Starting phenix.real_space_refine on Sat Aug 23 11:45:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyj_43662/08_2025/8vyj_43662.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyj_43662/08_2025/8vyj_43662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vyj_43662/08_2025/8vyj_43662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyj_43662/08_2025/8vyj_43662.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vyj_43662/08_2025/8vyj_43662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyj_43662/08_2025/8vyj_43662.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 89 5.16 5 C 7746 2.51 5 N 1803 2.21 5 O 2075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 11715 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1395, 11210 Classifications: {'peptide': 1395} Link IDs: {'PTRANS': 49, 'TRANS': 1345} Chain breaks: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" 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: "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: "A" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 351 Unusual residues: {'6OU': 2, 'NAG': 3, 'Y01': 7} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'Y01:plan-1': 1, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 2.83, per 1000 atoms: 0.24 Number of scatterers: 11715 At special positions: 0 Unit cell: (139.345, 132.153, 137.547, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 89 16.00 P 2 15.00 O 2075 8.00 N 1803 7.00 C 7746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 335 " distance=2.04 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 341 " distance=2.03 Simple disulfide: pdb=" SG CYS A 683 " - pdb=" SG CYS A 686 " distance=2.03 Simple disulfide: pdb=" SG CYS A 906 " - pdb=" SG CYS A 915 " distance=2.03 Simple disulfide: pdb=" SG CYS A1176 " - pdb=" SG CYS A1178 " distance=2.03 Simple disulfide: pdb=" SG CYS A1363 " - pdb=" SG CYS A1384 " distance=2.03 Simple disulfide: pdb=" SG CYS A1728 " - pdb=" SG CYS A1742 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG B 3 " - " NAG B 4 " " NAG B 4 " - " NAG B 5 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2109 " - " ASN A 318 " " NAG A2110 " - " ASN A 283 " " NAG A2111 " - " ASN A 291 " " NAG E 1 " - " ASN A1365 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 507.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 5 sheets defined 64.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 4.190A pdb=" N ARG A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.961A pdb=" N ALA A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 4.262A pdb=" N LEU A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 180 removed outlier: 4.094A pdb=" N VAL A 160 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.972A pdb=" N PHE A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 199 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.880A pdb=" N ARG A 222 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.937A pdb=" N LYS A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 removed outlier: 3.541A pdb=" N GLN A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.530A pdb=" N TYR A 314 " --> pdb=" O PRO A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 352 Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.998A pdb=" N PHE A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 433 removed outlier: 3.579A pdb=" N THR A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 695 removed outlier: 3.821A pdb=" N ARG A 693 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 714 Processing helix chain 'A' and resid 715 through 736 removed outlier: 5.557A pdb=" N LEU A 721 " --> pdb=" O PRO A 717 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 722 " --> pdb=" O PHE A 718 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN A 730 " --> pdb=" O CYS A 726 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 771 removed outlier: 3.980A pdb=" N GLU A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 removed outlier: 4.396A pdb=" N PHE A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 798 Processing helix chain 'A' and resid 810 through 820 removed outlier: 3.715A pdb=" N ARG A 814 " --> pdb=" O ARG A 811 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 818 " --> pdb=" O VAL A 815 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 820 " --> pdb=" O LYS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 835 removed outlier: 3.880A pdb=" N LEU A 828 " --> pdb=" O THR A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 862 removed outlier: 4.355A pdb=" N THR A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 844 " --> pdb=" O GLY A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 865 No H-bonds generated for 'chain 'A' and resid 863 through 865' Processing helix chain 'A' and resid 883 through 897 Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 914 through 943 Processing helix chain 'A' and resid 1171 through 1175 removed outlier: 4.154A pdb=" N ARG A1174 " --> pdb=" O GLY A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1204 removed outlier: 4.304A pdb=" N TRP A1191 " --> pdb=" O PRO A1187 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP A1192 " --> pdb=" O GLY A1188 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS A1204 " --> pdb=" O HIS A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1221 removed outlier: 3.744A pdb=" N GLU A1208 " --> pdb=" O HIS A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1225 removed outlier: 3.927A pdb=" N GLU A1225 " --> pdb=" O LEU A1222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1222 through 1225' Processing helix chain 'A' and resid 1226 through 1230 removed outlier: 4.202A pdb=" N GLU A1230 " --> pdb=" O ILE A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1261 removed outlier: 3.598A pdb=" N THR A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1291 removed outlier: 4.206A pdb=" N TRP A1273 " --> pdb=" O ASN A1269 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU A1274 " --> pdb=" O ALA A1270 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP A1275 " --> pdb=" O TRP A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1305 removed outlier: 4.088A pdb=" N LEU A1302 " --> pdb=" O PRO A1298 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A1303 " --> pdb=" O ILE A1299 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A1304 " --> pdb=" O LYS A1300 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1305 " --> pdb=" O SER A1301 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1298 through 1305' Processing helix chain 'A' and resid 1306 through 1315 Proline residue: A1310 - end of helix removed outlier: 4.268A pdb=" N SER A1315 " --> pdb=" O ARG A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1329 removed outlier: 4.432A pdb=" N VAL A1323 " --> pdb=" O GLY A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1356 removed outlier: 3.601A pdb=" N ILE A1334 " --> pdb=" O ALA A1330 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A1340 " --> pdb=" O ASN A1336 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A1348 " --> pdb=" O PHE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1387 removed outlier: 3.597A pdb=" N CYS A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1417 removed outlier: 3.540A pdb=" N THR A1417 " --> pdb=" O LEU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1430 removed outlier: 4.124A pdb=" N ILE A1424 " --> pdb=" O GLY A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1445 No H-bonds generated for 'chain 'A' and resid 1443 through 1445' Processing helix chain 'A' and resid 1446 through 1458 removed outlier: 4.149A pdb=" N PHE A1450 " --> pdb=" O MET A1446 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A1458 " --> pdb=" O ILE A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1481 Processing helix chain 'A' and resid 1488 through 1500 removed outlier: 3.744A pdb=" N LYS A1500 " --> pdb=" O ASN A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1520 removed outlier: 3.752A pdb=" N GLN A1518 " --> pdb=" O LEU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1527 Processing helix chain 'A' and resid 1527 through 1547 removed outlier: 4.425A pdb=" N ASP A1531 " --> pdb=" O LYS A1527 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A1547 " --> pdb=" O VAL A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1577 removed outlier: 3.921A pdb=" N ILE A1557 " --> pdb=" O SER A1553 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A1559 " --> pdb=" O GLU A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1611 removed outlier: 3.975A pdb=" N PHE A1596 " --> pdb=" O ASN A1592 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A1601 " --> pdb=" O VAL A1597 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER A1602 " --> pdb=" O VAL A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1627 removed outlier: 4.167A pdb=" N VAL A1624 " --> pdb=" O THR A1620 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE A1625 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A1626 " --> pdb=" O PHE A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1640 removed outlier: 3.613A pdb=" N LEU A1634 " --> pdb=" O GLY A1631 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A1635 " --> pdb=" O ARG A1632 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A1636 " --> pdb=" O ILE A1633 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A1637 " --> pdb=" O LEU A1634 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1676 Proline residue: A1655 - end of helix removed outlier: 3.952A pdb=" N ASN A1659 " --> pdb=" O PRO A1655 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE A1660 " --> pdb=" O ALA A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1696 through 1708 Processing helix chain 'A' and resid 1713 through 1718 Processing helix chain 'A' and resid 1744 through 1777 removed outlier: 3.720A pdb=" N GLY A1748 " --> pdb=" O SER A1744 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A1750 " --> pdb=" O ALA A1746 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A1755 " --> pdb=" O PHE A1751 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1802 Processing helix chain 'A' and resid 1810 through 1818 removed outlier: 4.692A pdb=" N ASP A1816 " --> pdb=" O SER A1812 " (cutoff:3.500A) Processing helix chain 'A' and resid 1828 through 1834 removed outlier: 3.782A pdb=" N SER A1834 " --> pdb=" O PRO A1830 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1838 removed outlier: 3.677A pdb=" N MET A1838 " --> pdb=" O LEU A1835 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1835 through 1838' Processing helix chain 'A' and resid 1850 through 1860 Processing helix chain 'A' and resid 1868 through 1882 removed outlier: 3.789A pdb=" N LYS A1872 " --> pdb=" O MET A1868 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A1882 " --> pdb=" O LYS A1878 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 282 Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 296 Processing sheet with id=AA4, first strand: chain 'A' and resid 1362 through 1365 Processing sheet with id=AA5, first strand: chain 'A' and resid 1808 through 1809 removed outlier: 4.193A pdb=" N VAL A1843 " --> pdb=" O ARG A1847 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2273 1.33 - 1.45: 2979 1.45 - 1.58: 6606 1.58 - 1.70: 4 1.70 - 1.83: 145 Bond restraints: 12007 Sorted by residual: bond pdb=" C PRO A 684 " pdb=" N PRO A 685 " ideal model delta sigma weight residual 1.334 1.365 -0.032 2.34e-02 1.83e+03 1.82e+00 bond pdb=" CG1 ILE A1600 " pdb=" CD1 ILE A1600 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" CB LYS A1505 " pdb=" CG LYS A1505 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CB MET A 135 " pdb=" CG MET A 135 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" CB GLU A 346 " pdb=" CG GLU A 346 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.58e-01 ... (remaining 12002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 16071 2.12 - 4.23: 192 4.23 - 6.35: 29 6.35 - 8.47: 8 8.47 - 10.59: 2 Bond angle restraints: 16302 Sorted by residual: angle pdb=" CB MET A 135 " pdb=" CG MET A 135 " pdb=" SD MET A 135 " ideal model delta sigma weight residual 112.70 123.29 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CA MET A1498 " pdb=" CB MET A1498 " pdb=" CG MET A1498 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 angle pdb=" C ALA A1330 " pdb=" N ILE A1331 " pdb=" CA ILE A1331 " ideal model delta sigma weight residual 120.33 122.94 -2.61 8.00e-01 1.56e+00 1.07e+01 angle pdb=" N ILE A1593 " pdb=" CA ILE A1593 " pdb=" C ILE A1593 " ideal model delta sigma weight residual 112.35 107.81 4.54 1.41e+00 5.03e-01 1.04e+01 angle pdb=" CB LYS A1505 " pdb=" CG LYS A1505 " pdb=" CD LYS A1505 " ideal model delta sigma weight residual 111.30 118.14 -6.84 2.30e+00 1.89e-01 8.84e+00 ... (remaining 16297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.25: 