1984 Dihedral : 10.147 59.890 1940 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.52 % Favored : 96.27 % Rotamer: Outliers : 9.32 % Allowed : 24.07 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.22), residues: 1421 helix: 1.89 (0.17), residues: 845 sheet: 0.40 (0.47), residues: 124 loop : -0.79 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 115 TYR 0.025 0.002 TYR A 157 PHE 0.022 0.002 PHE B 54 TRP 0.014 0.002 TRP A1382 HIS 0.004 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00409 (12040) covalent geometry : angle 0.65817 (16317) SS BOND : bond 0.00481 ( 10) SS BOND : angle 1.80011 ( 20) hydrogen bonds : bond 0.05099 ( 716) hydrogen bonds : angle 4.95657 ( 2079) link_BETA1-4 : bond 0.01253 ( 2) link_BETA1-4 : angle 4.10275 ( 6) link_NAG-ASN : bond 0.00562 ( 9) link_NAG-ASN : angle 4.10365 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 228 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 47 ARG cc_start: 0.5268 (ttt90) cc_final: 0.4706 (ttt90) REVERT: C 70 GLN cc_start: 0.6360 (mt0) cc_final: 0.5414 (tt0) REVERT: C 113 MET cc_start: 0.5838 (ppp) cc_final: 0.5522 (ttt) REVERT: C 148 MET cc_start: 0.3161 (mmm) cc_final: 0.2533 (tmm) REVERT: A 145 MET cc_start: 0.8409 (tpp) cc_final: 0.7924 (mpp) REVERT: A 192 ASP cc_start: 0.8870 (t0) cc_final: 0.8077 (m-30) REVERT: A 243 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7592 (mptt) REVERT: A 244 LYS cc_start: 0.8485 (mptt) cc_final: 0.8221 (mptt) REVERT: A 294 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5658 (mt-10) REVERT: A 300 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7475 (mtp85) REVERT: A 354 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8683 (mm) REVERT: A 738 TYR cc_start: 0.6230 (OUTLIER) cc_final: 0.5902 (m-80) REVERT: A 742 MET cc_start: 0.3698 (mtt) cc_final: 0.3318 (ttm) REVERT: A 766 HIS cc_start: 0.7245 (OUTLIER) cc_final: 0.7019 (t-170) REVERT: A 791 MET cc_start: 0.7996 (ttp) cc_final: 0.7407 (tmm) REVERT: A 845 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7689 (mp) REVERT: A 900 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7571 (m-40) REVERT: A 1177 ILE cc_start: 0.8432 (mm) cc_final: 0.7953 (tp) REVERT: A 1182 ARG cc_start: 0.8632 (mmm160) cc_final: 0.8372 (mtp-110) REVERT: A 1183 LYS cc_start: 0.8136 (ptpt) cc_final: 0.7710 (ptpt) REVERT: A 1262 ASP cc_start: 0.8318 (m-30) cc_final: 0.8078 (m-30) REVERT: A 1399 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 1505 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7878 (mm-40) REVERT: A 1522 MET cc_start: 0.8034 (tpp) cc_final: 0.7660 (mmp) REVERT: A 1543 MET cc_start: 0.8990 (tpt) cc_final: 0.8637 (tpt) REVERT: A 1602 TYR cc_start: 0.7008 (m-10) cc_final: 0.6212 (t80) REVERT: A 1603 PHE cc_start: 0.7793 (m-80) cc_final: 0.7347 (t80) REVERT: A 1634 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8729 (mm) REVERT: A 1711 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7696 (pttt) REVERT: B 65 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7440 (pt0) REVERT: B 96 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8010 (mpp80) REVERT: B 131 ASN cc_start: 0.7337 (OUTLIER) cc_final: 0.7101 (t0) REVERT: B 184 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7454 (mtmt) REVERT: B 190 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6509 (tp30) REVERT: B 191 THR cc_start: 0.5737 (OUTLIER) cc_final: 0.5352 (m) outliers start: 120 outliers final: 71 residues processed: 308 average time/residue: 0.0978 time to fit residues: 44.6625 Evaluate side-chains 300 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 213 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1505 GLN Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1639 MET Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 191 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 106 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 117 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 0.0060 chunk 135 optimal weight: 6.9990 chunk 53 optimal weight: 0.3980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.157344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114975 restraints weight = 17562.296| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.21 r_work: 0.3288 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12061 Z= 0.130 Angle : 0.641 10.933 16370 Z= 0.320 Chirality : 0.042 