Starting phenix.real_space_refine on Fri Sep 11 20:56:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6j8e_9780/09_2026/6j8e_9780.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j8e_9780/09_2026/6j8e_9780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6j8e_9780/09_2026/6j8e_9780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j8e_9780/09_2026/6j8e_9780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6j8e_9780/09_2026/6j8e_9780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j8e_9780/09_2026/6j8e_9780.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6j8e_9780/09_2026/6j8e_9780.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6j8e_9780/09_2026/6j8e_9780.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 974 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 94 5.16 5 Na 1 4.78 5 C 6904 2.51 5 N 1646 2.21 5 O 1837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10482 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 1004 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 992 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 122, 992 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 998 Chain: "A" Number of atoms: 9193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1139, 9193 Classifications: {'peptide': 1139} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 27, 'TRANS': 1105} Chain breaks: 3 Chain: "D" Number of atoms: 136 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Conformer: "B" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} bond proxies already assigned to first conformer: 115 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' NA': 1, '9Z9': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG D 10 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 10 " occ=0.50 Time building chain proxies: 2.33, per 1000 atoms: 0.22 Number of scatterers: 10482 At special positions: 0 Unit cell: (140.739, 140.739, 109.1, 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 94 16.00 Na 1 11.00 O 1837 8.00 N 1646 7.00 C 6904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=1.84 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS A 910 " distance=2.09 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 918 " distance=2.04 Simple disulfide: pdb=" SG CYS A 950 " - pdb=" SG CYS A 959 " distance=2.05 Simple disulfide: pdb=" SG CYS A1366 " - pdb=" SG CYS A1386 " distance=2.01 Simple disulfide: pdb=" SG CYS A1731 " - pdb=" SG CYS A1746 " distance=2.03 Simple disulfide: pdb=" SG CYS D 1 " - pdb=" SG CYS D 15 " distance=2.03 Simple disulfide: pdb=" SG CYS D 2 " - pdb=" SG CYS D 9 " distance=2.03 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 16 " 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 " - " BMA B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2106 " - " ASN A1393 " " NAG B 1 " - " ASN A 340 " " NAG E 1 " - " ASN A1382 " " NAG F 1 " - " ASN A1368 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 610.6 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2422 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 5 sheets defined 67.0% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'A' and resid 118 through 122 Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.928A pdb=" N VAL A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 128' Processing helix chain 'A' and resid 128 through 146 removed outlier: 3.549A pdb=" N ASN A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 140 " --> pdb=" O MET A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 removed outlier: 3.523A pdb=" N THR A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.863A pdb=" N TRP A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 207 removed outlier: 3.884A pdb=" N PHE A 207 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.531A pdb=" N VAL A 221 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 223 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 233 through 246 removed outlier: 3.991A pdb=" N ILE A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 250 through 270 removed outlier: 3.545A pdb=" N LEU A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.795A pdb=" N ALA A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.881A pdb=" N LEU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 412 removed outlier: 3.832A pdb=" N PHE A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 441 removed outlier: 3.540A pdb=" N GLU A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 754 removed outlier: 4.451A pdb=" N LEU A 751 " --> pdb=" O LYS A 747 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 778 removed outlier: 4.105A pdb=" N THR A 766 " --> pdb=" O ASP A 762 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 774 " --> pdb=" O VAL A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 808 removed outlier: 3.509A pdb=" N ASN A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 805 " --> pdb=" O ILE A 801 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 841 removed outlier: 3.528A pdb=" N LEU A 840 " --> pdb=" O MET A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 863 removed outlier: 3.854A pdb=" N LEU A 849 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG A 853 " --> pdb=" O ARG A 850 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 855 " --> pdb=" O PHE A 852 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 856 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A 857 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 858 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 862 " --> pdb=" O LYS A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 879 removed outlier: 3.663A pdb=" N ASN A 868 " --> pdb=" O TRP A 864 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 869 " --> pdb=" O PRO A 865 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 878 " --> pdb=" O ILE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 903 removed outlier: 3.623A pdb=" N MET A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 910 removed outlier: 4.121A pdb=" N LYS A 908 " --> pdb=" O GLY A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 939 