6957 28.25 - 56.50: 559 56.50 - 84.74: 79 84.74 - 112.99: 34 112.99 - 141.24: 10 Dihedral angle restraints: 7639 sinusoidal: 3561 harmonic: 4078 Sorted by residual: dihedral pdb=" CB CYS A 280 " pdb=" SG CYS A 280 " pdb=" SG CYS A 335 " pdb=" CB CYS A 335 " ideal model delta sinusoidal sigma weight residual -86.00 -164.36 78.36 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS A1363 " pdb=" SG CYS A1363 " pdb=" SG CYS A1384 " pdb=" CB CYS A1384 " ideal model delta sinusoidal sigma weight residual -86.00 -155.25 69.25 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS A1728 " pdb=" SG CYS A1728 " pdb=" SG CYS A1742 " pdb=" CB CYS A1742 " ideal model delta sinusoidal sigma weight residual 93.00 160.12 -67.12 1 1.00e+01 1.00e-02 5.87e+01 ... (remaining 7636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1173 0.029 - 0.058: 479 0.058 - 0.087: 187 0.087 - 0.116: 52 0.116 - 0.146: 11 Chirality restraints: 1902 Sorted by residual: chirality pdb=" C1 NAG A2110 " pdb=" ND2 ASN A 283 " pdb=" C2 NAG A2110 " pdb=" O5 NAG A2110 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.36 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" C3 NAG D 1 " pdb=" C2 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O3 NAG D 1 " both_signs ideal model delta sigma weight residual False 2.45 2.31 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 1899 not shown) Planarity restraints: 1965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A1725 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A1726 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A1726 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1726 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 222 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C ARG A 222 " 0.030 2.00e-02 2.50e+03 pdb=" O ARG A 222 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 223 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 403 " 0.012 2.00e-02 2.50e+03 1.17e-02 2.75e+00 pdb=" CG TYR A 403 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 403 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 403 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 403 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 403 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 403 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 403 " -0.000 2.00e-02 2.50e+03 ... (remaining 1962 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 373 2.71 - 3.26: 11812 3.26 - 3.81: 17249 3.81 - 4.35: 19458 4.35 - 4.90: 32854 Nonbonded interactions: 81746 Sorted by model distance: nonbonded pdb=" O LYS A1264 " pdb=" OG1 THR A1268 " model vdw 2.169 3.040 nonbonded pdb=" OG1 THR A1390 " pdb=" OE2 GLU A1392 " model vdw 2.202 3.040 nonbonded pdb=" N GLU A 346 " pdb=" OE1 GLU A 346 " model vdw 2.287 3.120 nonbonded pdb=" O GLY A 180 " pdb=" OG1 THR A 187 " model vdw 2.320 3.040 nonbonded pdb=" N ASP A1714 " pdb=" OD1 ASP A1714 " model vdw 2.324 3.120 ... (remaining 81741 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 'C' selection = 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.910 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 : 0.003 0.047 12025 Z= 0.141 Angle : 0.622 10.586 16349 Z= 0.325 Chirality : 0.038 0.146 1902 Planarity : 0.004 0.046 1961 Dihedral : 20.756 141.240 4980 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.16 % Allowed : 29.41 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.24), residues: 1387 helix: 0.91 (0.19), residues: 815 sheet: -1.92 (0.76), residues: 36 loop : -2.16 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1626 TYR 0.025 0.001 TYR A 403 PHE 0.022 0.001 PHE A 942 TRP 0.017 0.001 TRP A1258 HIS 0.004 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00303 (12007) covalent geometry : angle 0.61493 (16302) SS BOND : bond 0.00274 ( 7) SS BOND : angle 1.54480 ( 14) hydrogen bonds : bond 0.16751 ( 588) hydrogen bonds : angle 5.79048 ( 1665) link_BETA1-4 : bond 0.00647 ( 7) link_BETA1-4 : angle 1.25431 ( 21) link_NAG-ASN : bond 0.00335 ( 4) link_NAG-ASN : angle 2.66673 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 382 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.7487 (m-30) cc_final: 0.7250 (m-30) REVERT: A 790 ILE cc_start: 0.8917 (tp) cc_final: 0.8415 (tp) REVERT: A 876 LEU cc_start: 0.8887 (tp) cc_final: 0.8652 (mp) REVERT: A 1222 LEU cc_start: 0.8241 (mt) cc_final: 0.7821 (mp) REVERT: A 1351 MET cc_start: 0.7812 (tpt) cc_final: 0.7577 (tpt) REVERT: A 1539 CYS cc_start: 0.8868 (m) cc_final: 0.8657 (p) REVERT: A 1653 SER cc_start: 0.8426 (m) cc_final: 0.8003 (p) REVERT: A 1851 MET cc_start: 0.3901 (mtp) cc_final: 0.3494 (mpp) outliers start: 2 outliers final: 0 residues processed: 383 average time/residue: 0.1166 time to fit residues: 63.2548 Evaluate side-chains 276 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.0070 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN A 740 ASN A 753 ASN A 834 ASN A1564 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.173957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.138463 restraints weight = 26723.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142136 restraints weight = 12879.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.144484 restraints weight = 7847.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145962 restraints weight = 5577.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.146932 restraints weight = 4459.591| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12025 Z= 0.152 Angle : 0.687 8.821 16349 Z= 0.339 Chirality : 0.041 0.212 1902 Planarity : 0.004 0.064 1961 Dihedral : 16.019 131.975 2342 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.09 % Allowed : 27.94 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.23), residues: 1387 helix: 1.11 (0.19), residues: 822 sheet: -1.78 (0.80), residues: 36 loop : -2.31 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1623 TYR 0.018 0.001 TYR A 403 PHE 0.022 0.002 PHE A 392 TRP 0.015 0.001 TRP A 781 HIS 0.005 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00320 (12007) covalent geometry : angle 0.67602 (16302) SS BOND : bond 0.00268 ( 7) SS BOND : angle 1.54597 ( 14) hydrogen bonds : bond 0.06010 ( 588) hydrogen bonds : angle 4.30227 ( 1665) link_BETA1-4 : bond 0.00497 ( 7) link_BETA1-4 : angle 2.45664 ( 21) link_NAG-ASN : bond 0.00463 ( 4) link_NAG-ASN : angle 3.10559 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 288 