0.387 1907 Planarity : 0.004 0.043 1984 Dihedral : 9.166 59.938 1916 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 7.22 % Allowed : 24.61 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.22), residues: 1421 helix: 2.00 (0.17), residues: 853 sheet: 0.36 (0.47), residues: 124 loop : -0.73 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.028 0.001 TYR A 157 PHE 0.023 0.001 PHE A1509 TRP 0.014 0.001 TRP A1382 HIS 0.004 0.001 HIS A1721 Details of bonding type rmsd covalent geometry : bond 0.00268 (12040) covalent geometry : angle 0.61612 (16317) SS BOND : bond 0.00373 ( 10) SS BOND : angle 2.08376 ( 20) hydrogen bonds : bond 0.04444 ( 716) hydrogen bonds : angle 4.71014 ( 2079) link_BETA1-4 : bond 0.01201 ( 2) link_BETA1-4 : angle 3.68211 ( 6) link_NAG-ASN : bond 0.00594 ( 9) link_NAG-ASN : angle 3.65303 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 231 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 47 ARG cc_start: 0.5424 (ttt90) cc_final: 0.4891 (ttt90) REVERT: C 70 GLN cc_start: 0.6342 (mt0) cc_final: 0.5164 (tt0) REVERT: C 148 MET cc_start: 0.3132 (mmm) cc_final: 0.2478 (tmm) REVERT: A 145 MET cc_start: 0.8440 (tpp) cc_final: 0.7939 (mpp) REVERT: A 243 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7541 (mptt) REVERT: A 244 LYS cc_start: 0.8549 (mptt) cc_final: 0.8255 (mptt) REVERT: A 300 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7511 (ttm-80) REVERT: A 354 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8613 (mm) REVERT: A 358 MET cc_start: 0.8966 (tmm) cc_final: 0.8298 (ttt) REVERT: A 738 TYR cc_start: 0.6036 (OUTLIER) cc_final: 0.5728 (m-80) REVERT: A 791 MET cc_start: 0.7883 (ttp) cc_final: 0.7426 (tmm) REVERT: A 845 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7564 (mp) REVERT: A 900 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7644 (m-40) REVERT: A 1177 ILE cc_start: 0.8544 (mm) cc_final: 0.8072 (tp) REVERT: A 1182 ARG cc_start: 0.8617 (mmm160) cc_final: 0.5914 (ttt-90) REVERT: A 1183 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7772 (ptpt) REVERT: A 1262 ASP cc_start: 0.8349 (m-30) cc_final: 0.8068 (m-30) REVERT: A 1514 ASN cc_start: 0.7378 (OUTLIER) cc_final: 0.6207 (m110) REVERT: A 1522 MET cc_start: 0.8090 (tpp) cc_final: 0.7782 (mmp) REVERT: A 1602 TYR cc_start: 0.6895 (m-10) cc_final: 0.5990 (t80) REVERT: A 1603 PHE cc_start: 0.7796 (m-80) cc_final: 0.7424 (t80) REVERT: A 1634 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8647 (mm) REVERT: A 1711 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7754 (pttt) REVERT: A 1719 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7556 (tttm) REVERT: B 65 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7476 (pt0) REVERT: B 96 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8197 (mpp80) REVERT: B 131 ASN cc_start: 0.7386 (t0) cc_final: 0.7125 (t0) REVERT: B 184 LYS cc_start: 0.7606 (mtmm) cc_final: 0.7182 (mtmm) REVERT: B 190 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6477 (tp30) outliers start: 93 outliers final: 48 residues processed: 296 average time/residue: 0.1120 time to fit residues: 47.9982 Evaluate side-chains 273 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 88 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 ASN A1709 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.149799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106958 restraints weight = 17671.377| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.19 r_work: 0.3168 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 12061 Z= 0.321 Angle : 0.794 12.130 16370 Z= 0.402 Chirality : 0.050 0.583 1907 Planarity : 0.005 0.046 1984 Dihedral : 9.014 59.723 1896 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 9.24 % Allowed : 23.29 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.21), residues: 1421 helix: 1.51 (0.17), residues: 848 sheet: -0.03 (0.44), residues: 124 loop : -1.20 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 277 TYR 0.028 0.003 TYR A1739 PHE 0.022 0.003 PHE B 54 TRP 0.013 0.002 TRP C 67 HIS 0.009 0.002 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00763 (12040) covalent geometry : angle 0.76607 (16317) SS BOND : bond 0.00834 ( 10) SS BOND : angle 2.71907 ( 20) hydrogen bonds : bond 0.05622 ( 716) hydrogen bonds : angle 5.12119 ( 2079) link_BETA1-4 : bond 0.01870 ( 2) link_BETA1-4 : angle 4.68986 ( 6) link_NAG-ASN : bond 0.00466 ( 9) link_NAG-ASN : angle 4.16935 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 203 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 47 ARG cc_start: 0.5414 (ttt90) cc_final: 0.5155 (ttt90) REVERT: C 113 MET cc_start: 0.5729 (ttp) cc_final: 0.4699 (ppp) REVERT: C 148 MET cc_start: 0.3467 (mmm) cc_final: 0.2896 (tmm) REVERT: A 122 ILE cc_start: 0.8551 (tp) cc_final: 0.8309 (tp) REVERT: A 125 HIS cc_start: 0.6645 (t-90) cc_final: 0.6320 (t-90) REVERT: A 145 MET cc_start: 0.8663 (tpp) cc_final: 0.8224 (mpp) REVERT: A 222 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.8952 (tt) REVERT: A 243 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7697 (mptt) REVERT: A 244 LYS cc_start: 0.8634 (mptt) cc_final: 0.8295 (mptt) REVERT: A 300 ARG cc_start: 0.8054 (ttm-80) cc_final: 0.7738 (ttm-80) REVERT: A 354 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8791 (mm) REVERT: A 357 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8501 (mt) REVERT: A 358 MET cc_start: 0.9030 (tmm) cc_final: 0.8494 (ttt) REVERT: A 738 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.5823 (m-80) REVERT: A 791 MET cc_start: 0.7985 (ttp) cc_final: 0.7536 (tmm) REVERT: A 845 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7721 (mp) REVERT: A 900 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7843 (m-40) REVERT: A 968 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7097 (mp) REVERT: A 1177 ILE cc_start: 0.8574 (mm) cc_final: 0.8065 (tp) REVERT: A 1399 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8425 (mt) REVERT: A 1514 ASN cc_start: 0.7330 (OUTLIER) cc_final: 0.6295 (m110) REVERT: A 1522 MET cc_start: 0.8183 (tpp) cc_final: 0.7938 (tpp) REVERT: A 1602 TYR cc_start: 0.6904 (m-10) cc_final: 0.6021 (t80) REVERT: A 1603 PHE cc_start: 0.7822 (m-80) cc_final: 0.7431 (t80) REVERT: A 1634 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8774 (mm) REVERT: A 1637 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8766 (tp) REVERT: A 1711 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7839 (pttt) REVERT: A 1719 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7731 (tttm) REVERT: B 65 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7530 (pt0) REVERT: B 96 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7732 (mpp80) REVERT: B 131 ASN cc_start: 0.7668 (t0) cc_final: 0.7424 (t0) REVERT: B 184 LYS cc_start: 0.7736 (mtmm) cc_final: 0.7482 (mtpp) REVERT: B 190 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6483 (tp30) outliers start: 119 outliers final: 69 residues processed: 294 average time/residue: 0.1046 time to fit residues: 45.0731 Evaluate side-chains 282 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 196 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1601 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1707 ILE Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1764 SER Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 47 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 92 optimal weight: 0.0980 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 85 optimal weight: 0.0970 chunk 111 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 911 ASN B 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.155138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119026 restraints weight = 17296.948| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.40 r_work: 0.3233 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12061 Z= 0.138 Angle : 0.661 10.547 16370 Z= 0.332 Chirality : 0.042 0.395 1907 Planarity : 0.004 0.038 1984 Dihedral : 8.490 59.815 1892 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.80 % Favored : 95.99 % Rotamer: Outliers : 6.44 % Allowed : 25.62 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.22), residues: 1421 helix: 1.89 (0.17), residues: 850 sheet: 0.03 (0.45), residues: 124 loop : -1.02 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 838 TYR 0.028 0.001 TYR A 157 PHE 0.020 0.001 PHE B 54 TRP 0.015 0.001 TRP A1382 HIS 0.003 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00290 (12040) covalent geometry : angle 0.63855 (16317) SS BOND : bond 0.00337 ( 10) SS BOND : angle 1.84418 ( 20) hydrogen bonds : bond 0.04513 ( 716) hydrogen bonds : angle 4.73580 ( 2079) link_BETA1-4 : bond 0.01285 ( 2) link_BETA1-4 : angle 3.72457 ( 6) link_NAG-ASN : bond 0.00631 ( 9) link_NAG-ASN : angle 3.60684 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 224 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.4648 (ppp) REVERT: C 148 MET cc_start: 0.3403 (mmm) cc_final: 0.2951 (tmm) REVERT: A 125 HIS cc_start: 0.6621 (t-90) cc_final: 0.6365 (t-90) REVERT: A 145 MET cc_start: 0.8704 (tpp) cc_final: 0.8226 (mpp) REVERT: A 169 VAL cc_start: 0.8054 (p) cc_final: 0.7852 (p) REVERT: A 222 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.8700 (tt) REVERT: A 243 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7656 (mptt) REVERT: A 244 LYS cc_start: 0.8641 (mptt) cc_final: 0.8360 (mptt) REVERT: A 300 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7632 (ttm-80) REVERT: A 357 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8449 (mt) REVERT: A 407 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7846 (tt0) REVERT: A 738 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5742 (m-80) REVERT: A 760 PHE cc_start: 0.8658 (t80) cc_final: 0.8257 (t80) REVERT: A 791 MET cc_start: 0.7966 (ttp) cc_final: 0.7502 (tmm) REVERT: A 845 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7543 (mp) REVERT: A 900 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7621 (m-40) REVERT: A 1177 ILE cc_start: 0.8579 (mm) cc_final: 0.8139 (tp) REVERT: A 1182 ARG cc_start: 0.8692 (mmm160) cc_final: 0.5836 (ttt-90) REVERT: A 1262 ASP cc_start: 0.8465 (m-30) cc_final: 0.8150 (m-30) REVERT: A 1399 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8315 (mt) REVERT: A 1514 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.6366 (m110) REVERT: A 1522 MET cc_start: 0.8170 (tpp) cc_final: 0.7830 (mmp) REVERT: A 1543 MET cc_start: 0.9045 (tpt) cc_final: 0.8827 (tpt) REVERT: A 1602 TYR cc_start: 0.6887 (m-10) cc_final: 0.5877 (t80) REVERT: A 1603 PHE cc_start: 0.7873 (m-80) cc_final: 0.7442 (t80) REVERT: A 1634 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8688 (mm) REVERT: A 1637 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8625 (tp) REVERT: A 1711 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7940 (pttt) REVERT: A 1719 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7586 (tttm) REVERT: A 1739 TYR cc_start: 0.8726 (t80) cc_final: 0.8138 (t80) REVERT: B 65 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7467 (pt0) REVERT: B 96 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8128 (mpp80) REVERT: B 131 ASN cc_start: 0.7519 (t0) cc_final: 0.7290 (t0) REVERT: B 190 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6660 (tp30) outliers start: 83 outliers final: 51 residues processed: 282 average time/residue: 0.0995 time to fit residues: 41.1792 Evaluate side-chains 283 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 217 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 132 optimal weight: 0.0980 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.152702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109957 restraints weight = 17579.042| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.18 r_work: 0.3215 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12061 Z= 0.199 Angle : 0.691 10.111 16370 Z= 0.348 Chirality : 0.045 0.464 1907 Planarity : 0.004 0.035 1984 Dihedral : 8.290 59.772 1888 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.08 % Favored : 95.71 % Rotamer: Outliers : 6.44 % Allowed : 25.62 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.22), residues: 1421 helix: 1.78 (0.17), residues: 850 sheet: -0.10 (0.45), residues: 124 loop : -1.15 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 838 TYR 0.026 0.002 TYR A 157 PHE 0.020 0.002 PHE B 54 TRP 0.023 0.001 TRP A 190 HIS 0.005 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00466 (12040) covalent geometry : angle 0.66815 (16317) SS BOND : bond 0.00325 ( 10) SS BOND : angle 1.97338 ( 20) hydrogen bonds : bond 0.04771 ( 716) hydrogen bonds : angle 4.84046 ( 2079) link_BETA1-4 : bond 0.01291 ( 2) link_BETA1-4 : angle 3.99822 ( 6) link_NAG-ASN : bond 0.00531 ( 9) link_NAG-ASN : angle 3.60294 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 216 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 70 GLN cc_start: 0.6000 (mt0) cc_final: 0.5262 (tt0) REVERT: C 113 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.4696 (ppp) REVERT: C 148 MET cc_start: 0.3452 (mmm) cc_final: 0.2999 (tmm) REVERT: A 145 MET