Starting phenix.real_space_refine on Tue Jul 29 19:12:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j8e_9780/07_2025/6j8e_9780.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j8e_9780/07_2025/6j8e_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6j8e_9780/07_2025/6j8e_9780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j8e_9780/07_2025/6j8e_9780.map" model { file = "/net/cci-nas-00/data/ceres_data/6j8e_9780/07_2025/6j8e_9780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j8e_9780/07_2025/6j8e_9780.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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: 7.35, per 1000 atoms: 0.70 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: 2.73 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.11 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: 3.45 Time building geometry restraints manager: 3.24 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: 6084 22.99 - 45.98: 337 45.98 - 68.97: 65 68.97 - 91.95: 9 91.95 - 114.94: 7 Dihedral angle restraints: 6502 sinusoidal: 2750 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 6499 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.170 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 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 : 14.773 114.942 4047 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.040 0.003 TRP A1348 HIS 0.017 0.002 HIS A 128 PHE 0.047 0.004 PHE A1359 TYR 0.068 0.004 TYR A 907 ARG 0.016 0.002 ARG A1435 Details of bonding type rmsd link_NAG-ASN : bond 0.00816 ( 4) link_NAG-ASN : angle 4.19445 ( 12) link_BETA1-4 : bond 0.01230 ( 4) link_BETA1-4 : angle 7.91912 ( 12) hydrogen bonds : bond 0.30412 ( 541) hydrogen bonds : angle 10.43248 ( 1525) SS BOND : bond 0.06145 ( 11) SS BOND : angle 8.50588 ( 22) covalent geometry : bond 0.00831 (10745) covalent geometry : angle 1.43212 (14573) *********************** 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 : 1.197 Fit side-chains REVERT: A 120 LYS cc_start: 0.5385 (OUTLIER) cc_final: 0.3872 (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: 1.0366 time to fit residues: 317.9376 Evaluate side-chains 157 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 106 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN C 82 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.136592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.090864 restraints weight = 43078.756| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.86 r_work: 0.2968 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- 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 = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10764 Z= 0.173 Angle : 0.854 10.306 14619 Z= 0.428 Chirality : 0.044 0.228 1683 Planarity : 0.006 0.068 1778 Dihedral : 10.299 106.607 1665 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.74 % Favored : 94.62 % Rotamer: Outliers : 4.36 % Allowed : 16.81 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.21), residues: 1272 helix: -1.78 (0.16), residues: 782 sheet: -0.78 (0.53), residues: 80 loop : -2.47 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 67 HIS 0.004 0.001 HIS C 136 PHE 0.016 0.002 PHE A 986 TYR 0.020 0.002 TYR A 390 ARG 0.007 0.001 ARG A 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 4) link_NAG-ASN : angle 2.32663 ( 12) link_BETA1-4 : bond 0.00930 ( 4) link_BETA1-4 : angle 4.86697 ( 12) hydrogen bonds : bond 0.05666 ( 541) hydrogen bonds : angle 4.87886 ( 1525) SS BOND : bond 0.00938 ( 11) SS BOND : angle 1.78230 ( 22) covalent geometry : bond 0.00379 (10745) covalent geometry : angle 0.83821 (14573) *********************** 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 220 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: C 71 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5739 (mm-30) REVERT: C 107 LYS cc_start: 0.8659 (mttt) cc_final: 0.8447 (mmtm) REVERT: C 108 TYR cc_start: 0.7526 (m-80) cc_final: 0.7071 (m-80) REVERT: C 128 TYR cc_start: 0.6005 (m-80) cc_final: 0.5767 (m-80) REVERT: A 187 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7557 (mm) REVERT: A 217 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8027 (pmt170) REVERT: A 369 THR cc_start: 0.8204 (m) cc_final: 0.7816 (p) REVERT: A 749 LYS cc_start: 0.6030 (OUTLIER) cc_final: 0.5595 (mmtm) REVERT: A 758 ASP cc_start: 0.1084 (OUTLIER) cc_final: 0.0307 (t70) REVERT: A 919 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8386 (mt-10) REVERT: A 1220 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8759 (tp) REVERT: A 1677 PHE cc_start: 0.8786 (m-80) cc_final: 0.8436 (t80) REVERT: D 3 ASN cc_start: 0.8441 (t0) cc_final: 0.8012 (t0) outliers start: 49 outliers final: 7 residues processed: 207 average