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 ASN cc_start: 0.7437 (t0) cc_final: 0.7054 (t0) REVERT: A 744 GLU cc_start: 0.8422 (mp0) cc_final: 0.7448 (tt0) REVERT: A 790 ILE cc_start: 0.8663 (tp) cc_final: 0.8084 (tp) REVERT: A 794 MET cc_start: 0.9199 (mmp) cc_final: 0.8700 (mmp) REVERT: A 876 LEU cc_start: 0.9058 (tp) cc_final: 0.8794 (mp) REVERT: A 1258 TRP cc_start: 0.8805 (t60) cc_final: 0.8562 (t60) REVERT: A 1309 ARG cc_start: 0.8997 (ttp-170) cc_final: 0.8615 (ttp80) REVERT: A 1392 GLU cc_start: 0.7295 (pt0) cc_final: 0.7088 (pt0) REVERT: A 1534 ILE cc_start: 0.8597 (mm) cc_final: 0.8218 (mt) REVERT: A 1539 CYS cc_start: 0.9040 (m) cc_final: 0.8432 (p) REVERT: A 1546 MET cc_start: 0.8084 (mmm) cc_final: 0.7561 (mmm) REVERT: A 1623 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.8095 (mpp80) REVERT: A 1653 SER cc_start: 0.8636 (m) cc_final: 0.8345 (p) REVERT: A 1765 ASN cc_start: 0.9155 (t0) cc_final: 0.8935 (t0) outliers start: 38 outliers final: 23 residues processed: 308 average time/residue: 0.0911 time to fit residues: 41.3040 Evaluate side-chains 285 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 262 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1344 PHE Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1662 LEU Chi-restraints excluded: chain A residue 1668 MET Chi-restraints excluded: chain A residue 1750 LEU Chi-restraints excluded: chain A residue 1775 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 9 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 0.0870 chunk 104 optimal weight: 0.9980 chunk 122 optimal weight: 0.0570 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A1289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.172683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137118 restraints weight = 26718.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140823 restraints weight = 12832.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143147 restraints weight = 7776.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.144670 restraints weight = 5518.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.145512 restraints weight = 4384.017| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12025 Z= 0.137 Angle : 0.663 13.036 16349 Z= 0.324 Chirality : 0.040 0.225 1902 Planarity : 0.005 0.095 1961 Dihedral : 14.452 133.146 2342 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.57 % Allowed : 26.97 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.23), residues: 1387 helix: 0.92 (0.19), residues: 846 sheet: -1.99 (0.76), residues: 36 loop : -2.36 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1626 TYR 0.021 0.001 TYR A1426 PHE 0.029 0.001 PHE A1246 TRP 0.012 0.001 TRP A 781 HIS 0.008 0.001 HIS A1849 Details of bonding type rmsd covalent geometry : bond 0.00290 (12007) covalent geometry : angle 0.65120 (16302) SS BOND : bond 0.00263 ( 7) SS BOND : angle 1.32895 ( 14) hydrogen bonds : bond 0.05275 ( 588) hydrogen bonds : angle 4.07423 ( 1665) link_BETA1-4 : bond 0.00579 ( 7) link_BETA1-4 : angle 2.51883 ( 21) link_NAG-ASN : bond 0.00519 ( 4) link_NAG-ASN : angle 3.15075 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5775 (mmt) cc_final: 0.5464 (mmt) REVERT: A 118 HIS cc_start: 0.4298 (OUTLIER) cc_final: 0.3446 (t-90) REVERT: A 138 MET cc_start: 0.6050 (tpp) cc_final: 0.5849 (tpp) REVERT: A 194 ASN cc_start: 0.7465 (m-40) cc_final: 0.7102 (t0) REVERT: A 431 GLU cc_start: 0.6241 (mm-30) cc_final: 0.5834 (mt-10) REVERT: A 744 GLU cc_start: 0.8450 (mp0) cc_final: 0.7522 (tt0) REVERT: A 790 ILE cc_start: 0.8682 (tp) cc_final: 0.8074 (tp) REVERT: A 794 MET cc_start: 0.9263 (mmp) cc_final: 0.8794 (mmp) REVERT: A 892 PHE cc_start: 0.9157 (t80) cc_final: 0.8954 (t80) REVERT: A 907 MET cc_start: 0.8455 (mtp) cc_final: 0.8215 (mtp) REVERT: A 1443 ASN cc_start: 0.8728 (t0) cc_final: 0.8464 (t0) REVERT: A 1534 ILE cc_start: 0.8599 (mm) cc_final: 0.8201 (mt) REVERT: A 1539 CYS cc_start: 0.9012 (m) cc_final: 0.8437 (p) REVERT: A 1653 SER cc_start: 0.8648 (m) cc_final: 0.8339 (p) REVERT: A 1741 ASP cc_start: 0.6910 (m-30) cc_final: 0.6662 (m-30) REVERT: A 1765 ASN cc_start: 0.9148 (t0) cc_final: 0.8872 (t0) outliers start: 44 outliers final: 27 residues processed: 307 average time/residue: 0.0908 time to fit residues: 41.4891 Evaluate side-chains 288 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1289 ASN Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1344 PHE Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1598 VAL Chi-restraints excluded: chain A residue 1622 PHE Chi-restraints excluded: chain A residue 1648 PHE Chi-restraints excluded: chain A residue 1662 LEU Chi-restraints excluded: chain A residue 1668 MET Chi-restraints excluded: chain A residue 1750 LEU Chi-restraints excluded: chain A residue 1775 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 108 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.0070 chunk 52 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A1472 ASN A1765 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.170880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134904 restraints weight = 27146.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138543 restraints weight = 13277.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140847 restraints weight = 8126.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.142333 restraints weight = 5811.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.143152 restraints weight = 4653.312| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12025 Z= 0.138 Angle : 0.664 9.991 16349 Z= 0.325 Chirality : 0.040 0.248 1902 Planarity : 0.004 0.056 1961 Dihedral : 13.456 140.975 2342 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.98 % Allowed : 27.86 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.23), residues: 1387 helix: 0.87 (0.18), residues: 854 sheet: -2.10 (0.74), residues: 36 loop : -2.49 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1623 TYR 0.015 0.001 TYR A 403 PHE 0.031 0.001 PHE A1246 TRP 0.011 0.001 TRP A 781 HIS 0.004 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00299 (12007) covalent geometry : angle 0.65079 (16302) SS BOND : bond 0.00185 ( 7) SS BOND : angle 1.42368 ( 14) hydrogen bonds : bond 0.04933 ( 588) hydrogen bonds : angle 4.02105 ( 1665) link_BETA1-4 : bond 0.00622 ( 7) link_BETA1-4 : angle 2.68140 ( 21) link_NAG-ASN : bond 0.00533 ( 4) link_NAG-ASN : angle 3.17597 