cc_start: 0.8724 (tpp) cc_final: 0.8226 (mpp) REVERT: A 166 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7115 (pp20) REVERT: A 190 TRP cc_start: 0.7636 (m-90) cc_final: 0.6872 (m-90) REVERT: A 222 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.8677 (tt) REVERT: A 243 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7670 (mptt) REVERT: A 244 LYS cc_start: 0.8606 (mptt) cc_final: 0.8288 (mptt) REVERT: A 300 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7751 (ttm-80) REVERT: A 357 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8486 (mt) REVERT: A 358 MET cc_start: 0.9000 (tmm) cc_final: 0.8405 (ttt) REVERT: A 407 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7774 (tt0) REVERT: A 738 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.5772 (m-80) REVERT: A 760 PHE cc_start: 0.8678 (t80) cc_final: 0.8278 (t80) REVERT: A 791 MET cc_start: 0.7936 (ttp) cc_final: 0.7504 (tmm) REVERT: A 845 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7595 (mp) REVERT: A 900 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7709 (m-40) REVERT: A 968 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7109 (mp) REVERT: A 1177 ILE cc_start: 0.8579 (mm) cc_final: 0.8120 (tp) REVERT: A 1182 ARG cc_start: 0.8706 (mmm160) cc_final: 0.8391 (mtp-110) REVERT: A 1188 ILE cc_start: 0.9160 (mm) cc_final: 0.8886 (mt) REVERT: A 1223 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8058 (ttpt) REVERT: A 1262 ASP cc_start: 0.8509 (m-30) cc_final: 0.8278 (m-30) REVERT: A 1399 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8343 (mt) REVERT: A 1491 LYS cc_start: 0.7350 (pptt) cc_final: 0.6964 (pptt) REVERT: A 1514 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.6379 (m110) REVERT: A 1522 MET cc_start: 0.8137 (tpp) cc_final: 0.7798 (mmp) REVERT: A 1543 MET cc_start: 0.9005 (tpt) cc_final: 0.8798 (tpt) REVERT: A 1602 TYR cc_start: 0.6595 (m-10) cc_final: 0.5780 (t80) REVERT: A 1603 PHE cc_start: 0.7806 (m-80) cc_final: 0.7356 (t80) REVERT: A 1634 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8642 (mm) REVERT: A 1637 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8663 (tp) REVERT: A 1711 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7909 (pttt) REVERT: A 1719 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7679 (tttm) REVERT: A 1739 TYR cc_start: 0.8757 (t80) cc_final: 0.8207 (t80) REVERT: B 65 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: B 96 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7947 (mpp80) REVERT: B 131 ASN cc_start: 0.7600 (t0) cc_final: 0.7364 (t0) REVERT: B 184 LYS cc_start: 0.7971 (mtpp) cc_final: 0.7752 (mttm) REVERT: B 190 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6677 (tp30) outliers start: 83 outliers final: 55 residues processed: 274 average time/residue: 0.1012 time to fit residues: 40.6998 Evaluate side-chains 284 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 211 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1201 MET Chi-restraints excluded: chain A residue 1223 LYS Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 23 optimal weight: 0.0870 chunk 86 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.155394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119499 restraints weight = 17422.832| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.42 r_work: 0.3240 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12061 Z= 0.133 Angle : 0.646 10.109 16370 Z= 0.320 Chirality : 0.042 0.379 1907 Planarity : 0.003 0.038 1984 Dihedral : 7.998 59.619 1887 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.08 % Favored : 95.71 % Rotamer: Outliers : 5.90 % Allowed : 26.16 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.22), residues: 1421 helix: 1.90 (0.17), residues: 857 sheet: -0.06 (0.45), residues: 124 loop : -1.11 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 838 TYR 0.029 0.001 TYR A 157 PHE 0.054 0.001 PHE A 843 TRP 0.019 0.001 TRP A 190 HIS 0.003 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00287 (12040) covalent geometry : angle 0.62560 (16317) SS BOND : bond 0.00323 ( 10) SS BOND : angle 1.66205 ( 20) hydrogen bonds : bond 0.04291 ( 716) hydrogen bonds : angle 4.68826 ( 2079) link_BETA1-4 : bond 0.01200 ( 2) link_BETA1-4 : angle 3.63502 ( 6) link_NAG-ASN : bond 0.00569 ( 9) link_NAG-ASN : angle 3.33865 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 