time/residue: 0.9485 time to fit residues: 216.2409 Evaluate side-chains 157 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 217 ARG 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 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 1737 HIS Chi-restraints excluded: chain A residue 1751 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1207 HIS A1292 ASN A1475 ASN A1725 ASN A1778 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.130786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.084086 restraints weight = 43242.323| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.03 r_work: 0.2856 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10764 Z= 0.300 Angle : 0.869 11.306 14619 Z= 0.435 Chirality : 0.049 0.258 1683 Planarity : 0.006 0.073 1778 Dihedral : 9.530 99.690 1644 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.85 % Favored : 93.52 % Rotamer: Outliers : 7.67 % Allowed : 16.64 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.23), residues: 1272 helix: -0.38 (0.18), residues: 769 sheet: -0.82 (0.51), residues: 80 loop : -2.07 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 864 HIS 0.004 0.002 HIS A 924 PHE 0.028 0.002 PHE A 963 TYR 0.037 0.003 TYR A 907 ARG 0.006 0.001 ARG A1435 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 4) link_NAG-ASN : angle 2.43756 ( 12) link_BETA1-4 : bond 0.00500 ( 4) link_BETA1-4 : angle 5.28783 ( 12) hydrogen bonds : bond 0.05561 ( 541) hydrogen bonds : angle 4.42929 ( 1525) SS BOND : bond 0.00740 ( 11) SS BOND : angle 1.66539 ( 22) covalent geometry : bond 0.00708 (10745) covalent geometry : angle 0.85213 (14573) *********************** 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 236 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 149 time to evaluate : 1.106 Fit side-chains REVERT: C 79 MET cc_start: 0.5603 (mtp) cc_final: 0.5329 (ttt) REVERT: C 108 TYR cc_start: 0.7423 (m-80) cc_final: 0.6713 (m-80) REVERT: A 187 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7688 (mm) REVERT: A 217 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7871 (pmt170) REVERT: A 220 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8220 (mtm-85) REVERT: A 268 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8493 (mp10) REVERT: A 757 MET cc_start: 0.4775 (OUTLIER) cc_final: 0.4176 (tpt) REVERT: A 758 ASP cc_start: 0.1495 (OUTLIER) cc_final: 0.0753 (t70) REVERT: A 1508 LYS cc_start: 0.5929 (OUTLIER) cc_final: 0.5209 (mmtp) REVERT: A 1677 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8490 (t80) REVERT: A 1694 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8927 (ttt) REVERT: D 3 ASN cc_start: 0.8544 (t0) cc_final: 0.8283 (t0) outliers start: 87 outliers final: 24 residues processed: 213 average time/residue: 0.9554 time to fit residues: 223.6340 Evaluate side-chains 168 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 390 TYR 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 848 VAL Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 919 GLU 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 1305 LEU Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain A residue 1504 LEU Chi-restraints excluded: chain A residue 1508 LYS Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1579 VAL Chi-restraints excluded: chain A residue 1628 ILE 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 1768 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 11 optimal weight: 40.0000 chunk 12 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 120 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.134564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.088377 restraints weight = 39088.031| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.82 r_work: 0.2937 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3968 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= 0.135 Angle : 0.723 9.867 14619 Z= 0.357 Chirality : 0.042 0.195 1683 Planarity : 0.004 0.069 1778 Dihedral : 8.919 102.763 1644 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.22 % Favored : 94.23 % Rotamer: Outliers : 4.44 % Allowed : 19.