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5940 (mmt) cc_final: 0.5617 (mmt) REVERT: A 118 HIS cc_start: 0.4132 (OUTLIER) cc_final: 0.3287 (t-90) REVERT: A 138 MET cc_start: 0.6044 (tpp) cc_final: 0.5819 (tpp) REVERT: A 194 ASN cc_start: 0.7540 (m-40) cc_final: 0.7209 (t0) REVERT: A 431 GLU cc_start: 0.6261 (mm-30) cc_final: 0.5886 (mt-10) REVERT: A 713 VAL cc_start: 0.7173 (m) cc_final: 0.6912 (m) REVERT: A 744 GLU cc_start: 0.8480 (mp0) cc_final: 0.7465 (tt0) REVERT: A 790 ILE cc_start: 0.8730 (tp) cc_final: 0.8119 (tp) REVERT: A 794 MET cc_start: 0.9264 (mmp) cc_final: 0.8791 (mmp) REVERT: A 892 PHE cc_start: 0.9212 (t80) cc_final: 0.8994 (t80) REVERT: A 912 GLN cc_start: 0.7271 (tt0) cc_final: 0.6752 (pm20) REVERT: A 932 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8155 (m110) REVERT: A 1253 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6973 (mp0) REVERT: A 1419 LYS cc_start: 0.8545 (mmtm) cc_final: 0.8269 (mmtp) REVERT: A 1443 ASN cc_start: 0.8766 (t0) cc_final: 0.8515 (t0) REVERT: A 1534 ILE cc_start: 0.8591 (mm) cc_final: 0.8212 (mt) REVERT: A 1539 CYS cc_start: 0.9022 (m) cc_final: 0.8420 (p) REVERT: A 1653 SER cc_start: 0.8682 (m) cc_final: 0.8331 (p) REVERT: A 1662 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7477 (tp) REVERT: A 1741 ASP cc_start: 0.7126 (m-30) cc_final: 0.6859 (m-30) REVERT: A 1765 ASN cc_start: 0.9185 (t0) cc_final: 0.8966 (t0) outliers start: 49 outliers final: 34 residues processed: 298 average time/residue: 0.0945 time to fit residues: 42.2286 Evaluate side-chains 293 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1344 PHE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1598 VAL Chi-restraints excluded: chain A residue 1648 PHE Chi-restraints excluded: chain A residue 1662 LEU Chi-restraints excluded: chain A residue 1668 MET Chi-restraints excluded: chain A residue 1750 LEU Chi-restraints excluded: chain A residue 1775 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 61 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 88 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 120 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.170827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.134592 restraints weight = 27096.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138245 restraints weight = 13283.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140547 restraints weight = 8153.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142016 restraints weight = 5835.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142927 restraints weight = 4678.040| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12025 Z= 0.130 Angle : 0.660 9.528 16349 Z= 0.324 Chirality : 0.041 0.248 1902 Planarity : 0.004 0.059 1961 Dihedral : 12.742 147.537 2342 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.47 % Allowed : 28.19 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.23), residues: 1387 helix: 0.97 (0.19), residues: 841 sheet: -2.28 (0.77), residues: 34 loop : -2.52 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1623 TYR 0.014 0.001 TYR A 403 PHE 0.019 0.001 PHE A 816 TRP 0.011 0.001 TRP A 781 HIS 0.002 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00278 (12007) covalent geometry : angle 0.64590 (16302) SS BOND : bond 0.00521 ( 7) SS BOND : angle 1.82007 ( 14) hydrogen bonds : bond 0.04675 ( 588) hydrogen bonds : angle 3.94608 ( 1665) link_BETA1-4 : bond 0.00637 ( 7) link_BETA1-4 : angle 2.83640 ( 21) link_NAG-ASN : bond 0.00544 ( 4) link_NAG-ASN : angle 3.10414 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5858 (mmt) cc_final: 0.5573 (mmt) REVERT: A 118 HIS cc_start: 0.4054 (OUTLIER) cc_final: 0.3213 (t-90) REVERT: A 138 MET cc_start: 0.6071 (tpp) cc_final: 0.5820 (tpp) REVERT: A 194 ASN cc_start: 0.7501 (m-40) cc_final: 0.7179 (t0) REVERT: A 431 GLU cc_start: 0.6275 (mm-30) cc_final: 0.5930 (mt-10) REVERT: A 744 GLU cc_start: 0.8564 (mp0) cc_final: 0.7735 (tt0) REVERT: A 790 ILE cc_start: 0.8732 (tp) cc_final: 0.8104 (tp) REVERT: A 794 MET cc_start: 0.9270 (mmp) cc_final: 0.8768 (mmp) REVERT: A 907 MET cc_start: 0.8541 (mtp) cc_final: 0.8262 (mtp) REVERT: A 912 GLN cc_start: 0.7309 (tt0) cc_final: 0.6724 (pm20) REVERT: A 932 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8129 (m-40) REVERT: A 1253 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6920 (mp0) REVERT: A 1419 LYS cc_start: 0.8519 (mmtm) cc_final: 0.8261 (mmtp) REVERT: A 1443 ASN cc_start: 0.8819 (t0) cc_final: 0.8586 (t0) REVERT: A 1534 ILE cc_start: 0.8612 (mm) cc_final: 0.8249 (mt) REVERT: A 1539 CYS cc_start: 0.9001 (m) cc_final: 0.8351 (p) REVERT: A 1623 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.8034 (mtm-85) REVERT: A 1653 SER cc_start: 0.8750 (m) cc_final: 0.8322 (p) REVERT: A 1662 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7469 (tp) REVERT: A 1741 ASP cc_start: 0.7160 (m-30) cc_final: 0.6906 (m-30) REVERT: A 1765 ASN cc_start: 0.9184 (t0) cc_final: 0.8966 (t0) outliers start: 55 outliers final: 39 residues processed: 306 average time/residue: 0.0987 time to fit residues: 44.9218 Evaluate side-chains 300 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1344 PHE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1537 LEU Chi-restraints excluded: chain A residue 1546 MET Chi-restraints excluded: chain A residue 1598 VAL Chi-restraints excluded: chain A residue 1629 ARG Chi-restraints excluded: chain A residue 1662 LEU Chi-restraints excluded: chain A residue 1668 MET Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1750 LEU Chi-restraints excluded: chain A residue 1775 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 25 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.166575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.130549 restraints weight = 27038.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.134006 restraints weight = 13418.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.136251 restraints weight = 8288.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137686 restraints weight = 5952.