removed outlier: 3.574A pdb=" N VAL A 935 " --> pdb=" O SER A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 955 removed outlier: 3.699A pdb=" N MET A 947 " --> pdb=" O TRP A 943 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP A 949 " --> pdb=" O GLU A 945 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 953 " --> pdb=" O ASP A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 986 removed outlier: 3.685A pdb=" N VAL A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 971 " --> pdb=" O MET A 967 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 986 " --> pdb=" O LEU A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1206 removed outlier: 3.587A pdb=" N ARG A1198 " --> pdb=" O TRP A1194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A1199 " --> pdb=" O TRP A1195 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR A1200 " --> pdb=" O ASN A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1224 removed outlier: 3.886A pdb=" N GLU A1211 " --> pdb=" O HIS A1207 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A1212 " --> pdb=" O ASN A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1228 removed outlier: 3.768A pdb=" N GLU A1228 " --> pdb=" O LEU A1225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1225 through 1228' Processing helix chain 'A' and resid 1231 through 1236 removed outlier: 4.306A pdb=" N LYS A1236 " --> pdb=" O ILE A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1265 removed outlier: 3.944A pdb=" N LYS A1247 " --> pdb=" O GLU A1243 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A1250 " --> pdb=" O ASP A1246 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A1257 " --> pdb=" O PHE A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1270 Processing helix chain 'A' and resid 1272 through 1295 removed outlier: 3.530A pdb=" N ILE A1281 " --> pdb=" O LEU A1277 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A1282 " --> pdb=" O ASP A1278 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1288 " --> pdb=" O VAL A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1306 removed outlier: 3.754A pdb=" N ARG A1306 " --> pdb=" O ILE A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1317 removed outlier: 3.697A pdb=" N ALA A1310 " --> pdb=" O THR A1307 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A1311 " --> pdb=" O LEU A1308 " (cutoff:3.500A) Proline residue: A1313 - end of helix Processing helix chain 'A' and resid 1320 through 1331 removed outlier: 3.789A pdb=" N VAL A1326 " --> pdb=" O GLY A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1359 removed outlier: 3.738A pdb=" N VAL A1343 " --> pdb=" O ASN A1339 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A1351 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1391 Processing helix chain 'A' and resid 1408 through 1421 removed outlier: 3.540A pdb=" N LEU A1413 " --> pdb=" O GLY A1409 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A1417 " --> pdb=" O LEU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1433 removed outlier: 3.657A pdb=" N ILE A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1448 No H-bonds generated for 'chain 'A' and resid 1446 through 1448' Processing helix chain 'A' and resid 1449 through 1460 removed outlier: 3.820A pdb=" N PHE A1453 " --> pdb=" O MET A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1483 removed outlier: 3.595A pdb=" N GLN A1478 " --> pdb=" O ASP A1474 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A1483 " --> pdb=" O GLN A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1497 removed outlier: 3.968A pdb=" N LYS A1496 " --> pdb=" O GLU A1492 " (cutoff:3.500A) Processing helix chain 'A' and resid 1500 through 1506 removed outlier: 3.591A pdb=" N SER A1506 " --> pdb=" O LYS A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1529 removed outlier: 4.182A pdb=" N MET A1523 " --> pdb=" O LYS A1519 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A1529 " --> pdb=" O PHE A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1550 removed outlier: 3.840A pdb=" N ILE A1537 " --> pdb=" O PHE A1533 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A1538 " --> pdb=" O ASP A1534 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A1547 " --> pdb=" O LEU A1543 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A1549 " --> pdb=" O MET A1545 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A1550 " --> pdb=" O VAL A1546 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1585 removed outlier: 3.504A pdb=" N ILE A1571 " --> pdb=" O ASN A1567 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A1582 " --> pdb=" O CYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1616 removed outlier: 3.791A pdb=" N ILE A1596 " --> pdb=" O ILE A1592 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A1600 " --> pdb=" O ILE A1596 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA A1612 " --> pdb=" O GLY A1608 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A1613 " --> pdb=" O MET A1609 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A1614 " --> pdb=" O PHE A1610 " (cutoff:3.500A) Processing helix chain 'A' and resid 1621 through 1629 removed outlier: 3.502A pdb=" N PHE A1625 " --> pdb=" O SER A1621 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A1627 " --> pdb=" O THR A1623 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A1629 " --> pdb=" O PHE A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1634 Processing helix chain 'A' and resid 1635 through 1642 removed outlier: 4.048A pdb=" N GLY A1642 " --> pdb=" O LEU A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1655 Processing helix chain 'A' and resid 1656 through 1682 removed outlier: 3.589A pdb=" N ILE A1663 " --> pdb=" O ALA A1659 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A1666 " --> pdb=" O ASN A1662 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1670 " --> pdb=" O LEU A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1711 removed outlier: 3.614A pdb=" N ILE A1705 " --> pdb=" O GLY A1701 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A1709 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1715 