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1272 helix: 0.46 (0.19), residues: 775 sheet: -0.83 (0.51), residues: 80 loop : -2.01 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1716 HIS 0.009 0.001 HIS A 750 PHE 0.014 0.001 PHE C 83 TYR 0.017 0.001 TYR A 390 ARG 0.003 0.000 ARG A 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 4) link_NAG-ASN : angle 1.90339 ( 12) link_BETA1-4 : bond 0.01131 ( 4) link_BETA1-4 : angle 4.75196 ( 12) hydrogen bonds : bond 0.04052 ( 541) hydrogen bonds : angle 4.01465 ( 1525) SS BOND : bond 0.00826 ( 11) SS BOND : angle 1.10376 ( 22) covalent geometry : bond 0.00298 (10745) covalent geometry : angle 0.70798 (14573) *********************** 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 210 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 160 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 79 MET cc_start: 0.5765 (mtp) cc_final: 0.5507 (ttt) REVERT: C 108 TYR cc_start: 0.7505 (m-80) cc_final: 0.6988 (m-80) REVERT: A 217 ARG cc_start: 0.8276 (pmt170) cc_final: 0.8033 (pmt170) REVERT: A 387 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: A 751 LEU cc_start: 0.8010 (mp) cc_final: 0.7791 (mm) REVERT: A 754 LEU cc_start: 0.5541 (OUTLIER) cc_final: 0.4447 (tp) REVERT: A 755 VAL cc_start: 0.3331 (OUTLIER) cc_final: 0.2983 (p) REVERT: A 758 ASP cc_start: 0.1146 (OUTLIER) cc_final: 0.0557 (t70) REVERT: A 852 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8682 (t80) REVERT: A 1243 GLU cc_start: 0.8285 (tp30) cc_final: 0.7750 (tm-30) REVERT: A 1551 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8126 (mp0) REVERT: A 1577 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: A 1677 PHE cc_start: 0.8744 (m-80) cc_final: 0.8403 (t80) REVERT: D 3 ASN cc_start: 0.8513 (t0) cc_final: 0.8271 (t0) outliers start: 50 outliers final: 19 residues processed: 193 average time/residue: 1.0251 time to fit residues: 216.1532 Evaluate side-chains 169 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 LEU 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 210 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 754 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 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 983 LEU Chi-restraints excluded: chain A residue 1283 ASP Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1577 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 1 optimal weight: 0.0670 chunk 2 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A1207 HIS A1778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.135385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.089671 restraints weight = 38691.413| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.87 r_work: 0.2961 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4205 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= 0.124 Angle : 0.692 9.377 14619 Z= 0.341 Chirality : 0.042 0.204 1683 Planarity : 0.004 0.069 1778 Dihedral : 8.427 101.716 1642 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.14 % Favored : 94.39 % Rotamer: Outliers : 4.62 % Allowed : 20.47 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1272 helix: 0.98 (0.19), residues: 783 sheet: -0.60 (0.52), residues: 80 loop : -1.94 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 67 HIS 0.008 0.001 HIS A 750 PHE 0.017 0.001 PHE C 63 TYR 0.028 0.001 TYR A1564 ARG 0.011 0.001 ARG A 358 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 4) link_NAG-ASN : angle 1.84566 ( 12) link_BETA1-4 : bond 0.01040 ( 4) link_BETA1-4 : angle 4.72207 ( 12) hydrogen bonds : bond 0.03666 ( 541) hydrogen bonds : angle 3.82556 ( 1525) SS BOND : bond 0.00331 ( 11) SS BOND : angle 1.24945 ( 22) covalent geometry : bond 0.00270 (10745) covalent geometry : angle 0.67551 (14573) *********************** 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 210 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: C 79 MET cc_start: 0.5673 (mtp) cc_final: 0.5413 (ttt) REVERT: C 108 TYR cc_start: 0.7557 (m-80) cc_final: 0.7005 (m-80) REVERT: A 187 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7501 (mm) REVERT: A 220 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.8305 (mtm-85) REVERT: A 387 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: A 751 LEU cc_start: 0.8133 (mp) cc_final: 0.7931 (mm) REVERT: A 754 LEU cc_start: 0.5443 (OUTLIER) cc_final: 0.4394 (tp) REVERT: A 755 VAL cc_start: 0.3389 (OUTLIER) cc_final: 0.3106 (p) REVERT: A 758 ASP cc_start: 0.0961 (OUTLIER) cc_final: 0.0358 (t70) REVERT: A 855 LEU cc_start: 0.9384 (mt) cc_final: 0.9114 (mm) REVERT: A 1243 GLU cc_start: 0.8296 (tp30) cc_final: 0.7734 (tm-30) REVERT: A 1508 LYS cc_start: 0.5849 (OUTLIER) cc_final: 0.5041 (mmtm) REVERT: A 1551 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8193 (mp0) REVERT: A 1577 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: A 1677 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8403 (t80) REVERT: D 3 ASN cc_start: 0.8521 (t0) cc_final: 0.8260 (t0) outliers start: 52 outliers final: 17 residues processed: 193 average time/residue: 0.9070 time to fit residues: 192.5350 Evaluate side-chains 167 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 65 LEU 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 187 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 754 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 869 