214 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASN cc_start: 0.5458 (t0) cc_final: 0.4784 (t0) REVERT: C 113 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.4693 (ppp) REVERT: C 148 MET cc_start: 0.3157 (mmm) cc_final: 0.2903 (tmm) REVERT: A 133 MET cc_start: 0.7757 (ttt) cc_final: 0.7551 (ttp) REVERT: A 166 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7237 (pp20) REVERT: A 190 TRP cc_start: 0.7548 (m-90) cc_final: 0.6866 (m-90) REVERT: A 192 ASP cc_start: 0.8967 (t0) cc_final: 0.8088 (m-30) REVERT: A 222 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8657 (tt) REVERT: A 243 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7668 (mptt) REVERT: A 244 LYS cc_start: 0.8635 (mptt) cc_final: 0.8316 (mptt) REVERT: A 300 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7690 (ttm-80) REVERT: A 357 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8444 (mt) REVERT: A 358 MET cc_start: 0.8998 (tmm) cc_final: 0.8409 (ttt) REVERT: A 364 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: A 407 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7759 (tt0) REVERT: A 738 TYR cc_start: 0.6079 (OUTLIER) cc_final: 0.5735 (m-80) REVERT: A 760 PHE cc_start: 0.8575 (t80) cc_final: 0.8289 (t80) REVERT: A 791 MET cc_start: 0.7924 (ttp) cc_final: 0.7299 (ttt) REVERT: A 845 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7377 (mp) REVERT: A 900 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7630 (m-40) REVERT: A 1177 ILE cc_start: 0.8532 (mm) cc_final: 0.8103 (tp) REVERT: A 1182 ARG cc_start: 0.8698 (mmm160) cc_final: 0.5895 (ttt-90) REVERT: A 1188 ILE cc_start: 0.9167 (mm) cc_final: 0.8876 (mt) REVERT: A 1262 ASP cc_start: 0.8459 (m-30) cc_final: 0.8151 (m-30) REVERT: A 1399 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8336 (mt) REVERT: A 1491 LYS cc_start: 0.7489 (pptt) cc_final: 0.7135 (ptpp) REVERT: A 1514 ASN cc_start: 0.7287 (OUTLIER) cc_final: 0.6314 (m110) REVERT: A 1522 MET cc_start: 0.8103 (tpp) cc_final: 0.7775 (mmp) REVERT: A 1602 TYR cc_start: 0.6510 (m-10) cc_final: 0.5747 (t80) REVERT: A 1603 PHE cc_start: 0.7750 (m-80) cc_final: 0.7366 (t80) REVERT: A 1634 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8673 (mm) REVERT: A 1637 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8608 (tp) REVERT: A 1691 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8801 (mm) REVERT: A 1711 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7927 (pttt) REVERT: A 1719 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7642 (tttm) REVERT: B 65 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: B 96 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8121 (mpp80) REVERT: B 131 ASN cc_start: 0.7480 (t0) cc_final: 0.7230 (t0) REVERT: B 184 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7581 (mtmt) REVERT: B 190 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6647 (tp30) outliers start: 76 outliers final: 50 residues processed: 267 average time/residue: 0.1051 time to fit residues: 40.9929 Evaluate side-chains 280 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1663 MET Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1764 SER Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 122 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118387 restraints weight = 17586.036| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.40 r_work: 0.3229 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12061 Z= 0.151 Angle : 0.655 10.050 16370 Z= 0.326 Chirality : 0.043 0.403 1907 Planarity : 0.003 0.037 1984 Dihedral : 7.903 59.412 1886 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.08 % Favored : 95.78 % Rotamer: Outliers : 5.51 % Allowed : 26.63 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.22), residues: 1421 helix: 1.88 (0.17), residues: 858 sheet: -0.30 (0.43), residues: 134 loop : -1.09 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 838 TYR 0.028 0.002 TYR A 157 PHE 0.019 0.001 PHE B 54 TRP 0.015 0.001 TRP A 190 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00342 (12040) covalent geometry : angle 0.63483 (16317) SS BOND : bond 0.00344 ( 10) SS BOND : angle 1.96896 ( 20) hydrogen bonds : bond 0.04359 ( 716) hydrogen bonds : angle 4.71322 ( 2079) link_BETA1-4 : bond 0.01268 ( 2) link_BETA1-4 : angle 3.76085 ( 6) link_NAG-ASN : bond 0.00537 ( 9) link_NAG-ASN : angle 3.29321 