through 1721 removed outlier: 3.777A pdb=" N LEU A1719 " --> pdb=" O GLY A1715 " (cutoff:3.500A) Processing helix chain 'A' and resid 1748 through 1785 removed outlier: 3.507A pdb=" N MET A1770 " --> pdb=" O VAL A1766 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A1777 " --> pdb=" O ALA A1773 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A1780 " --> pdb=" O LEU A1776 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A1782 " --> pdb=" O ASN A1778 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A1784 " --> pdb=" O SER A1780 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 13 removed outlier: 3.719A pdb=" N BARG D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.302A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 65 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN C 82 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TRP C 67 " --> pdb=" O PHE C 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 276 through 280 Processing sheet with id=AA5, first strand: chain 'A' and resid 1365 through 1367 541 hydrogen bonds defined for protein. 1525 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: 1.71 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 3223 1.36 - 1.52: 5746 1.52 - 1.69: 1626 1.69 - 1.85: 149 1.85 - 2.01: 1 Bond restraints: 10745 Sorted by residual: bond pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " ideal model delta sigma weight residual 1.808 2.011 -0.203 3.30e-02 9.18e+02 3.77e+01 bond pdb=" C ILE A1334 " pdb=" N PRO A1335 " ideal model delta sigma weight residual 1.336 1.407 -0.072 1.23e-02 6.61e+03 3.40e+01 bond pdb=" C GLN C 96 " pdb=" N ASP C 97 " ideal model delta sigma weight residual 1.332 1.245 0.086 1.52e-02 4.33e+03 3.23e+01 bond pdb=" N PRO A 921 " pdb=" CD PRO A 921 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.68e+01 bond pdb=" CA AARG D 10 " pdb=" C AARG D 10 " ideal model delta sigma weight residual 1.524 1.585 -0.061 1.27e-02 6.20e+03 2.32e+01 ... (remaining 10740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.07: 14467 6.07 - 12.14: 87 12.14 - 18.21: 13 18.21 - 24.29: 5 24.29 - 30.36: 1 Bond angle restraints: 14573 Sorted by residual: angle pdb=" CA AARG D 10 " pdb=" C AARG D 10 " pdb=" O AARG D 10 " ideal model delta sigma weight residual 120.82 136.81 -15.99 1.05e+00 9.07e-01 2.32e+02 angle pdb=" O GLN C 96 " pdb=" C GLN C 96 " pdb=" N ASP C 97 " ideal model delta sigma weight residual 122.59 142.68 -20.09 1.33e+00 5.65e-01 2.28e+02 angle pdb=" CA AARG D 10 " pdb=" C AARG D 10 " pdb=" N ASP D 11 " ideal model delta sigma weight residual 117.07 102.57 14.50 1.14e+00 7.69e-01 1.62e+02 angle pdb=" N AARG D 10 " pdb=" CA AARG D 10 " pdb=" C AARG D 10 " ideal model delta sigma weight residual 111.07 124.56 -13.49 1.07e+00 8.73e-01 1.59e+02 angle pdb=" N ASN A 212 " pdb=" CA ASN A 212 " pdb=" CB ASN A 212 " ideal model delta sigma weight residual 110.49 131.53 -21.04 1.69e+00 3.50e-01 1.55e+02 ... (remaining 14568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.99: 5875 22.99 - 45.98: 318 45.98 - 68.97: 52 68.97 - 91.95: 7 91.95 - 114.94: 1 Dihedral angle restraints: 6253 sinusoidal: 2501 harmonic: 3752 Sorted by residual: dihedral pdb=" N ASN A 212 " pdb=" C ASN A 212 " pdb=" CA ASN A 212 " pdb=" CB ASN A 212 " ideal model delta harmonic sigma weight residual 122.80 157.90 -35.10 0 2.50e+00 1.60e-01 1.97e+02 dihedral pdb=" C ASN A 212 " pdb=" N ASN A 212 " pdb=" CA ASN A 212 " pdb=" CB ASN A 212 " ideal model delta harmonic sigma weight residual -122.60 -151.91 29.31 0 2.50e+00 1.60e-01 1.37e+02 dihedral pdb=" CA PRO A1514 " pdb=" C PRO A1514 " pdb=" N ARG A1515 " pdb=" CA ARG A1515 " ideal model delta harmonic sigma weight residual 180.00 135.66 44.34 0 5.00e+00 4.00e-02 7.86e+01 ... (remaining 6250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.281: 1673 0.281 - 0.563: 7 0.563 - 0.844: 2 0.844 - 1.126: 0 1.126 - 1.407: 1 Chirality restraints: 1683 Sorted by residual: chirality pdb=" CA ASN A 212 " pdb=" N ASN A 212 " pdb=" C ASN A 212 " pdb=" CB ASN A 212 " both_signs ideal model delta sigma weight residual False 2.51 1.10 1.41 2.00e-01 2.50e+01 4.95e+01 chirality pdb=" CA TRP A 316 " pdb=" N TRP A 316 " pdb=" C TRP A 316 " pdb=" CB TRP A 316 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.98e+00 chirality pdb=" CA PRO A 744 " pdb=" N PRO A 744 " pdb=" C PRO A 744 " pdb=" CB PRO A 744 " both_signs ideal model delta sigma weight residual False 2.72 2.13 0.58 2.00e-01 2.50e+01 8.55e+00 ... (remaining 1680 not shown) Planarity restraints: 1782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 743 " -0.152 5.00e-02 4.00e+02 2.35e-01 8.82e+01 pdb=" N PRO A 744 " 0.405 5.00e-02 4.00e+02 pdb=" CA PRO A 744 " -0.150 5.00e-02 4.00e+02 pdb=" CD PRO A 744 " -0.104 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA BARG D 10 " 0.033 2.00e-02 2.50e+03 6.79e-02 4.61e+01 pdb=" C BARG D 10 " -0.117 2.00e-02 2.50e+03 pdb=" O BARG D 10 " 0.045 2.00e-02 2.50e+03 pdb=" N ASP D 11 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AARG D 10 " 0.025 2.00e-02 2.50e+03 4.82e-02 2.33e+01 pdb=" C AARG D 10 " -0.083 2.00e-02 2.50e+03 pdb=" O AARG D 10 " 0.035 2.00e-02 2.50e+03 pdb=" N ASP D 11 " 0.023 2.00e-02 2.50e+03 ... (remaining 1779 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 54 2.52 - 3.12: 7227 3.12 - 3.71: 15821 3.71 - 4.31: 22749 4.31 - 4.90: 36721 Nonbonded interactions: 82572 Sorted by model distance: nonbonded pdb=" O THR A1712 " pdb=" OG SER A1713 " model vdw 1.927 3.040 nonbonded pdb=" CG LYS A 743 " pdb=" CD PRO A 744 " model vdw 2.186 3.840 nonbonded pdb=" O LEU A1416 " pdb=" OG1 THR A1420 " model vdw 2.236 3.040 nonbonded pdb=" O LEU A 380 " pdb=" OG SER A 413 " model vdw 2.256 3.040 nonbonded pdb=" CD1 LEU A 436 " pdb=" OE2 GLU A 440 " model vdw 2.299 3.460 ... (remaining 82567 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 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.14 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.560 Find NCS groups from input model: 0.190 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 0.009 0.203 10764 