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1508 LYS 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 1737 HIS Chi-restraints excluded: chain A residue 1778 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 40.0000 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 chunk 79 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A1778 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.133332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.087878 restraints weight = 55467.203| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.42 r_work: 0.2906 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10764 Z= 0.161 Angle : 0.704 9.924 14619 Z= 0.348 Chirality : 0.043 0.212 1683 Planarity : 0.004 0.068 1778 Dihedral : 8.163 99.063 1639 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.14 % Favored : 94.31 % Rotamer: Outliers : 5.14 % Allowed : 20.64 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1272 helix: 1.19 (0.19), residues: 782 sheet: -0.58 (0.52), residues: 80 loop : -1.84 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1716 HIS 0.007 0.001 HIS A 750 PHE 0.014 0.001 PHE A 963 TYR 0.017 0.001 TYR A 390 ARG 0.006 0.001 ARG A 358 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 4) link_NAG-ASN : angle 1.87479 ( 12) link_BETA1-4 : bond 0.00946 ( 4) link_BETA1-4 : angle 4.76218 ( 12) hydrogen bonds : bond 0.03801 ( 541) hydrogen bonds : angle 3.84102 ( 1525) SS BOND : bond 0.00372 ( 11) SS BOND : angle 1.21069 ( 22) covalent geometry : bond 0.00375 (10745) covalent geometry : angle 0.68805 (14573) *********************** 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 208 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 150 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: C 108 TYR cc_start: 0.7532 (m-80) cc_final: 0.6787 (m-80) REVERT: A 187 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7564 (mm) REVERT: A 220 ARG cc_start: 0.8636 (mtm-85) cc_final: 0.8273 (mtm-85) REVERT: A 268 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8602 (mp10) REVERT: A 387 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8471 (pm20) REVERT: A 411 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9049 (mm) REVERT: A 754 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.4410 (tp) REVERT: A 755 VAL cc_start: 0.3520 (OUTLIER) cc_final: 0.3288 (p) REVERT: A 758 ASP cc_start: 0.1043 (OUTLIER) cc_final: 0.0390 (t70) REVERT: A 817 TYR cc_start: 0.7161 (m-80) cc_final: 0.6880 (m-80) REVERT: A 855 LEU cc_start: 0.9418 (mt) cc_final: 0.9186 (mm) REVERT: A 905 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9052 (ttmt) REVERT: A 960 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9046 (mm) REVERT: A 1211 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7530 (pt0) REVERT: A 1243 GLU cc_start: 0.8378 (tp30) cc_final: 0.7810 (tm-30) REVERT: A 1508 LYS cc_start: 0.5860 (OUTLIER) cc_final: 0.5025 (mmtm) REVERT: A 1577 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7906 (tp30) REVERT: A 1677 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8446 (t80) REVERT: D 3 ASN cc_start: 0.8489 (t0) cc_final: 0.8216 (t0) outliers start: 58 outliers final: 20 residues processed: 193 average time/residue: 0.9493 time to fit residues: 200.9053 Evaluate side-chains 174 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 ARG 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 187 LEU 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 754 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 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 960 LEU Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain A residue 1283 ASP 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 1577 GLU Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1677 PHE 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 7 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.132083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.085419 restraints weight = 43635.968| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.84 r_work: 0.2909 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10764 Z= 0.201 Angle : 0.758 14.975 14619 Z= 0.374 Chirality : 0.045 0.216 1683 Planarity : 0.005 0.068 1778 Dihedral : 9.195 174.059 1639 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.69 % Favored : 93.83 % Rotamer: Outliers : 5.23 % Allowed : 21.08 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1272 helix: 1.25 (0.19), residues: 783 sheet: -0.61 (0.52), residues: 80 loop : -1.74 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 67 HIS 0.006 0.001 HIS A 750 PHE 0.031 0.002 PHE C 83 TYR 0.025 0.002 TYR A1564 ARG 0.016 0.001 ARG C 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 4) link_NAG-ASN : angle 1.86783 ( 