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138628 restraints weight = 4788.371| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12025 Z= 0.178 Angle : 0.724 11.926 16349 Z= 0.359 Chirality : 0.043 0.265 1902 Planarity : 0.005 0.060 1961 Dihedral : 12.357 149.891 2342 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.87 % Allowed : 28.84 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.23), residues: 1387 helix: 0.79 (0.18), residues: 855 sheet: -2.41 (0.75), residues: 34 loop : -2.69 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1623 TYR 0.024 0.002 TYR A 403 PHE 0.031 0.002 PHE A1246 TRP 0.013 0.001 TRP A 781 HIS 0.005 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00399 (12007) covalent geometry : angle 0.70848 (16302) SS BOND : bond 0.00302 ( 7) SS BOND : angle 2.09298 ( 14) hydrogen bonds : bond 0.05341 ( 588) hydrogen bonds : angle 4.13073 ( 1665) link_BETA1-4 : bond 0.00571 ( 7) link_BETA1-4 : angle 3.02818 ( 21) link_NAG-ASN : bond 0.00552 ( 4) link_NAG-ASN : angle 3.32565 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 260 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 HIS cc_start: 0.4038 (OUTLIER) cc_final: 0.3151 (t-90) REVERT: A 194 ASN cc_start: 0.7493 (m-40) cc_final: 0.7191 (t0) REVERT: A 357 SER cc_start: 0.6863 (p) cc_final: 0.6623 (m) REVERT: A 431 GLU cc_start: 0.6294 (mm-30) cc_final: 0.5934 (mt-10) REVERT: A 744 GLU cc_start: 0.8655 (mp0) cc_final: 0.7549 (tt0) REVERT: A 764 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.6303 (ttt) REVERT: A 790 ILE cc_start: 0.8736 (tp) cc_final: 0.8112 (tp) REVERT: A 794 MET cc_start: 0.9239 (mmp) cc_final: 0.8727 (mmp) REVERT: A 811 ARG cc_start: 0.7315 (ptt180) cc_final: 0.6976 (mtp180) REVERT: A 932 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8151 (m110) REVERT: A 1253 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6925 (mp0) REVERT: A 1419 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8454 (mmtm) REVERT: A 1439 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: A 1443 ASN cc_start: 0.8938 (t0) cc_final: 0.8617 (t0) REVERT: A 1539 CYS cc_start: 0.8989 (m) cc_final: 0.8758 (t) REVERT: A 1555 GLU cc_start: 0.7517 (mp0) cc_final: 0.6400 (mm-30) REVERT: A 1653 SER cc_start: 0.8843 (m) cc_final: 0.8460 (p) REVERT: A 1662 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7814 (tp) REVERT: A 1689 ASP cc_start: 0.7557 (t0) cc_final: 0.7344 (t0) outliers start: 60 outliers final: 41 residues processed: 295 average time/residue: 0.1013 time to fit residues: 44.2468 Evaluate side-chains 294 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1424 ILE Chi-restraints excluded: chain A residue 1439 GLN Chi-restraints excluded: chain A residue 1546 MET Chi-restraints excluded: chain A residue 1598 VAL Chi-restraints excluded: chain A residue 1629 ARG Chi-restraints excluded: chain A residue 1662 LEU Chi-restraints excluded: chain A residue 1668 MET Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1750 LEU Chi-restraints excluded: chain A residue 1775 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 137 optimal weight: 0.1980 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 chunk 61 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.167816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132113 restraints weight = 26720.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.135708 restraints weight = 12966.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137986 restraints weight = 7885.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.139446 restraints weight = 5610.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140394 restraints weight = 4471.346| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12025 Z= 0.136 Angle : 0.708 15.784 16349 Z= 0.345 Chirality : 0.041 0.233 1902 Planarity : 0.004 0.063 1961 Dihedral : 11.927 151.152 2342 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.82 % Allowed : 29.49 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.23), residues: 1387 helix: 1.01 (0.19), residues: 826 sheet: -2.40 (0.76), residues: 34 loop : -2.70 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1623 TYR 0.028 0.001 TYR A 403 PHE 0.022 0.001 PHE A 198 TRP 0.012 0.001 TRP A 781 HIS 0.003 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00296 (12007) covalent geometry : angle 0.69369 (16302) SS BOND : bond 0.00268 ( 7) SS BOND : angle 1.54820 ( 14) hydrogen bonds : bond 0.04935 ( 588) hydrogen bonds : angle 4.01314 ( 1665) link_BETA1-4 : bond 0.00595 ( 7) link_BETA1-4 : angle 3.04561 ( 21) link_NAG-ASN : bond 0.00573 ( 4) link_NAG-ASN : angle 3.22569 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 258 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 HIS cc_start: 0.3962 (OUTLIER) cc_final: 0.3073 (t-90) REVERT: A 194 ASN cc_start: 0.7483 (m-40) cc_final: 0.7200 (t0) REVERT: A 254 MET cc_start: 0.7504 (pmm) cc_final: 0.7242 (ttp) REVERT: A 390 MET cc_start: 0.8563 (tmm) cc_final: 0.8319 (tmm) REVERT: A 431 GLU cc_start: 0.6264 (mm-30) cc_final: 0.5938 (mt-10) REVERT: A 744 GLU cc_start: 0.8644 (mp0) cc_final: 0.7431 (tt0) REVERT: A 764 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6393 (ttt) REVERT: A 790 ILE cc_start: 0.8755 (tp) cc_final: 0.8074 (tp) REVERT: A 794 MET cc_start: 0.9246 (mmp) cc_final: 0.8673 (mmp) REVERT: A 932 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8118 (m-40) REVERT: A 1253 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6996 (mp0) REVERT: A 1309 ARG cc_start: 0.8977 (ttt180) cc_final: 0.8713 (ttt-90) REVERT: A 1419 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8366 (mmtm) REVERT: A 1443 ASN cc_start: 0.8900 (t0) cc_final: 0.8567 (t0) REVERT: A 1539 CYS cc_start: 0.8977 (m) cc_final: 0.8735 (t) REVERT: A 1546 MET cc_start: 0.8427 (tpt) cc_final: 0.8128 (mmm) REVERT: A 1626 ARG cc_start: 0.8542 (ptm-80) cc_final: 0.8261 (ttm-80) REVERT: A 1653 SER cc_start: 0.8749 (m) cc_final: 0.8323 (p) REVERT: A 1662 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7762 (tp) outliers start: 47 outliers final: 36 residues processed: 288 average time/residue: 0.1005 time to fit residues: 43.0363 Evaluate side-chains 291 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1344 PHE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1598 VAL Chi-restraints excluded: chain A residue 1620 THR Chi-restraints excluded: chain A residue 1629 ARG Chi-restraints excluded: chain A residue 1648 PHE Chi-restraints excluded: chain A residue 1651 MET Chi-restraints excluded: chain A residue 1662 LEU Chi-restraints excluded: chain A residue 1668 MET Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1750 LEU Chi-restraints excluded: chain A residue 1775 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 38 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 105 optimal weight: 0.0770 chunk 87 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 131 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.167431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.132053 restraints weight = 26800.