Z= 0.406 Angle : 1.490 30.358 14619 Z= 0.817 Chirality : 0.078 1.407 1683 Planarity : 0.009 0.235 1778 Dihedral : 13.942 114.942 3798 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 1.03 % Allowed : 6.40 % Favored : 92.57 % Rotamer: Outliers : 5.14 % Allowed : 8.71 % Favored : 86.15 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 5.71 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.60 (0.17), residues: 1272 helix: -4.19 (0.09), residues: 774 sheet: -0.78 (0.53), residues: 85 loop : -2.87 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A1435 TYR 0.068 0.004 TYR A 907 PHE 0.047 0.004 PHE A1359 TRP 0.040 0.003 TRP A1348 HIS 0.017 0.002 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.39 (10745) covalent geometry : angle 1.43212 / 0.80 (14573) SS BOND : bond 0.06145 / 3.82 ( 11) SS BOND : angle 8.50588 / 3.97 ( 22) hydrogen bonds : bond 0.30412 / 19.96 ( 541) hydrogen bonds : angle 10.43248 / 7.35 ( 1525) link_BETA1-4 : bond 0.01230 / 0.69 ( 4) link_BETA1-4 : angle 7.91912 / 4.63 ( 12) link_NAG-ASN : bond 0.00816 / 0.50 ( 4) link_NAG-ASN : angle 4.19445 / 2.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 236 time to evaluate : 0.376 Fit side-chains REVERT: A 120 LYS cc_start: 0.5385 (OUTLIER) cc_final: 0.3871 (mptt) REVERT: A 758 ASP cc_start: -0.0337 (OUTLIER) cc_final: -0.0778 (t0) REVERT: A 919 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6547 (mt-10) outliers start: 58 outliers final: 12 residues processed: 282 average time/residue: 0.4811 time to fit residues: 147.3911 Evaluate side-chains 159 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 744 PRO Chi-restraints excluded: chain A residue 750 HIS Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 919 GLU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain D residue 5 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 70 GLN C 118 GLN A 132 ASN A 383 GLN A 388 ASN A 418 ASN A 441 GLN A 868 ASN A 876 ASN A 924 HIS A 971 ASN A1196 ASN A1207 HIS A1208 ASN A1272 ASN A1292 ASN A1466 ASN A1595 ASN A1702 ASN A1748 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.137318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.092679 restraints weight = 31341.034| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.31 r_work: 0.3003 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10764 Z= 0.163 Angle : 0.846 10.350 14619 Z= 0.425 Chirality : 0.044 0.225 1683 Planarity : 0.006 0.068 1778 Dihedral : 7.660 91.928 1416 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.90 % Favored : 94.47 % Rotamer: Outliers : 3.92 % Allowed : 17.42 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.20), residues: 1272 helix: -1.78 (0.16), residues: 784 sheet: -0.78 (0.53), residues: 80 loop : -2.53 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 119 TYR 0.019 0.002 TYR A 907 PHE 0.016 0.002 PHE A 986 TRP 0.026 0.001 TRP C 67 HIS 0.004 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (10745) covalent geometry : angle 0.83185 / 0.42 (14573) SS BOND : bond 0.01189 / 0.85 ( 11) SS BOND : angle 1.85796 / 1.09 ( 22) hydrogen bonds : bond 0.05967 / 3.92 ( 541) hydrogen bonds : angle 4.92420 / 3.39 ( 1525) link_BETA1-4 : bond 0.01071 / 0.57 ( 4) link_BETA1-4 : angle 4.42478 / 2.57 ( 12) link_NAG-ASN : bond 0.00318 / 0.22 ( 4) link_NAG-ASN : angle 2.27778 / 1.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: C 79 MET cc_start: 0.5490 (mtp) cc_final: 0.5222 (ttt) REVERT: C 107 LYS cc_start: 0.8654 (mttt) cc_final: 0.8453 (mmtm) REVERT: C 108 TYR cc_start: 0.7488 (m-80) cc_final: 0.7145 (m-80) REVERT: C 128 TYR cc_start: 0.5986 (m-80) cc_final: 0.5750 (m-80) REVERT: A 187 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7426 (mm) REVERT: A 217 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8002 (pmt170) REVERT: A 268 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8385 (mp10) REVERT: A 369 THR cc_start: 0.8130 (m) cc_final: 0.7760 (p) REVERT: A 749 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5769 (mmtm) REVERT: A 758 ASP cc_start: 0.0961 (OUTLIER) cc_final: 0.0253 (t70) REVERT: A 813 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6540 (ttt) REVERT: A 919 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8247 (mt-10) REVERT: A 1220 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8742 (tp) REVERT: A 1598 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8386 (t70) REVERT: A 1677 PHE cc_start: 0.8777 (m-80) cc_final: 0.8383 (t80) REVERT: D 3 ASN cc_start: 0.8367 (t0) cc_final: 0.7970 (t0) outliers start: 44 outliers final: 6 residues processed: 200 average time/residue: 0.4647 time to fit residues: 102.1314 Evaluate side-chains 154 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 919 GLU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1737 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 66 optimal weight: 0.0030 chunk 51 optimal weight: 9.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 GLN A 976 ASN A1207 HIS A1357 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.135921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.089423 restraints weight = 48858.307| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.25 r_work: 0.2944 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 0.043 10764 Z= 0.150 Angle : 0.737 9.448 14619 Z= 0.368 Chirality : 0.042 0.214 1683 Planarity : 0.005 0.069 1778 Dihedral : 6.899 100.378 1395 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.22 % Favored : 94.15 % Rotamer: Outliers : 5.92 % Allowed : 16.99 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.23), residues: 1272 helix: -0.22 (0.18), residues: 772 sheet: -0.80 (0.52), residues: 80 loop : -2.13 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 119 TYR 0.019 0.002 TYR A 390 PHE 0.018 0.001 PHE A 186 TRP 0.013 0.001 TRP C 67 HIS 0.003 0.001 HIS D 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (10745) covalent geometry : angle 0.72427 / 0.37 (14573) SS BOND : bond 0.00596 / 0.38 ( 11) SS BOND : angle 1.23939 / 0.79 ( 22) hydrogen bonds : bond 0.04513 / 2.96 ( 541) hydrogen bonds : angle 4.22000 / 2.88 ( 1525) link_BETA1-4 : bond 0.00971 / 0.51 ( 4) link_BETA1-4 : angle 4.20339 / 2.44 ( 12) link_NAG-ASN : bond 0.00248 / 0.15 ( 4) link_NAG-ASN : angle 1.93888 / 1.