Starting phenix.real_space_refine on Thu Aug 6 05:26:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9thi_55928/08_2026/9thi_55928.cif Found real_map, /net/cci-nas-00/data/ceres_data/9thi_55928/08_2026/9thi_55928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9thi_55928/08_2026/9thi_55928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9thi_55928/08_2026/9thi_55928.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9thi_55928/08_2026/9thi_55928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9thi_55928/08_2026/9thi_55928.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.037 sd= 0.244 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 8350 2.51 5 N 2257 2.21 5 O 2511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13177 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 849, 6488 Classifications: {'peptide': 849} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 797} Chain breaks: 1 Chain: "B" Number of atoms: 6689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 6689 Classifications: {'peptide': 878} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 822} Chain breaks: 1 Time building chain proxies: 2.44, per 1000 atoms: 0.19 Number of scatterers: 13177 At special positions: 0 Unit cell: (116.144, 139.944, 98.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 2511 8.00 N 2257 7.00 C 8350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 434.8 milliseconds 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 28 sheets defined 31.7% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 802 through 808 Processing helix chain 'A' and resid 818 through 828 removed outlier: 4.298A pdb=" N THR A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE A 825 " --> pdb=" O GLU A 821 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 826 " --> pdb=" O ILE A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 912 through 917 Processing helix chain 'A' and resid 935 through 940 Processing helix chain 'A' and resid 953 through 968 Processing helix chain 'A' and resid 972 through 976 removed outlier: 3.546A pdb=" N ILE A 976 " --> pdb=" O ALA A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 982 removed outlier: 3.794A pdb=" N TYR A 981 " --> pdb=" O ARG A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1043 removed outlier: 3.670A pdb=" N ALA A1043 " --> pdb=" O LYS A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1054 removed outlier: 3.690A pdb=" N LEU A1051 " --> pdb=" O PRO A1047 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A1054 " --> pdb=" O ILE A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1066 removed outlier: 3.959A pdb=" N ALA A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1178 removed outlier: 3.634A pdb=" N SER A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TRP A1178 " --> pdb=" O TYR A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1198 removed outlier: 3.737A pdb=" N THR A1196 " --> pdb=" O GLY A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1216 Processing helix chain 'A' and resid 1272 through 1281 Processing helix chain 'A' and resid 1293 through 1297 removed outlier: 3.609A pdb=" N VAL A1297 " --> pdb=" O SER A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1312 Processing helix chain 'A' and resid 1313 through 1328 removed outlier: 4.276A pdb=" N MET A1317 " --> pdb=" O GLN A1313 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG A1328 " --> pdb=" O TYR A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1338 Processing helix chain 'A' and resid 1345 through 1355 removed outlier: 3.548A pdb=" N LYS A1349 " --> pdb=" O LYS A1345 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A1351 " --> pdb=" O LEU A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1382 Processing helix chain 'A' and resid 1402 through 1404 No H-bonds generated for 'chain 'A' and resid 1402 through 1404' Processing helix chain 'A' and resid 1431 through 1438 removed outlier: 3.654A pdb=" N CYS A1435 " --> pdb=" O PRO A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1447 removed outlier: 3.565A pdb=" N GLY A1447 " --> pdb=" O LEU A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1501 through 1515 removed outlier: 4.191A pdb=" N GLY A1515 " --> pdb=" O TRP A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1581 No H-bonds generated for 'chain 'A' and resid 1579 through 1581' Processing helix chain 'A' and resid 1582 through 1590 removed outlier: 3.644A pdb=" N VAL A1586 " --> pdb=" O SER A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1626 Processing helix chain 'A' and resid 1626 through 1640 removed outlier: 3.688A pdb=" N VAL A1633 " --> pdb=" O SER A1629 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A1638 " --> pdb=" O ALA A1634 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 799 removed outlier: 3.551A pdb=" N VAL B 797 " --> pdb=" O ASP B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 807 Processing helix chain 'B' and resid 819 through 827 removed outlier: 4.115A pdb=" N GLN B 823 " --> pdb=" O GLY B 819 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 825 " --> pdb=" O GLU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 919 Processing helix chain 'B' and resid 920 through 922 No H-bonds generated