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.135681 restraints weight = 12941.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137987 restraints weight = 7838.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139463 restraints weight = 5540.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140313 restraints weight = 4402.988| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12025 Z= 0.142 Angle : 0.732 16.044 16349 Z= 0.356 Chirality : 0.041 0.279 1902 Planarity : 0.004 0.056 1961 Dihedral : 11.566 152.390 2342 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.47 % Allowed : 29.08 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.23), residues: 1387 helix: 1.00 (0.19), residues: 826 sheet: -2.43 (0.77), residues: 34 loop : -2.74 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1623 TYR 0.028 0.001 TYR A 403 PHE 0.019 0.001 PHE A1267 TRP 0.011 0.001 TRP A 781 HIS 0.003 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00312 (12007) covalent geometry : angle 0.71871 (16302) SS BOND : bond 0.00279 ( 7) SS BOND : angle 1.51803 ( 14) hydrogen bonds : bond 0.04825 ( 588) hydrogen bonds : angle 4.03247 ( 1665) link_BETA1-4 : bond 0.00587 ( 7) link_BETA1-4 : angle 3.05077 ( 21) link_NAG-ASN : bond 0.00556 ( 4) link_NAG-ASN : angle 3.17149 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 HIS cc_start: 0.4139 (OUTLIER) cc_final: 0.3241 (t-90) REVERT: A 194 ASN cc_start: 0.7502 (m-40) cc_final: 0.7240 (t0) REVERT: A 254 MET cc_start: 0.7486 (pmm) cc_final: 0.7192 (ttp) REVERT: A 431 GLU cc_start: 0.6315 (mm-30) cc_final: 0.5990 (mt-10) REVERT: A 744 GLU cc_start: 0.8554 (mp0) cc_final: 0.7456 (tt0) REVERT: A 790 ILE cc_start: 0.8757 (tp) cc_final: 0.8039 (tp) REVERT: A 794 MET cc_start: 0.9261 (mmp) cc_final: 0.8657 (mmp) REVERT: A 932 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8126 (m-40) REVERT: A 1253 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7023 (mp0) REVERT: A 1254 MET cc_start: 0.7647 (tmm) cc_final: 0.7400 (tmm) REVERT: A 1274 LEU cc_start: 0.8768 (tp) cc_final: 0.8560 (tp) REVERT: A 1309 ARG cc_start: 0.8991 (ttt180) cc_final: 0.8508 (ttt-90) REVERT: A 1392 GLU cc_start: 0.7466 (pt0) cc_final: 0.7076 (pm20) REVERT: A 1419 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8352 (mmtm) REVERT: A 1439 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: A 1443 ASN cc_start: 0.8884 (t0) cc_final: 0.8603 (t0) REVERT: A 1539 CYS cc_start: 0.8980 (m) cc_final: 0.8716 (t) REVERT: A 1546 MET cc_start: 0.8454 (tpt) cc_final: 0.8135 (mmm) REVERT: A 1626 ARG cc_start: 0.8531 (ptm-80) cc_final: 0.8268 (ttm-80) REVERT: A 1653 SER cc_start: 0.8783 (m) cc_final: 0.8370 (p) REVERT: A 1662 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7774 (tp) REVERT: A 1701 MET cc_start: 0.8857 (tpp) cc_final: 0.8631 (tpp) outliers start: 55 outliers final: 43 residues processed: 293 average time/residue: 0.1017 time to fit residues: 44.3984 Evaluate side-chains 298 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1344 PHE Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1439 GLN Chi-restraints excluded: chain A residue 1488 THR Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1598 VAL Chi-restraints excluded: chain A residue 1620 THR Chi-restraints excluded: chain A residue 1629 ARG Chi-restraints excluded: chain A residue 1648 PHE Chi-restraints excluded: chain A residue 1662 LEU Chi-restraints excluded: chain A residue 1668 MET Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1742 CYS Chi-restraints excluded: chain A residue 1750 LEU Chi-restraints excluded: chain A residue 1775 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 31 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 110 optimal weight: 0.0370 chunk 51 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 129 optimal weight: 0.0010 chunk 11 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 overall best weight: 0.2264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.170069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134377 restraints weight = 26683.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138055 restraints weight = 12889.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140382 restraints weight = 7809.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.141879 restraints weight = 5529.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.142769 restraints weight = 4396.243| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12025 Z= 0.126 Angle : 0.729 16.126 16349 Z= 0.354 Chirality : 0.040 0.229 1902 Planarity : 0.004 0.066 1961 Dihedral : 11.192 153.452 2342 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.84 % Allowed : 31.03 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.23), residues: 1387 helix: 1.06 (0.19), residues: 826 sheet: -2.19 (0.75), residues: 36 loop : -2.73 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1623 TYR 0.015 0.001 TYR A 162 PHE 0.034 0.001 PHE A1246 TRP 0.009 0.001 TRP A 195 HIS 0.002 0.000 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00262 (12007) covalent geometry : angle 0.71596 (16302) SS BOND : bond 0.00283 ( 7) SS BOND : angle 1.21617 ( 14) hydrogen bonds : bond 0.04352 ( 588) hydrogen bonds : angle 3.95047 ( 1665) link_BETA1-4 : bond 0.00588 ( 7) link_BETA1-4 : angle 3.09637 ( 21) link_NAG-ASN : bond 0.00571 ( 4) link_NAG-ASN : angle 2.99858 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 HIS cc_start: 0.4058 (OUTLIER) cc_final: 0.3217 (t-90) REVERT: A 194 ASN cc_start: 0.7438 (m-40) cc_final: 0.7167 (t0) REVERT: A 254 MET cc_start: 0.7483 (pmm) cc_final: 0.7242 (ttp) REVERT: A 431 GLU cc_start: 0.6252 (mm-30) cc_final: 0.5966 (mt-10) REVERT: A 744 GLU cc_start: 0.8464 (mp0) cc_final: 0.7437 (tt0) REVERT: A 790 ILE cc_start: 0.8748 (tp) cc_final: 0.7979 (tp) REVERT: A 794 MET cc_start: 0.9261 (mmp) cc_final: 0.8621 (mmp) REVERT: A 932 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8108 (m-40) REVERT: A 1249 VAL cc_start: 0.7924 (p) cc_final: 0.7554 (p) REVERT: A 1253 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6983 (mp0) REVERT: A 1258 TRP cc_start: 0.8709 (t60) cc_final: 0.8458 (t60) REVERT: A 1305 LEU cc_start: 0.9070 (tt) cc_final: 0.8866 (tt) REVERT: A 1309 ARG cc_start: 0.9016 (ttt180) cc_final: 