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 211 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASN cc_start: 0.5433 (t0) cc_final: 0.4844 (t0) REVERT: C 113 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.4720 (ppp) REVERT: C 148 MET cc_start: 0.3160 (mmm) cc_final: 0.2899 (tmm) REVERT: A 145 MET cc_start: 0.8724 (tpp) cc_final: 0.8207 (mpp) REVERT: A 166 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7105 (pp20) REVERT: A 243 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7672 (mptt) REVERT: A 244 LYS cc_start: 0.8659 (mptt) cc_final: 0.8371 (mptt) REVERT: A 300 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: A 357 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8434 (mt) REVERT: A 358 MET cc_start: 0.9004 (tmm) cc_final: 0.8459 (ttt) REVERT: A 364 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: A 407 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7781 (tt0) REVERT: A 738 TYR cc_start: 0.6214 (OUTLIER) cc_final: 0.5870 (m-80) REVERT: A 742 MET cc_start: 0.3658 (mtt) cc_final: 0.3338 (mtp) REVERT: A 760 PHE cc_start: 0.8551 (t80) cc_final: 0.8215 (t80) REVERT: A 791 MET cc_start: 0.7880 (ttp) cc_final: 0.7289 (ttt) REVERT: A 845 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7300 (mp) REVERT: A 900 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7724 (m-40) REVERT: A 1177 ILE cc_start: 0.8560 (mm) cc_final: 0.8147 (tp) REVERT: A 1182 ARG cc_start: 0.8689 (mmm160) cc_final: 0.8410 (mtp-110) REVERT: A 1188 ILE cc_start: 0.9181 (mm) cc_final: 0.8894 (mt) REVERT: A 1262 ASP cc_start: 0.8474 (m-30) cc_final: 0.8151 (m-30) REVERT: A 1399 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8353 (mt) REVERT: A 1491 LYS cc_start: 0.7598 (pptt) cc_final: 0.7218 (ptpp) REVERT: A 1514 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.6403 (m110) REVERT: A 1522 MET cc_start: 0.8125 (tpp) cc_final: 0.7793 (mmp) REVERT: A 1602 TYR cc_start: 0.6542 (m-10) cc_final: 0.5750 (t80) REVERT: A 1603 PHE cc_start: 0.7757 (m-80) cc_final: 0.7360 (t80) REVERT: A 1634 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8709 (mm) REVERT: A 1637 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8641 (tp) REVERT: A 1691 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8808 (mm) REVERT: A 1719 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7682 (tttm) REVERT: A 1739 TYR cc_start: 0.8681 (t80) cc_final: 0.8251 (t80) REVERT: B 65 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: B 96 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8120 (mpp80) REVERT: B 131 ASN cc_start: 0.7503 (t0) cc_final: 0.7255 (t0) REVERT: B 184 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7616 (mtpp) outliers start: 71 outliers final: 50 residues processed: 259 average time/residue: 0.1064 time to fit residues: 40.4675 Evaluate side-chains 271 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 730 TRP Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1663 MET Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1764 SER Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 174 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 26 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118454 restraints weight = 17446.232| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.33 r_work: 0.3236 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12061 Z= 0.156 Angle : 0.657 9.992 16370 Z= 0.326 Chirality : 0.043 0.408 1907 Planarity : 0.003 0.036 1984 Dihedral : 7.585 59.511 1877 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 5.28 % Allowed : 26.79 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.22), residues: 1421 helix: 1.88 (0.17), residues: 857 sheet: -0.32 (0.43), residues: 134 loop : -1.12 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 838 TYR 0.027 0.001 TYR A 157 PHE 0.019 0.001 PHE B 54 TRP 0.012 0.001 TRP A 190 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00358 (12040) covalent geometry : angle 0.63701 (16317) SS BOND : bond 0.00302 ( 10) SS BOND : angle 1.88842 ( 20) hydrogen bonds : bond 0.04385 ( 716) hydrogen bonds : angle 4.71196 ( 2079) link_BETA1-4 : bond 0.01339 ( 2) link_BETA1-4 : angle 3.76369 ( 6) link_NAG-ASN : bond 0.00537 ( 9) link_NAG-ASN : angle 3.25450 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3796.52 seconds wall clock time: 65 minutes 28.06 seconds (3928.06 seconds total)