for 'chain 'B' and resid 920 through 922' Processing helix chain 'B' and resid 935 through 943 Processing helix chain 'B' and resid 953 through 968 Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 1031 through 1035 removed outlier: 3.885A pdb=" N THR B1034 " --> pdb=" O THR B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1052 removed outlier: 3.509A pdb=" N ILE B1050 " --> pdb=" O PRO B1047 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B1052 " --> pdb=" O ALA B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1069 Processing helix chain 'B' and resid 1125 through 1131 removed outlier: 3.617A pdb=" N ALA B1131 " --> pdb=" O VAL B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1170 through 1179 removed outlier: 3.590A pdb=" N TRP B1178 " --> pdb=" O TYR B1174 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1182 No H-bonds generated for 'chain 'B' and resid 1180 through 1182' Processing helix chain 'B' and resid 1183 through 1198 removed outlier: 4.013A pdb=" N THR B1196 " --> pdb=" O GLY B1192 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET B1197 " --> pdb=" O ARG B1193 " (cutoff:3.500A) Processing helix chain 'B' and resid 1200 through 1216 removed outlier: 3.865A pdb=" N TRP B1205 " --> pdb=" O LYS B1201 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B1206 " --> pdb=" O ASP B1202 " (cutoff:3.500A) Processing helix chain 'B' and resid 1235 through 1240 Processing helix chain 'B' and resid 1272 through 1281 Processing helix chain 'B' and resid 1288 through 1290 No H-bonds generated for 'chain 'B' and resid 1288 through 1290' Processing helix chain 'B' and resid 1305 through 1327 removed outlier: 3.931A pdb=" N ILE B1315 " --> pdb=" O ARG B1311 " (cutoff:3.500A) Proline residue: B1316 - end of helix Processing helix chain 'B' and resid 1332 through 1337 removed outlier: 3.759A pdb=" N ASN B1337 " --> pdb=" O LEU B1333 " (cutoff:3.500A) Processing helix chain 'B' and resid 1344 through 1353 removed outlier: 3.545A pdb=" N LYS B1349 " --> pdb=" O LYS B1345 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1381 Processing helix chain 'B' and resid 1431 through 1438 removed outlier: 4.170A pdb=" N CYS B1435 " --> pdb=" O PRO B1431 " (cutoff:3.500A) Processing helix chain 'B' and resid 1443 through 1447 Processing helix chain 'B' and resid 1501 through 1513 Processing helix chain 'B' and resid 1578 through 1590 removed outlier: 3.843A pdb=" N VAL B1583 " --> pdb=" O THR B1579 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE B1584 " --> pdb=" O ALA B1580 " (cutoff:3.500A) Proline residue: B1585 - end of helix Processing helix chain 'B' and resid 1626 through 1639 removed outlier: 4.036A pdb=" N ASP B1632 " --> pdb=" O SER B1628 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B1636 " --> pdb=" O ASP B1632 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B1637 " --> pdb=" O VAL B1633 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B1639 " --> pdb=" O LYS B1635 " (cutoff:3.500A) Processing helix chain 'B' and resid 1657 through 1660 Processing helix chain 'B' and resid 1661 through 1666 removed outlier: 3.690A pdb=" N SER B1665 " --> pdb=" O LEU B1661 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 857 through 864 removed outlier: 5.591A pdb=" N GLN A 859 " --> pdb=" O GLN A 850 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN A 850 " --> pdb=" O GLN A 859 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN A 849 " --> pdb=" O LEU A1601 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 870 through 872 Processing sheet with id=AA3, first strand: chain 'A' and resid 874 through 876 Processing sheet with id=AA4, first strand: chain 'A' and resid 1102 through 1103 removed outlier: 7.212A pdb=" N THR A 891 " --> pdb=" O HIS A1103 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A1266 " --> pdb=" O GLU A 892 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 904 through 905 Processing sheet with id=AA6, first strand: chain 'A' and resid 989 through 990 Processing sheet with id=AA7, first strand: chain 'A' and resid 1025 through 1029 removed outlier: 6.246A pdb=" N ALA A1025 " --> pdb=" O LEU A1110 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU A1112 " --> pdb=" O ALA A1025 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA A1027 " --> pdb=" O LEU A1112 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A1044 " --> pdb=" O ILE A1113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 1218 through 1219 Processing sheet with id=AA9, first strand: chain 'A' and resid 1222 through 1224 removed outlier: 3.614A pdb=" N THR A1222 " --> pdb=" O VAL A1539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1387 through 1391 Processing sheet with id=AB2, first strand: chain 'A' and resid 1414 through 1415 Processing sheet with id=AB3, first strand: chain 'A' and resid 1468 through 1469 Processing sheet with id=AB4, first strand: chain 'A' and resid 1518 through 1520 Processing sheet with id=AB5, first strand: chain 'B' and resid 815 through 816 removed outlier: 5.626A pdb=" N LYS B 815 " --> pdb=" O ALA B1384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 857 through 864 removed outlier: 4.369A pdb=" N ASN B 860 " --> pdb=" O GLY B 848 