0.8795 (ttt180) REVERT: A 1392 GLU cc_start: 0.7434 (pt0) cc_final: 0.7109 (pm20) REVERT: A 1419 LYS cc_start: 0.8490 (mmtm) cc_final: 0.8230 (mmtm) REVERT: A 1439 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: A 1443 ASN cc_start: 0.8865 (t0) cc_final: 0.8599 (t0) REVERT: A 1539 CYS cc_start: 0.8944 (m) cc_final: 0.8667 (t) REVERT: A 1546 MET cc_start: 0.8373 (tpt) cc_final: 0.8046 (mmm) REVERT: A 1653 SER cc_start: 0.8615 (m) cc_final: 0.8230 (p) REVERT: A 1662 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7779 (tp) REVERT: A 1701 MET cc_start: 0.8866 (tpp) cc_final: 0.8632 (tpp) outliers start: 35 outliers final: 26 residues processed: 296 average time/residue: 0.0935 time to fit residues: 41.4877 Evaluate side-chains 292 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 262 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1344 PHE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1439 GLN Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1598 VAL Chi-restraints excluded: chain A residue 1648 PHE Chi-restraints excluded: chain A residue 1662 LEU Chi-restraints excluded: chain A residue 1668 MET Chi-restraints excluded: chain A residue 1742 CYS Chi-restraints excluded: chain A residue 1750 LEU Chi-restraints excluded: chain A residue 1775 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 77 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.166448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.130339 restraints weight = 27040.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.133862 restraints weight = 13198.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.136171 restraints weight = 8087.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137630 restraints weight = 5753.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138549 restraints weight = 4601.934| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12025 Z= 0.167 Angle : 0.769 15.998 16349 Z= 0.379 Chirality : 0.042 0.273 1902 Planarity : 0.005 0.069 1961 Dihedral : 11.167 153.538 2342 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.68 % Allowed : 31.11 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.23), residues: 1387 helix: 0.97 (0.19), residues: 823 sheet: -2.35 (0.73), residues: 36 loop : -2.83 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A1629 TYR 0.018 0.002 TYR A 403 PHE 0.026 0.002 PHE A 259 TRP 0.012 0.001 TRP A 195 HIS 0.005 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00376 (12007) covalent geometry : angle 0.75529 (16302) SS BOND : bond 0.00323 ( 7) SS BOND : angle 1.59577 ( 14) hydrogen bonds : bond 0.04986 ( 588) hydrogen bonds : angle 4.11677 ( 1665) link_BETA1-4 : bond 0.00549 ( 7) link_BETA1-4 : angle 3.14334 ( 21) link_NAG-ASN : bond 0.00570 ( 4) link_NAG-ASN : angle 3.10752 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 HIS cc_start: 0.4031 (OUTLIER) cc_final: 0.3150 (t-90) REVERT: A 194 ASN cc_start: 0.7378 (m-40) cc_final: 0.7108 (t0) REVERT: A 431 GLU cc_start: 0.6424 (mm-30) cc_final: 0.6121 (mt-10) REVERT: A 744 GLU cc_start: 0.8471 (mp0) cc_final: 0.7444 (tt0) REVERT: A 790 ILE cc_start: 0.8761 (tp) cc_final: 0.8011 (tp) REVERT: A 794 MET cc_start: 0.9269 (mmp) cc_final: 0.8661 (mmp) REVERT: A 932 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8102 (m-40) REVERT: A 1253 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7037 (mp0) REVERT: A 1274 LEU cc_start: 0.8761 (tp) cc_final: 0.8551 (tp) REVERT: A 1309 ARG cc_start: 0.9018 (ttt180) cc_final: 0.8476 (ttt-90) REVERT: A 1419 LYS cc_start: 0.8657 (mmtm) cc_final: 0.8392 (mmtm) REVERT: A 1439 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: A 1443 ASN cc_start: 0.8960 (t0) cc_final: 0.8663 (t0) REVERT: A 1539 CYS cc_start: 0.8949 (m) cc_final: 0.8650 (t) REVERT: A 1546 MET cc_start: 0.8509 (tpt) cc_final: 0.8167 (mmm) REVERT: A 1626 ARG cc_start: 0.8424 (ptm-80) cc_final: 0.8086 (ttm-80) REVERT: A 1653 SER cc_start: 0.8788 (m) cc_final: 0.8414 (p) REVERT: A 1662 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7585 (tp) REVERT: A 1688 ILE cc_start: 0.9380 (mt) cc_final: 0.9121 (tp) outliers start: 33 outliers final: 27 residues processed: 277 average time/residue: 0.0955 time to fit residues: 39.9700 Evaluate side-chains 280 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1439 GLN Chi-restraints excluded: chain A residue 1488 THR Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1598 VAL Chi-restraints excluded: chain A residue 1648 PHE Chi-restraints excluded: chain A residue 1662 LEU Chi-restraints excluded: chain A residue 1668 MET Chi-restraints excluded: chain A residue 1742 CYS Chi-restraints excluded: chain A residue 1750 LEU Chi-restraints excluded: chain A residue 1775 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 42 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 99 optimal weight: 0.0970 chunk 16 optimal weight: 0.0970 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.168452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132427 restraints weight = 26746.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136030 restraints weight = 13035.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138303 restraints weight = 7958.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139789 restraints weight = 5684.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140624 restraints weight = 4521.062| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12025 Z= 0.136 Angle : 0.754 16.214 16349 Z= 0.366 Chirality : 0.041 0.242 1902 Planarity : 0.004 0.068 1961 Dihedral : 10.842 153.506 2342 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.01 % Allowed : 31.44 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.23), residues: 1387 helix: 1.05 (0.19), residues: 821 sheet: -2.27 (0.75), residues: 36 loop : -2.81 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1623 TYR 0.016 0.001 TYR A 378 PHE 0.044 0.001 PHE A1246 TRP 0.011 0.001 TRP A 195 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00301 (12007) covalent geometry : angle 0.74133 (16302) SS BOND : bond 0.00286 ( 7) SS BOND : angle 1.33857 ( 14) hydrogen bonds : bond 0.04671 ( 588) hydrogen bonds : angle 4.05100 ( 1665) link_BETA1-4 : bond 0.00555 ( 7) link_BETA1-4 : angle 3.12337 ( 21) link_NAG-ASN : bond 0.00569 ( 4) link_NAG-ASN : angle 3.01390 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2927.19 seconds wall clock time: 51 minutes 6.55 seconds (3066.55 seconds total)