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 160 time to evaluate : 0.411 Fit side-chains REVERT: C 107 LYS cc_start: 0.8645 (mttt) cc_final: 0.8430 (mmtm) REVERT: C 108 TYR cc_start: 0.7559 (m-80) cc_final: 0.6937 (m-80) REVERT: A 757 MET cc_start: 0.4722 (OUTLIER) cc_final: 0.4132 (tpt) REVERT: A 758 ASP cc_start: 0.0933 (OUTLIER) cc_final: 0.0356 (t70) REVERT: A 852 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8798 (t80) REVERT: A 1220 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8697 (tp) REVERT: A 1243 GLU cc_start: 0.8300 (tp30) cc_final: 0.7752 (tm-30) REVERT: A 1577 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: A 1655 MET cc_start: 0.8925 (mmp) cc_final: 0.8704 (tpt) REVERT: A 1677 PHE cc_start: 0.8798 (m-80) cc_final: 0.8429 (t80) REVERT: D 3 ASN cc_start: 0.8482 (t0) cc_final: 0.8132 (t0) outliers start: 67 outliers final: 19 residues processed: 206 average time/residue: 0.4349 time to fit residues: 98.7402 Evaluate side-chains 171 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1577 GLU Chi-restraints excluded: chain A residue 1579 VAL Chi-restraints excluded: chain A residue 1768 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 116 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1207 HIS A1725 ASN A1778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.135230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089478 restraints weight = 42500.345| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.05 r_work: 0.2948 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10764 Z= 0.150 Angle : 0.714 9.933 14619 Z= 0.355 Chirality : 0.042 0.209 1683 Planarity : 0.004 0.073 1778 Dihedral : 6.512 102.071 1390 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.22 % Favored : 94.23 % Rotamer: Outliers : 5.40 % Allowed : 18.29 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.24), residues: 1272 helix: 0.47 (0.19), residues: 783 sheet: -0.73 (0.52), residues: 80 loop : -2.00 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1629 TYR 0.016 0.001 TYR A 390 PHE 0.018 0.001 PHE A 186 TRP 0.012 0.001 TRP C 67 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (10745) covalent geometry : angle 0.70163 / 0.35 (14573) SS BOND : bond 0.00760 / 0.54 ( 11) SS BOND : angle 1.14030 / 0.76 ( 22) hydrogen bonds : bond 0.04048 / 2.68 ( 541) hydrogen bonds : angle 3.99615 / 2.71 ( 1525) link_BETA1-4 : bond 0.01001 / 0.51 ( 4) link_BETA1-4 : angle 4.09825 / 2.36 ( 12) link_NAG-ASN : bond 0.00221 / 0.14 ( 4) link_NAG-ASN : angle 1.83693 / 1.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 158 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: C 79 MET cc_start: 0.5554 (mtp) cc_final: 0.5292 (ttt) REVERT: C 108 TYR cc_start: 0.7616 (m-80) cc_final: 0.7009 (m-80) REVERT: A 755 VAL cc_start: 0.2994 (OUTLIER) cc_final: 0.2529 (p) REVERT: A 758 ASP cc_start: 0.0843 (OUTLIER) cc_final: 0.0255 (t70) REVERT: A 813 MET cc_start: 0.6883 (ttt) cc_final: 0.6618 (ttt) REVERT: A 852 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8777 (t80) REVERT: A 1220 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8692 (tp) REVERT: A 1243 GLU cc_start: 0.8337 (tp30) cc_final: 0.7775 (tm-30) REVERT: A 1508 LYS cc_start: 0.5902 (OUTLIER) cc_final: 0.5143 (mmtm) REVERT: A 1551 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8119 (mp0) REVERT: A 1577 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7937 (tp30) REVERT: A 1677 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8540 (t80) REVERT: A 1694 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8626 (ttt) REVERT: D 3 ASN cc_start: 0.8551 (t0) cc_final: 0.8241 (t0) outliers start: 61 outliers final: 23 residues processed: 197 average time/residue: 0.4896 time to fit residues: 105.5647 Evaluate side-chains 176 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1508 LYS Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1577 GLU Chi-restraints excluded: chain A residue 1579 VAL Chi-restraints excluded: chain A residue 1677 PHE Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1737 HIS Chi-restraints excluded: chain A residue 1751 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.135956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.090622 restraints weight = 42440.838| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.97 r_work: 0.2969 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10764 Z= 0.127 Angle : 0.676 9.370 14619 Z= 0.336 Chirality : 0.041 0.210 1683 Planarity : 0.004 0.071 1778 Dihedral : 6.397 104.359 1390 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.90 % Favored : 94.55 % Rotamer: Outliers : 4.62 % Allowed : 19.60 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1272 helix: 0.98 (0.19), residues: 783 sheet: -0.66 (0.53), residues: 80 loop : -1.94 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 358 TYR 0.026 0.001 TYR A1564 PHE 0.013 0.001 PHE A 186 TRP 0.007 0.001 TRP C 67 HIS 0.003 0.001 HIS A 750 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10745) covalent geometry : angle 0.66360 / 0.33 (14573) SS BOND : bond 0.00360 / 0.24 ( 11) SS BOND : angle 1.23652 / 0.92 ( 22) hydrogen bonds : bond 0.03684 / 2.43 ( 541) hydrogen bonds : angle 3.84445 / 2.59 ( 1525) link_BETA1-4 : bond 0.00969 / 0.50 ( 4) link_BETA1-4 : angle 3.98635 / 2.28 ( 12) link_NAG-ASN : bond 0.00178 / 0.11 ( 4) link_NAG-ASN : angle 1.76231 / 0.