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY B 848 " --> pdb=" O ASN B 860 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 862 " --> pdb=" O LEU B 846 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU B 846 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN B 849 " --> pdb=" O LEU B1601 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 870 through 872 removed outlier: 6.191A pdb=" N TYR B1076 " --> pdb=" O PRO B1097 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 870 through 872 removed outlier: 6.191A pdb=" N TYR B1076 " --> pdb=" O PRO B1097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 874 through 877 Processing sheet with id=AC1, first strand: chain 'B' and resid 1102 through 1103 removed outlier: 7.130A pdb=" N THR B 891 " --> pdb=" O HIS B1103 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET B1266 " --> pdb=" O GLU B 892 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 903 through 905 Processing sheet with id=AC3, first strand: chain 'B' and resid 1025 through 1029 removed outlier: 6.403A pdb=" N ALA B1025 " --> pdb=" O LEU B1110 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU B1112 " --> pdb=" O ALA B1025 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B1027 " --> pdb=" O LEU B1112 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B1044 " --> pdb=" O ILE B1113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 1218 through 1219 Processing sheet with id=AC5, first strand: chain 'B' and resid 1222 through 1224 removed outlier: 3.902A pdb=" N THR B1222 " --> pdb=" O VAL B1539 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B1229 " --> pdb=" O GLY B1540 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1359 through 1360 removed outlier: 3.643A pdb=" N SER B1360 " --> pdb=" O THR B1363 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1388 through 1392 Processing sheet with id=AC8, first strand: chain 'B' and resid 1414 through 1415 Processing sheet with id=AC9, first strand: chain 'B' and resid 1468 through 1469 Processing sheet with id=AD1, first strand: chain 'B' and resid 1518 through 1520 363 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2317 1.32 - 1.45: 3539 1.45 - 1.57: 7537 1.57 - 1.69: 2 1.69 - 1.81: 98 Bond restraints: 13493 Sorted by residual: bond pdb=" N ILE A 912 " pdb=" CA ILE A 912 " ideal model delta sigma weight residual 1.455 1.505 -0.050 1.38e-02 5.25e+03 1.31e+01 bond pdb=" CA SER A 913 " pdb=" CB SER A 913 " ideal model delta sigma weight residual 1.531 1.475 0.056 1.59e-02 3.96e+03 1.25e+01 bond pdb=" N ASN A 919 " pdb=" CA ASN A 919 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.10e+01 bond pdb=" CA SER A 922 " pdb=" CB SER A 922 " ideal model delta sigma weight residual 1.530 1.479 0.051 1.69e-02 3.50e+03 9.12e+00 bond pdb=" N VAL B1644 " pdb=" CA VAL B1644 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.23e-02 6.61e+03 8.98e+00 ... (remaining 13488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 18158 2.85 - 5.69: 262 5.69 - 8.54: 28 8.54 - 11.38: 9 11.38 - 14.23: 4 Bond angle restraints: 18461 Sorted by residual: angle pdb=" N GLN A 920 " pdb=" CA GLN A 920 " pdb=" CB GLN A 920 " ideal model delta sigma weight residual 110.35 101.03 9.32 1.15e+00 7.56e-01 6.56e+01 angle pdb=" N ASP B1652 " pdb=" CA ASP B1652 " pdb=" C ASP B1652 " ideal model delta sigma weight residual 113.88 104.22 9.66 1.23e+00 6.61e-01 6.16e+01 angle pdb=" C ASP A 914 " pdb=" CA ASP A 914 " pdb=" CB ASP A 914 " ideal model delta sigma weight residual 111.17 99.36 11.81 1.53e+00 4.27e-01 5.96e+01 angle pdb=" C THR B1124 " pdb=" N THR B1125 " pdb=" CA THR B1125 " ideal model delta sigma weight residual 121.54 135.77 -14.23 1.91e+00 2.74e-01 5.55e+01 angle pdb=" N THR B1651 " pdb=" CA THR B1651 " pdb=" C THR B1651 " ideal model delta sigma weight residual 112.59 103.69 8.90 1.22e+00 6.72e-01 5.32e+01 ... (remaining 18456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6770 17.76 - 35.53: 887 35.53 - 53.29: 282 53.29 - 71.06: 69 71.06 - 88.82: 13 Dihedral angle restraints: 8021 sinusoidal: 3004 harmonic: 5017 Sorted by residual: dihedral pdb=" CA PHE B1256 " pdb=" C PHE B1256 " pdb=" N PRO B1257 " pdb=" CA PRO B1257 " ideal model delta harmonic sigma weight residual 180.00 -131.39 -48.61 0 5.00e+00 4.00e-02 9.45e+01 dihedral pdb=" CD ARG A 926 " pdb=" NE ARG A 926 " pdb=" CZ ARG A 926 " pdb=" NH1 ARG A 926 " ideal model delta sinusoidal sigma weight residual 0.00 62.71 -62.71 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" C ASP A 914 " pdb=" N ASP A 914 " pdb=" CA ASP A 914 " pdb=" CB ASP A 914 " ideal model delta harmonic sigma weight residual -122.60 -108.38 -14.22 0 2.50e+00 1.60e-01 3.24e+01 ... (remaining 8018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1769 0.064 - 0.129: 312 0.129 - 0.193: 23 0.193 - 0.258: 4 0.258 - 0.322: 3 Chirality restraints: 2111 Sorted by residual: chirality pdb=" CA LEU B1650 " pdb=" N LEU B1650 " pdb=" C LEU B1650 " pdb=" CB LEU B1650 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ASP A 914 " pdb=" N ASP A 914 " pdb=" C ASP A 914 " pdb=" CB ASP A 914 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ASP B1652 " pdb=" N ASP B1652 " pdb=" C ASP B1652 " pdb=" CB ASP B1652 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2108 