12) link_BETA1-4 : bond 0.00896 ( 4) link_BETA1-4 : angle 4.83381 ( 12) hydrogen bonds : bond 0.04028 ( 541) hydrogen bonds : angle 3.89535 ( 1525) SS BOND : bond 0.00396 ( 11) SS BOND : angle 1.24418 ( 22) covalent geometry : bond 0.00475 (10745) covalent geometry : angle 0.74280 (14573) *********************** 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 207 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 148 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 108 TYR cc_start: 0.7568 (m-80) cc_final: 0.6851 (m-80) REVERT: A 220 ARG cc_start: 0.8605 (mtm-85) cc_final: 0.8263 (mtm-85) REVERT: A 268 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8401 (mp10) REVERT: A 387 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8420 (pm20) REVERT: A 411 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9030 (mm) REVERT: A 754 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.4531 (tp) REVERT: A 758 ASP cc_start: 0.1304 (OUTLIER) cc_final: 0.0545 (t70) REVERT: A 817 TYR cc_start: 0.7191 (m-80) cc_final: 0.6953 (m-80) REVERT: A 855 LEU cc_start: 0.9439 (mt) cc_final: 0.9236 (mm) REVERT: A 905 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8976 (ttmt) REVERT: A 960 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9056 (mm) REVERT: A 967 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8278 (ttp) REVERT: A 1211 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: A 1243 GLU cc_start: 0.8408 (tp30) cc_final: 0.7849 (tm-30) REVERT: A 1508 LYS cc_start: 0.5856 (OUTLIER) cc_final: 0.4968 (mmtm) REVERT: A 1551 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8127 (mp0) REVERT: A 1577 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7914 (tp30) REVERT: A 1677 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8464 (t80) REVERT: D 3 ASN cc_start: 0.8492 (t0) cc_final: 0.8214 (t0) outliers start: 59 outliers final: 23 residues processed: 187 average time/residue: 0.9832 time to fit residues: 201.2427 Evaluate side-chains 179 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain A residue 250 ASP 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 754 LEU 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 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 960 LEU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain A residue 1283 ASP Chi-restraints excluded: chain A residue 1284 VAL 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 1548 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 1737 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 3 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.134128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.089245 restraints weight = 34713.989| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.60 r_work: 0.2967 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4543 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= 0.129 Angle : 0.707 9.164 14619 Z= 0.347 Chirality : 0.043 0.301 1683 Planarity : 0.004 0.062 1778 Dihedral : 9.018 179.152 1639 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.01 % Favored : 93.68 % Rotamer: Outliers : 4.27 % Allowed : 22.04 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1272 helix: 1.49 (0.19), residues: 783 sheet: -0.56 (0.51), residues: 80 loop : -1.72 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 281 HIS 0.006 0.001 HIS A 750 PHE 0.014 0.001 PHE A1755 TYR 0.015 0.001 TYR A 390 ARG 0.005 0.001 ARG A 358 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 4) link_NAG-ASN : angle 1.79947 ( 12) link_BETA1-4 : bond 0.01069 ( 4) link_BETA1-4 : angle 4.68037 ( 12) hydrogen bonds : bond 0.03494 ( 541) hydrogen bonds : angle 3.77461 ( 1525) SS BOND : bond 0.00315 ( 11) SS BOND : angle 1.01034 ( 22) covalent geometry : bond 0.00287 (10745) covalent geometry : angle 0.69272 (14573) *********************** 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 204 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: C 108 TYR cc_start: 0.7555 (m-80) cc_final: 0.6813 (m-80) REVERT: A 119 ARG cc_start: 0.1913 (ptt-90) cc_final: 0.1546 (mpp-170) REVERT: A 220 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.8247 (mtm-85) REVERT: A 268 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8487 (mm-40) REVERT: A 387 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8364 (pm20) REVERT: A 411 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8963 (mm) REVERT: A 754 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.4595 (tp) REVERT: A 757 MET cc_start: 0.5173 (OUTLIER) cc_final: 0.4654 (mmm) REVERT: A 758 ASP cc_start: 0.1701 (OUTLIER) cc_final: 0.0701 (t70) REVERT: A 817 TYR cc_start: 0.7225 (m-80) cc_final: 0.7002 (m-80) REVERT: A 905 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8950 (ttmt) REVERT: A 960 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9054 (mm) REVERT: A 967 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8246 (ttp) REVERT: A 1211 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: A 1243 GLU cc_start: 0.8356 (tp30) cc_final: 0.7761 (tm-30) REVERT: A 1508 LYS cc_start: 0.5797 (OUTLIER) cc_final: 0.4983 (mmtm) REVERT: A 1551 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8114 (mp0) REVERT: A 1577 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7828 (tp30) REVERT: A 1653 LEU cc_start: 0.8142 (tm) cc_final: 0.7887 (tt) REVERT: A 1677 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8380 (t80) REVERT: D 3 ASN cc_start: 0.8483 (t0) cc_final: 0.8246 (t0) outliers start: 48 outliers final: 20 residues processed: 188 average time/residue: 1.0727 time to fit residues: 219.1012 Evaluate side-chains 182 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 250 ASP 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 754 LEU 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 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 960 LEU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain A residue 1334 ILE 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 1677 PHE 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 87 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 49 optimal weight: 0.0970 chunk 68 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.132102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.085236 restraints weight = 50392.143| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 4.06 r_work: 0.2907 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10764 Z= 0.176 Angle : 0.729 10.085 14619 Z= 0.359 Chirality : 0.044 0.266 1683 Planarity : 0.004 0.065 1778 Dihedral : 8.922 179.768 1639 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.01 % Favored : 93.52 % Rotamer: Outliers : 3.83 % Allowed : 23.08 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1272 helix: 1.49 (0.19), residues: 786 sheet: -0.52 (0.52), residues: 80 loop : -1.70 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 281 HIS 0.006 0.001 HIS A 750 PHE 0.017 0.001 PHE C 63 TYR 0.025 0.002 TYR A1564 ARG 0.004 0.001 ARG A1626 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 4) link_NAG-ASN : angle 1.82976 ( 12) link_BETA1-4 : bond 0.00870 ( 4) link_BETA1-4 : angle 4.81668 ( 12) hydrogen bonds : bond 0.03815 ( 541) hydrogen bonds : angle 3.83884 ( 1525) SS BOND : bond 0.00372 ( 11) SS BOND : angle 1.17645 ( 22) covalent geometry : bond 0.00414 (10745) covalent geometry : angle 0.71362 (14573) *********************** 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 196 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: C 108 TYR cc_start: 0.7495 (m-80) cc_final: 0.6706 (m-80) REVERT: A 220 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.8243 (mtm-85) REVERT: A 268 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8485 (mm-40) REVERT: A 387 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: A 411 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9018 (mm) REVERT: A 754 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.4418 (tp) REVERT: A 757 MET cc_start: 0.5113 (mpm) cc_final: 0.4179 (tpt) REVERT: A 905 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8967 (ttmt) REVERT: A 960 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9128 (mm) REVERT: A 967 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8314 (ttp) REVERT: A 1243 GLU cc_start: 0.8453 (tp30) cc_final: 0.7852 (tm-30) REVERT: A 1508 LYS cc_start: 0.5617 (OUTLIER) cc_final: 0.4694 (mmtm) REVERT: A 1551 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8156 (mp0) REVERT: A 1577 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: A 1653 LEU cc_start: 0.8173 (tm) cc_final: 0.7877 (tt) REVERT: A 1677 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8467 (t80) REVERT: D 3 ASN cc_start: 0.8455 (t0) cc_final: 0.8181 (t0) outliers start: 43 outliers final: 22 residues processed: 186 average time/residue: 1.2820 time to fit residues: 261.4803 Evaluate side-chains 179 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 136 HIS 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 250 ASP 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 754 LEU 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 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 960 LEU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1334 ILE 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 1677 PHE 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 80 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 118 optimal weight: 0.0370 chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.134128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.087358 restraints weight = 54990.447| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.23 r_work: 0.2929 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4755 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= 0.128 Angle : 0.700 8.847 14619 Z= 0.342 Chirality : 0.042 0.257 1683 Planarity : 0.004 0.061 1778 Dihedral : 8.633 173.562 1639 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.01 % Favored : 93.60 % Rotamer: Outliers : 3.14 % Allowed : 24.