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: C 79 MET cc_start: 0.5759 (mtp) cc_final: 0.5480 (ttt) REVERT: C 108 TYR cc_start: 0.7562 (m-80) cc_final: 0.7033 (m-80) REVERT: A 749 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5759 (mmtm) REVERT: A 755 VAL cc_start: 0.3332 (OUTLIER) cc_final: 0.3022 (p) REVERT: A 758 ASP cc_start: 0.0963 (OUTLIER) cc_final: 0.0219 (t0) REVERT: A 813 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6204 (ttt) REVERT: A 817 TYR cc_start: 0.7125 (m-80) cc_final: 0.6691 (m-80) REVERT: A 852 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8684 (t80) REVERT: A 1220 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8716 (tp) REVERT: A 1243 GLU cc_start: 0.8328 (tp30) cc_final: 0.7768 (tm-30) REVERT: A 1501 MET cc_start: 0.7759 (ttm) cc_final: 0.7556 (ttt) REVERT: A 1508 LYS cc_start: 0.5910 (OUTLIER) cc_final: 0.5314 (mmtm) REVERT: A 1551 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8104 (mp0) REVERT: A 1577 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7866 (tp30) REVERT: A 1628 ILE cc_start: 0.8719 (pt) cc_final: 0.8503 (mp) REVERT: A 1677 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8520 (t80) REVERT: A 1694 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8593 (ttt) REVERT: D 3 ASN cc_start: 0.8540 (t0) cc_final: 0.8230 (t0) outliers start: 52 outliers final: 21 residues processed: 194 average time/residue: 0.4445 time to fit residues: 94.7574 Evaluate side-chains 178 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1508 LYS Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1577 GLU Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1677 PHE Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1737 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 40.0000 chunk 77 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN A1207 HIS A1475 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.130672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.085100 restraints weight = 40947.396| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.80 r_work: 0.2880 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10764 Z= 0.270 Angle : 0.773 12.933 14619 Z= 0.387 Chirality : 0.046 0.220 1683 Planarity : 0.005 0.073 1778 Dihedral : 6.555 103.618 1390 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.69 % Favored : 93.75 % Rotamer: Outliers : 6.18 % Allowed : 19.25 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.24), residues: 1272 helix: 0.94 (0.19), residues: 781 sheet: -0.66 (0.52), residues: 80 loop : -1.85 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1306 TYR 0.027 0.002 TYR A 907 PHE 0.024 0.002 PHE A 963 TRP 0.008 0.001 TRP A 864 HIS 0.004 0.001 HIS A 750 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.27 (10745) covalent geometry : angle 0.76053 / 0.38 (14573) SS BOND : bond 0.00465 / 0.31 ( 11) SS BOND : angle 1.44834 / 1.06 ( 22) hydrogen bonds : bond 0.04558 / 3.03 ( 541) hydrogen bonds : angle 4.04299 / 2.74 ( 1525) link_BETA1-4 : bond 0.00744 / 0.38 ( 4) link_BETA1-4 : angle 4.33770 / 2.55 ( 12) link_NAG-ASN : bond 0.00451 / 0.31 ( 4) link_NAG-ASN : angle 1.93854 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 147 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 79 MET cc_start: 0.5604 (mtp) cc_final: 0.5310 (ttt) REVERT: C 108 TYR cc_start: 0.7567 (m-80) cc_final: 0.6765 (m-80) REVERT: A 268 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8592 (mp10) REVERT: A 387 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8441 (pm20) REVERT: A 411 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9131 (mt) REVERT: A 755 VAL cc_start: 0.3145 (OUTLIER) cc_final: 0.2900 (p) REVERT: A 758 ASP cc_start: 0.1153 (OUTLIER) cc_final: 0.0331 (t70) REVERT: A 813 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6484 (ttt) REVERT: A 817 TYR cc_start: 0.7110 (m-80) cc_final: 0.6683 (m-80) REVERT: A 1211 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7566 (pt0) REVERT: A 1220 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8726 (tp) REVERT: A 1243 GLU cc_start: 0.8439 (tp30) cc_final: 0.8221 (tp30) REVERT: A 1508 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5042 (mmtm) REVERT: A 1577 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7863 (tp30) REVERT: A 1677 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8447 (t80) REVERT: A 1694 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8892 (ttt) REVERT: D 3 ASN cc_start: 0.8510 (t0) cc_final: 0.8297 (t0) outliers start: 70 outliers final: 25 residues processed: 197 average time/residue: 0.4268 time to fit residues: 92.4698 Evaluate side-chains 175 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1323 MET Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain A residue 1508 LYS Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1577 GLU Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1677 PHE Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1737 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 85 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 118 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.135009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.089436 restraints weight = 39600.794| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.93 r_work: 0.2954 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10764 Z= 0.122 Angle : 0.684 10.112 14619 Z= 0.337 Chirality : 0.041 0.211 1683 Planarity : 0.004 0.068 1778 Dihedral : 6.418 108.613 1390 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.06 % Favored : 94.47 % Rotamer: Outliers : 4.62 % Allowed : 20.99 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1272 helix: 1.34 (0.19), residues: 787 sheet: -0.67 (0.51), residues: 80 loop : -1.74 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1626 TYR 0.024 0.001 TYR A1564 PHE 0.014 0.001 PHE A1755 TRP 0.009 0.001 TRP A1209 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10745) covalent geometry : angle 0.67301 / 0.33 (14573) SS BOND : bond 0.00283 / 0.19 ( 11) SS BOND : angle 0.98323 / 0.68 ( 22) hydrogen bonds : bond 0.03549 / 2.33 ( 541) hydrogen bonds : angle 3.78847 / 2.57 ( 1525) link_BETA1-4 : bond 0.00997 / 0.51 ( 4) link_BETA1-4 : angle 3.92492 / 2.22 ( 12) link_NAG-ASN : bond 0.00238 / 0.14 ( 4) link_NAG-ASN : angle 1.73028 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: C 108 TYR cc_start: 0.7496 (m-80) cc_final: 0.6897 (m-80) REVERT: A 220 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.8023 (mtm-85) REVERT: A 268 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8459 (mm-40) REVERT: A 387 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: A 411 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8975 (mm) REVERT: A 755 VAL cc_start: 0.3921 (OUTLIER) cc_final: 0.3213 (p) REVERT: A 758 ASP cc_start: 0.0966 (OUTLIER) cc_final: 0.0156 (t70) REVERT: A 813 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6317 (ttt) REVERT: A 817 TYR cc_start: 0.7089 (m-80) cc_final: 0.6735 (m-80) REVERT: A 869 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8137 (mmm) REVERT: A 905 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.9036 (ttmt) REVERT: A 967 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8345 (ttp) REVERT: A 1243 GLU cc_start: 0.8369 (tp30) cc_final: 0.7789 (tm-30) REVERT: A 1508 LYS cc_start: 0.5860 (OUTLIER) cc_final: 0.4975 (mmtm) REVERT: A 1551 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8115 (mp0) REVERT: A 1577 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: A 1694 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8638 (ttt) REVERT: D 3 ASN cc_start: 0.8547 (t0) cc_final: 0.8304 (t0) outliers start: 52 outliers final: 17 residues processed: 197 average time/residue: 0.4754 time to fit residues: 102.4587 Evaluate side-chains 175 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 905 LYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain A residue 1508 LYS Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1573 LEU Chi-restraints excluded: chain A residue 1577 GLU Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1737 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 80 optimal weight: 0.9990 chunk 99 optimal weight: 0.0060 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.090248 restraints weight = 35436.337| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.63 r_work: 0.2977 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10764 Z= 0.128 Angle : 0.696 10.429 14619 Z= 0.342 Chirality : 0.041 0.214 1683 Planarity : 0.004 0.066 1778 Dihedral : 6.358 106.465 1390 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.30 % Favored : 94.31 % Rotamer: Outliers : 4.18 % Allowed : 22.30 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1272 helix: 1.57 (0.19), residues: 784 sheet: -0.62 (0.52), residues: 80 loop : -1.75 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 84 TYR 0.015 0.001 TYR A 390 PHE 0.017 0.001 PHE C 63 TRP 0.009 0.001 TRP A1716 HIS 0.002 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (10745) covalent geometry : angle 0.68483 / 0.34 (14573) SS BOND : bond 0.00325 / 0.22 ( 11) SS BOND : angle 1.02128 / 0.71 ( 22) hydrogen bonds : bond 0.03463 / 2.26 ( 541) hydrogen bonds : angle 3.73905 / 2.55 ( 1525) link_BETA1-4 : bond 0.00999 / 0.51 ( 4) link_BETA1-4 : angle 3.91565 / 2.24 ( 12) link_NAG-ASN : bond 0.00154 / 0.09 ( 4) link_NAG-ASN : angle 1.67729 / 0.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 MET cc_start: 0.5904 (ttt) cc_final: 0.5664 (mtp) REVERT: C 85 MET cc_start: 0.7021 (mmm) cc_final: 0.6498 (tpp) REVERT: C 108 TYR cc_start: 0.7528 (m-80) cc_final: 0.6855 (m-80) REVERT: A 220 ARG cc_start: 0.8559 (mtm-85) cc_final: 0.8183 (mtm-85) REVERT: A 268 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8454 (mm-40) REVERT: A 387 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: A 411 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8969 (mm) REVERT: A 758 ASP cc_start: 0.1296 (OUTLIER) cc_final: 0.0244 (t70) REVERT: A 813 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6319 (ttt) REVERT: A 817 TYR cc_start: 0.7141 (m-80) cc_final: 0.6763 (m-80) REVERT: A 869 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8191 (mmm) REVERT: A 905 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.9003 (ttmt) REVERT: A 960 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9064 (mm) REVERT: A 967 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8223 (ttp) REVERT: A 1243 GLU cc_start: 0.8355 (tp30) cc_final: 0.7780 (tm-30) REVERT: A 1508 LYS cc_start: 0.5883 (OUTLIER) cc_final: 0.5163 (mmtm) REVERT: A 1551 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8072 (mp0) REVERT: A 1577 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7836 (tp30) REVERT: A 1694 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8615 (ttt) REVERT: D 3 ASN cc_start: 0.8516 (t0) cc_final: 0.8305 (t0) outliers start: 47 outliers final: 19 residues processed: 184 average time/residue: 0.4491 time to fit residues: 90.6883 Evaluate side-chains 178 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 905 LYS Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1508 LYS Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1577 GLU Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1737 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 25 optimal weight: 0.2980 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 0.0060 chunk 123 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1778 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.134194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.089563 restraints weight = 26182.325| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.02 r_work: 0.3001 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10764 Z= 0.142 Angle : 0.705 9.993 14619 Z= 0.346 Chirality : 0.042 0.218 1683 Planarity : 0.004 0.064 1778 Dihedral : 6.417 106.314 1390 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.69 % Favored : 93.99 % Rotamer: Outliers : 4.01 % Allowed : 23.17 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.25), residues: 1272 helix: 1.63 (0.19), residues: 786 sheet: -0.53 (0.53), residues: 79 loop : -1.78 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 84 TYR 0.023 0.001 TYR A1564 PHE 0.014 0.001 PHE A 186 TRP 0.012 0.001 TRP C 67 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10745) covalent geometry : angle 0.69470 / 0.34 (14573) SS BOND : bond 0.00313 / 0.21 ( 11) SS BOND : angle 1.03384 / 0.72 ( 22) hydrogen bonds : bond 0.03531 / 2.31 ( 541) hydrogen bonds : angle 3.74119 / 2.55 ( 1525) link_BETA1-4 : bond 0.00956 / 0.49 ( 4) link_BETA1-4 : angle 3.91216 / 2.23 ( 12) link_NAG-ASN : bond 0.00174 / 0.10 ( 4) link_NAG-ASN : angle 1.61069 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 108 TYR cc_start: 0.7566 (m-80) cc_final: 0.6878 (m-80) REVERT: A 220 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8232 (mtm-85) REVERT: A 268 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8560 (mm-40) REVERT: A 387 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: A 411 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8998 (mm) REVERT: A 757 MET cc_start: 0.4733 (mpp) cc_final: 0.4359 (mmm) REVERT: A 813 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6382 (ttt) REVERT: A 817 TYR cc_start: 0.7163 (m-80) cc_final: 0.6766 (m-80) REVERT: A 905 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9057 (ttmt) REVERT: A 967 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8455 (ttp) REVERT: A 1243 GLU cc_start: 0.8520 (tp30) cc_final: 0.7950 (tm-30) REVERT: A 1508 LYS cc_start: 0.5871 (OUTLIER) cc_final: 0.5192 (mmtm) REVERT: A 1551 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8288 (mp0) REVERT: A 1577 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: A 1694 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8696 (ttt) REVERT: D 3 ASN cc_start: 0.8553 (t0) cc_final: 0.8314 (t0) outliers start: 45 outliers final: 25 residues processed: 179 average time/residue: 0.4670 time to fit residues: 91.4441 Evaluate side-chains 177 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 905 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1508 LYS Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1577 GLU Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1737 HIS Chi-restraints excluded: chain A residue 1778 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 43 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1778 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.134869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.089621 restraints weight = 43317.716| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.00 r_work: 0.2957 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10764 Z= 0.132 Angle : 0.705 11.543 14619 Z= 0.347 Chirality : 0.042 0.219 1683 Planarity : 0.004 0.063 1778 Dihedral : 6.372 106.627 1390 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.53 % Favored : 94.23 % Rotamer: Outliers : 3.66 % Allowed : 23.08 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.25), residues: 1272 helix: 1.71 (0.19), residues: 786 sheet: -0.55 (0.53), residues: 79 loop : -1.77 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 84 TYR 0.015 0.001 TYR A 390 PHE 0.023 0.001 PHE A1779 TRP 0.009 0.001 TRP A1716 HIS 0.002 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10745) covalent geometry : angle 0.69462 / 0.34 (14573) SS BOND : bond 0.00286 / 0.19 ( 11) SS BOND : angle 0.98696 / 0.68 ( 22) hydrogen bonds : bond 0.03408 / 2.23 ( 541) hydrogen bonds : angle 3.73132 / 2.56 ( 1525) link_BETA1-4 : bond 0.00961 / 0.50 ( 4) link_BETA1-4 : angle 3.86552 / 2.20 ( 12) link_NAG-ASN : bond 0.00174 / 0.10 ( 4) link_NAG-ASN : angle 1.59412 / 0.87 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 65 LEU cc_start: 0.8039 (tp) cc_final: 0.7835 (tt) REVERT: C 108 TYR cc_start: 0.7474 (m-80) cc_final: 0.6768 (m-80) REVERT: A 220 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8183 (mtm-85) REVERT: A 268 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8461 (mm-40) REVERT: A 387 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8382 (pm20) REVERT: A 411 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8944 (mm) REVERT: A 757 MET cc_start: 0.4474 (mpp) cc_final: 0.4181 (mmm) REVERT: A 813 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6307 (ttt) REVERT: A 817 TYR cc_start: 0.7091 (m-80) cc_final: 0.6747 (m-80) REVERT: A 905 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.9006 (ttmt) REVERT: A 967 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8292 (ttp) REVERT: A 1243 GLU cc_start: 0.8444 (tp30) cc_final: 0.7869 (tm-30) REVERT: A 1508 LYS cc_start: 0.5878 (OUTLIER) cc_final: 0.5184 (mmtm) REVERT: A 1551 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8109 (mp0) REVERT: A 1577 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: A 1694 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8625 (ttt) REVERT: D 3 ASN cc_start: 0.8542 (t0) cc_final: 0.8314 (t0) outliers start: 41 outliers final: 26 residues processed: 180 average time/residue: 0.4687 time to fit residues: 92.2611 Evaluate side-chains 180 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 905 LYS Chi-restraints excluded: chain A residue 919 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1508 LYS Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1577 GLU Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1737 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 0.0170 chunk 109 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 GLN A1769 ASN A1778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.090601 restraints weight = 35589.834| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.43 r_work: 0.2975 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10764 Z= 0.130 Angle : 0.708 13.172 14619 Z= 0.345 Chirality : 0.042 0.219 1683 Planarity : 0.004 0.061 1778 Dihedral : 6.324 106.559 1390 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.69 % Favored : 94.07 % Rotamer: Outliers : 4.01 % Allowed : 22.82 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.25), residues: 1272 helix: 1.76 (0.19), residues: 787 sheet: -0.57 (0.53), residues: 79 loop : -1.77 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 850 TYR 0.015 0.001 TYR A 390 PHE 0.014 0.001 PHE A 186 TRP 0.008 0.001 TRP A1716 HIS 0.002 0.001 HIS A 750 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10745) covalent geometry : angle 0.69803 / 0.34 (14573) SS BOND : bond 0.00351 / 0.25 ( 11) SS BOND : angle 1.03261 / 0.72 ( 22) hydrogen bonds : bond 0.03368 / 2.20 ( 541) hydrogen bonds : angle 3.71011 / 2.54 ( 1525) link_BETA1-4 : bond 0.00966 / 0.50 ( 4) link_BETA1-4 : angle 3.84108 / 2.19 ( 12) link_NAG-ASN : bond 0.00166 / 0.09 ( 4) link_NAG-ASN : angle 1.58136 / 0.87 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4212.51 seconds wall clock time: 72 minutes 21.24 seconds (4341.24 seconds total)