not shown) Planarity restraints: 2417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 926 " -0.972 9.50e-02 1.11e+02 4.36e-01 1.15e+02 pdb=" NE ARG A 926 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG A 926 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 926 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 926 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B1256 " 0.105 5.00e-02 4.00e+02 1.60e-01 4.11e+01 pdb=" N PRO B1257 " -0.277 5.00e-02 4.00e+02 pdb=" CA PRO B1257 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO B1257 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 925 " -0.349 9.50e-02 1.11e+02 1.56e-01 1.50e+01 pdb=" NE ARG A 925 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 925 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 925 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 925 " -0.012 2.00e-02 2.50e+03 ... (remaining 2414 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4286 2.83 - 3.35: 12198 3.35 - 3.86: 22549 3.86 - 4.38: 27141 4.38 - 4.90: 45201 Nonbonded interactions: 111375 Sorted by model distance: nonbonded pdb=" O GLN A 920 " pdb=" N SER A 922 " model vdw 2.312 3.120 nonbonded pdb=" O ASN A 970 " pdb=" ND2 ASN A 970 " model vdw 2.351 3.120 nonbonded pdb=" O GLN A 920 " pdb=" OG1 THR A 923 " model vdw 2.362 3.040 nonbonded pdb=" O ASN B1604 " pdb=" OD1 ASN B1604 " model vdw 2.384 3.040 nonbonded pdb=" O ASP A 914 " pdb=" CB ASP A 914 " model vdw 2.421 2.752 ... (remaining 111370 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 'A' and (resid 789 through 1606 or resid 1619 through 1641)) selection = (chain 'B' and (resid 789 through 1126 or resid 1131 through 1641)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 18.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.110 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 13493 Z= 0.236 Angle : 0.883 14.225 18461 Z= 0.534 Chirality : 0.049 0.322 2111 Planarity : 0.011 0.436 2417 Dihedral : 18.382 88.820 4787 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.68 % Favored : 91.56 % Rotamer: Outliers : 5.61 % Allowed : 32.53 % Favored : 61.86 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.20), residues: 1719 helix: -1.06 (0.23), residues: 473 sheet: -0.94 (0.40), residues: 150 loop : -1.24 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1509 TYR 0.019 0.002 TYR A1204 PHE 0.021 0.002 PHE B 803 TRP 0.016 0.002 TRP A 924 HIS 0.004 0.001 HIS A1073 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.24 (13493) covalent geometry : angle 0.88274 / 0.53 (18461) hydrogen bonds : bond 0.19235 / 12.88 ( 355) hydrogen bonds : angle 7.37361 / 5.27 ( 975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 156 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 969 MET cc_start: 0.8578 (mpp) cc_final: 0.8299 (mmp) REVERT: A 1395 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7044 (tptm) REVERT: B 811 ASP cc_start: 0.6705 (m-30) cc_final: 0.6062 (m-30) REVERT: B 880 ILE cc_start: 0.8134 (mm) cc_final: 0.7906 (mt) REVERT: B 926 ARG cc_start: 0.5032 (ttp-170) cc_final: 0.4282 (ptt180) REVERT: B 969 MET cc_start: 0.7978 (mmt) cc_final: 0.7528 (mmt) REVERT: B 1194 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6461 (tp) REVERT: B 1240 ASP cc_start: 0.7839 (t0) cc_final: 0.7609 (t70) REVERT: B 1503 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8168 (mtt) outliers start: 79 outliers final: 55 residues processed: 217 average time/residue: 0.3729 time to fit residues: 92.5945 Evaluate side-chains 206 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 148 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 927 ASP Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1339 TYR Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1424 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1488 ASN Chi-restraints excluded: chain A residue 1579 THR Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 954 GLU Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1029 HIS Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1168 GLU Chi-restraints excluded: chain B residue 1169 TRP Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1198 VAL Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1283 LEU Chi-restraints excluded: chain B residue 1295 MET Chi-restraints excluded: chain B residue 1319 ILE Chi-restraints excluded: chain B residue 1354 THR Chi-restraints excluded: chain B residue 1358 THR Chi-restraints excluded: chain B residue 1503 MET Chi-restraints excluded: chain B residue 1516 ASN Chi-restraints excluded: chain B residue 1553 ILE Chi-restraints excluded: chain B residue 1554 GLU Chi-restraints excluded: chain B residue 1563 VAL Chi-restraints excluded: chain B residue 1575 THR Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 1650 LEU Chi-restraints excluded: chain B residue 1652 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 GLN A 970 ASN A 977 ASN A1413 ASN A1472 ASN A1475 ASN ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.122352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106384 restraints weight = 18702.550| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.61 r_work: 0.3215 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 13493 Z= 0.261 Angle : 0.754 13.026 18461 Z= 0.389 Chirality : 0.050 0.188 2111 Planarity : 0.007 0.162 2417 Dihedral : 9.408 58.208 1948 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.62 % Favored : 91.68 % Rotamer: Outliers : 11.58 % Allowed : 25.85 % Favored : 62.