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1272 helix: 1.61 (0.19), residues: 789 sheet: -0.47 (0.52), residues: 79 loop : -1.66 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.007 0.001 HIS A 750 PHE 0.014 0.001 PHE A1755 TYR 0.014 0.001 TYR A 390 ARG 0.010 0.001 ARG C 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 4) link_NAG-ASN : angle 1.75025 ( 12) link_BETA1-4 : bond 0.00990 ( 4) link_BETA1-4 : angle 4.71821 ( 12) hydrogen bonds : bond 0.03402 ( 541) hydrogen bonds : angle 3.75245 ( 1525) SS BOND : bond 0.00287 ( 11) SS BOND : angle 0.97988 ( 22) covalent geometry : bond 0.00280 (10745) covalent geometry : angle 0.68509 (14573) ********************** 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 193 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 108 TYR cc_start: 0.7432 (m-80) cc_final: 0.6602 (m-80) REVERT: A 119 ARG cc_start: 0.2390 (ptt-90) cc_final: 0.1168 (mtp-110) REVERT: A 220 ARG cc_start: 0.8617 (mtm-85) cc_final: 0.8210 (mtm-85) REVERT: A 268 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8513 (mm-40) REVERT: A 387 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: A 411 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8918 (mm) REVERT: A 754 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.4603 (tp) REVERT: A 813 MET cc_start: 0.6842 (ttt) cc_final: 0.6571 (tmt) REVERT: A 905 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8931 (ttmt) REVERT: A 960 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9092 (mm) REVERT: A 967 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8309 (ttp) REVERT: A 1243 GLU cc_start: 0.8461 (tp30) cc_final: 0.7866 (tm-30) REVERT: A 1508 LYS cc_start: 0.5676 (OUTLIER) cc_final: 0.4804 (mmtm) REVERT: A 1551 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8183 (mp0) REVERT: A 1577 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7915 (tp30) REVERT: A 1653 LEU cc_start: 0.8119 (tm) cc_final: 0.7833 (tt) REVERT: A 1677 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8416 (t80) REVERT: D 3 ASN cc_start: 0.8459 (t0) cc_final: 0.8174 (t0) outliers start: 35 outliers final: 22 residues processed: 182 average time/residue: 1.0120 time to fit residues: 201.2772 Evaluate side-chains 181 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 136 HIS 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 218 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 ASP 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 754 LEU 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 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 960 LEU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1334 ILE 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 1677 PHE 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 75 optimal weight: 5.9990 chunk 98 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.134067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.089228 restraints weight = 40192.496| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.83 r_work: 0.2952 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4824 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= 0.136 Angle : 0.707 8.796 14619 Z= 0.346 Chirality : 0.043 0.221 1683 Planarity : 0.004 0.061 1778 Dihedral : 8.617 179.351 1639 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.85 % Favored : 93.91 % Rotamer: Outliers : 3.66 % Allowed : 23.69 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1272 helix: 1.65 (0.19), residues: 789 sheet: -0.51 (0.52), residues: 79 loop : -1.63 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 281 HIS 0.007 0.001 HIS A 750 PHE 0.018 0.001 PHE C 83 TYR 0.015 0.001 TYR A 390 ARG 0.025 0.001 ARG C 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 4) link_NAG-ASN : angle 1.74604 ( 12) link_BETA1-4 : bond 0.00970 ( 4) link_BETA1-4 : angle 4.75578 ( 12) hydrogen bonds : bond 0.03433 ( 541) hydrogen bonds : angle 3.74663 ( 1525) SS BOND : bond 0.00295 ( 11) SS BOND : angle 1.00453 ( 22) covalent geometry : bond 0.00310 (10745) covalent geometry : angle 0.69155 (14573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8835.42 seconds wall clock time: 154 minutes 55.29 seconds (9295.29 seconds total)