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.20), residues: 1719 helix: -1.07 (0.23), residues: 473 sheet: -1.02 (0.38), residues: 152 loop : -1.27 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1181 TYR 0.021 0.002 TYR B1377 PHE 0.021 0.003 PHE B1402 TRP 0.012 0.002 TRP B1276 HIS 0.004 0.001 HIS A1103 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.26 (13493) covalent geometry : angle 0.75398 / 0.39 (18461) hydrogen bonds : bond 0.05405 / 3.51 ( 355) hydrogen bonds : angle 5.61304 / 3.84 ( 975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 154 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 808 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: A 926 ARG cc_start: 0.7888 (ttm110) cc_final: 0.6651 (mmt-90) REVERT: A 1118 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: A 1136 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7889 (tmt90) REVERT: A 1197 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7357 (ttp) REVERT: A 1383 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7174 (mmt-90) REVERT: A 1395 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7058 (tptm) REVERT: A 1455 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: B 811 ASP cc_start: 0.6639 (m-30) cc_final: 0.5988 (m-30) REVERT: B 880 ILE cc_start: 0.8034 (mm) cc_final: 0.7785 (mt) REVERT: B 926 ARG cc_start: 0.5169 (ttp-170) cc_final: 0.4396 (ptt180) REVERT: B 969 MET cc_start: 0.8137 (mmt) cc_final: 0.7747 (mmm) REVERT: B 1119 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.6845 (tt) REVERT: B 1240 ASP cc_start: 0.7948 (t0) cc_final: 0.7682 (t70) REVERT: B 1271 THR cc_start: 0.7638 (OUTLIER) cc_final: 0.7287 (p) REVERT: B 1372 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6677 (mp) REVERT: B 1503 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8164 (mtt) REVERT: B 1604 ASN cc_start: 0.7403 (p0) cc_final: 0.7156 (p0) REVERT: B 1635 LYS cc_start: 0.6374 (OUTLIER) cc_final: 0.5974 (tttt) outliers start: 163 outliers final: 90 residues processed: 288 average time/residue: 0.3541 time to fit residues: 117.4126 Evaluate side-chains 250 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 148 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 927 ASP Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1136 ARG Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1197 MET Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1239 SER Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1339 TYR Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1383 ARG Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1424 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1469 ILE Chi-restraints excluded: chain A residue 1488 ASN Chi-restraints excluded: chain A residue 1489 SER Chi-restraints excluded: chain A residue 1528 VAL Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1569 ASP Chi-restraints excluded: chain A residue 1579 THR Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 954 GLU Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1066 LEU Chi-restraints excluded: chain B residue 1119 ILE Chi-restraints excluded: chain B residue 1168 GLU Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1198 VAL Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 1279 VAL Chi-restraints excluded: chain B residue 1296 ASP Chi-restraints excluded: chain B residue 1306 THR Chi-restraints excluded: chain B residue 1307 SER Chi-restraints excluded: chain B residue 1319 ILE Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1354 THR Chi-restraints excluded: chain B residue 1358 THR Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1382 HIS Chi-restraints excluded: chain B residue 1403 GLU Chi-restraints excluded: chain B residue 1410 THR Chi-restraints excluded: chain B residue 1463 SER Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain B residue 1503 MET Chi-restraints excluded: chain B residue 1516 ASN Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1553 ILE Chi-restraints excluded: chain B residue 1554 GLU Chi-restraints excluded: chain B residue 1556 THR Chi-restraints excluded: chain B residue 1575 THR Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1624 THR Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1635 LYS Chi-restraints excluded: chain B residue 1677 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 122 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 ASN A 980 GLN A1014 ASN ** A1423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 GLN ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.126536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110522 restraints weight = 18762.915| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.62 r_work: 0.3277 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 13493 Z= 0.118 Angle : 0.601 11.668 18461 Z= 0.309 Chirality : 0.043 0.159 2111 Planarity : 0.006 0.158 2417 Dihedral : 7.934 59.821 1925 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.05 % Favored : 93.31 % Rotamer: Outliers : 7.46 % Allowed : 29.33 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.20), residues: 1719 helix: -0.47 (0.24), residues: 469 sheet: -0.77 (0.39), residues: 148 loop : -1.08 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1136 TYR 0.012 0.001 TYR A1204 PHE 0.013 0.001 PHE B1438 TRP 0.013 0.001 TRP A1511 HIS 0.003 0.001 HIS A1073 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (13493) covalent geometry : angle 0.60087 / 0.31 (18461) hydrogen bonds : bond 0.03951 / 2.62 ( 355) hydrogen bonds : angle 5.10063 / 3.46 ( 975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 172 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 926 ARG cc_start: 0.7989 (ttm110) cc_final: 0.6747 (mtt90) REVERT: A 969 MET cc_start: 0.8642 (mpp) cc_final: 0.8379 (mmp) REVERT: A 1124 THR cc_start: 0.8362 (m) cc_final: 0.8108 (t) REVERT: A 1132 MET cc_start: 0.4694 (mmm) cc_final: 0.4472 (mmm) REVERT: A 1336 ASP cc_start: 0.8157 (m-30) cc_final: 0.7935 (m-30) REVERT: A 1395 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7056 (tptm) REVERT: B 803 PHE cc_start: 0.6838 (t80) cc_final: 0.6629 (t80) REVERT: B 811 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6094 (m-30) REVERT: B 880 ILE cc_start: 0.8006 (mm) cc_final: 0.7737 (mt) REVERT: B 926 ARG cc_start: 0.5141 (ttp-170) cc_final: 0.4325 (ptt180) REVERT: B 969 MET cc_start: 0.8132 (mmt) cc_final: 0.7752 (mmm) REVERT: B 1119 ILE cc_start: 0.7293 (mp) cc_final: 0.6762 (tt) REVERT: B 1240 ASP cc_start: 0.7952 (t0) cc_final: 0.7667 (t70) REVERT: B 1503 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8290 (mtt) REVERT: B 1554 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7560 (pt0) outliers start: 105 outliers final: 50 residues processed: 248 average time/residue: 0.3530 time to fit residues: 100.5128 Evaluate side-chains 214 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 160 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1488 ASN Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1569 ASP Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 896 SER Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1029 HIS Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1168 GLU Chi-restraints excluded: chain B residue 1169 TRP Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1198 VAL Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1283 LEU Chi-restraints excluded: chain B residue 1301 VAL Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1354 THR Chi-restraints excluded: chain B residue 1358 THR Chi-restraints excluded: chain B residue 1382 HIS Chi-restraints excluded: chain B residue 1403 GLU Chi-restraints excluded: chain B residue 1428 VAL Chi-restraints excluded: chain B residue 1435 CYS Chi-restraints excluded: chain B residue 1503 MET Chi-restraints excluded: chain B residue 1516 ASN Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1554 GLU Chi-restraints excluded: chain B residue 1563 VAL Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1624 THR Chi-restraints excluded: chain B residue 1644 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 99 optimal weight: 0.0570 chunk 121 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 134 optimal weight: 0.0050 chunk 54 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 ASN A1013 ASN A1058 ASN ** A1423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1516 ASN ** B 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 GLN B1122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110149 restraints weight = 18603.212| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.63 r_work: 0.3268 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13493 Z= 0.124 Angle : 0.592 11.185 18461 Z= 0.303 Chirality : 0.043 0.203 2111 Planarity : 0.005 0.156 2417 Dihedral : 7.059 59.454 1896 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.63 % Favored : 92.73 % Rotamer: Outliers : 8.31 % Allowed : 28.20 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1719 helix: -0.29 (0.24), residues: 474 sheet: -0.70 (0.39), residues: 148 loop : -1.01 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 926 TYR 0.013 0.001 TYR A1204 PHE 0.018 0.001 PHE B1256 TRP 0.010 0.001 TRP B1276 HIS 0.003 0.001 HIS A1103 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 (13493) covalent geometry : angle 0.59227 / 0.30 (18461) hydrogen bonds : bond 0.03735 / 2.47 ( 355) hydrogen bonds : angle 4.94620 / 3.36 ( 975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 166 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 926 ARG cc_start: 0.7965 (ttm110) cc_final: 0.6659 (mmt-90) REVERT: A 969 MET cc_start: 0.8658 (mpp) cc_final: 0.8394 (mmp) REVERT: A 1383 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7057 (mmt-90) REVERT: A 1395 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7055 (tptm) REVERT: A 1455 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: B 811 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6160 (m-30) REVERT: B 880 ILE cc_start: 0.8019 (mm) cc_final: 0.7715 (mt) REVERT: B 926 ARG cc_start: 0.5187 (ttp-170) cc_final: 0.4368 (ptt180) REVERT: B 969 MET cc_start: 0.8110 (mmt) cc_final: 0.7670 (mmm) REVERT: B 1119 ILE cc_start: 0.7374 (mp) cc_final: 0.6794 (tt) REVERT: B 1240 ASP cc_start: 0.7982 (t0) cc_final: 0.7688 (t70) outliers start: 117 outliers final: 62 residues processed: 256 average time/residue: 0.3711 time to fit residues: 109.3669 Evaluate side-chains 219 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 153 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1339 TYR Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1383 ARG Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1424 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1488 ASN Chi-restraints excluded: chain A residue 1569 ASP Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 896 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 927 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 1029 HIS Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1124 THR Chi-restraints excluded: chain B residue 1133 CYS Chi-restraints excluded: chain B residue 1168 GLU Chi-restraints excluded: chain B residue 1169 TRP Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1198 VAL Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1283 LEU Chi-restraints excluded: chain B residue 1306 THR Chi-restraints excluded: chain B residue 1354 THR Chi-restraints excluded: chain B residue 1358 THR Chi-restraints excluded: chain B residue 1382 HIS Chi-restraints excluded: chain B residue 1403 GLU Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain B residue 1435 CYS Chi-restraints excluded: chain B residue 1516 ASN Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1556 THR Chi-restraints excluded: chain B residue 1563 VAL Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1624 THR Chi-restraints excluded: chain B residue 1644 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 163 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 119 optimal weight: 0.0770 chunk 57 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 overall best weight: 0.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 ASN ** A1423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 GLN ** B 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111643 restraints weight = 18741.332| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.64 r_work: 0.3293 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 13493 Z= 0.105 Angle : 0.569 10.603 18461 Z= 0.289 Chirality : 0.042 0.153 2111 Planarity : 0.005 0.154 2417 Dihedral : 6.497 56.640 1888 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.28 % Favored : 93.08 % Rotamer: Outliers : 6.61 % Allowed : 29.83 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.20), residues: 1719 helix: -0.06 (0.25), residues: 468 sheet: -0.82 (0.39), residues: 157 loop : -0.82 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1108 TYR 0.010 0.001 TYR A1204 PHE 0.015 0.001 PHE B1256 TRP 0.014 0.001 TRP A1511 HIS 0.002 0.001 HIS A1073 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.10 (13493) covalent geometry : angle 0.56921 / 0.29 (18461) hydrogen bonds : bond 0.03346 / 2.22 ( 355) hydrogen bonds : angle 4.77608 / 3.24 ( 975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 172 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 926 ARG cc_start: 0.7948 (ttm110) cc_final: 0.6612 (mmt-90) REVERT: A 969 MET cc_start: 0.8580 (mpp) cc_final: 0.8347 (mmp) REVERT: A 1124 THR cc_start: 0.8356 (m) cc_final: 0.7803 (p) REVERT: A 1134 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.5193 (tmt) REVERT: A 1395 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.6929 (tppp) REVERT: A 1455 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: B 811 ASP cc_start: 0.6667 (m-30) cc_final: 0.6055 (m-30) REVERT: B 880 ILE cc_start: 0.8038 (mm) cc_final: 0.7756 (mt) REVERT: B 926 ARG cc_start: 0.5174 (ttp-170) cc_final: 0.4443 (ptt180) REVERT: B 967 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.5350 (mptp) REVERT: B 969 MET cc_start: 0.7968 (mmt) cc_final: 0.7499 (mmt) REVERT: B 1240 ASP cc_start: 0.7986 (t0) cc_final: 0.7686 (t70) REVERT: B 1403 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8266 (mt-10) REVERT: B 1503 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8074 (mtt) outliers start: 93 outliers final: 46 residues processed: 245 average time/residue: 0.3808 time to fit residues: 107.4360 Evaluate side-chains 208 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1424 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1569 ASP Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 896 SER Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 967 LYS Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1168 GLU Chi-restraints excluded: chain B residue 1169 TRP Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1198 VAL Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1283 LEU Chi-restraints excluded: chain B residue 1307 SER Chi-restraints excluded: chain B residue 1354 THR Chi-restraints excluded: chain B residue 1358 THR Chi-restraints excluded: chain B residue 1382 HIS Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1403 GLU Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain B residue 1435 CYS Chi-restraints excluded: chain B residue 1463 SER Chi-restraints excluded: chain B residue 1503 MET Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1563 VAL Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1644 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 8 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 ASN ** A1342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1423 ASN B 889 GLN ** B 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107808 restraints weight = 18723.634| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.62 r_work: 0.3236 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13493 Z= 0.195 Angle : 0.664 13.723 18461 Z= 0.336 Chirality : 0.046 0.179 2111 Planarity : 0.006 0.157 2417 Dihedral : 6.701 59.246 1882 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.98 % Favored : 92.38 % Rotamer: Outliers : 7.95 % Allowed : 28.55 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.20), residues: 1719 helix: -0.26 (0.24), residues: 469 sheet: -0.99 (0.37), residues: 158 loop : -1.01 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1108 TYR 0.019 0.002 TYR B1377 PHE 0.023 0.002 PHE B1256 TRP 0.008 0.002 TRP B1335 HIS 0.005 0.001 HIS B1029 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (13493) covalent geometry : angle 0.66380 / 0.34 (18461) hydrogen bonds : bond 0.04178 / 2.72 ( 355) hydrogen bonds : angle 5.01230 / 3.40 ( 975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 155 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 926 ARG cc_start: 0.8022 (ttm110) cc_final: 0.6727 (mmt-90) REVERT: A 969 MET cc_start: 0.8708 (mpp) cc_final: 0.8382 (mmp) REVERT: A 1118 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8075 (pm20) REVERT: A 1134 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.5362 (tmt) REVERT: A 1293 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7310 (mm110) REVERT: A 1395 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.6853 (tppp) REVERT: A 1455 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: B 811 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6052 (m-30) REVERT: B 880 ILE cc_start: 0.8006 (mm) cc_final: 0.7711 (mt) REVERT: B 889 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7025 (mm110) REVERT: B 926 ARG cc_start: 0.5222 (ttp-110) cc_final: 0.4372 (ptt180) REVERT: B 969 MET cc_start: 0.7983 (mmt) cc_final: 0.7557 (mmt) REVERT: B 1078 VAL cc_start: 0.7580 (m) cc_final: 0.7380 (m) REVERT: B 1119 ILE cc_start: 0.7432 (mp) cc_final: 0.6863 (tt) REVERT: B 1240 ASP cc_start: 0.7995 (t0) cc_final: 0.7689 (t70) REVERT: B 1395 LYS cc_start: 0.6803 (tttp) cc_final: 0.6484 (tttm) REVERT: B 1503 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8164 (mtt) REVERT: B 1536 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7906 (mm-30) outliers start: 112 outliers final: 73 residues processed: 244 average time/residue: 0.3547 time to fit residues: 99.9236 Evaluate side-chains 233 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 151 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1293 GLN Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1424 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1469 ILE Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1569 ASP Chi-restraints excluded: chain A residue 1579 THR Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 889 GLN Chi-restraints excluded: chain B residue 896 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1133 CYS Chi-restraints excluded: chain B residue 1168 GLU Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1198 VAL Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1283 LEU Chi-restraints excluded: chain B residue 1301 VAL Chi-restraints excluded: chain B residue 1306 THR Chi-restraints excluded: chain B residue 1307 SER Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1354 THR Chi-restraints excluded: chain B residue 1358 THR Chi-restraints excluded: chain B residue 1382 HIS Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1416 SER Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain B residue 1435 CYS Chi-restraints excluded: chain B residue 1463 SER Chi-restraints excluded: chain B residue 1503 MET Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1516 ASN Chi-restraints excluded: chain B residue 1536 GLU Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1553 ILE Chi-restraints excluded: chain B residue 1556 THR Chi-restraints excluded: chain B residue 1563 VAL Chi-restraints excluded: chain B residue 1598 SER Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1624 THR Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 1677 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 71 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.4591 > 50:) chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 119 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 169 optimal weight: 0.0070 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 ASN A1342 ASN A1423 ASN ** B 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1557 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110549 restraints weight = 18589.623| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.61 r_work: 0.3276 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 13493 Z= 0.118 Angle : 0.598 10.958 18461 Z= 0.302 Chirality : 0.043 0.173 2111 Planarity : 0.005 0.155 2417 Dihedral : 6.378 58.087 1882 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.63 % Favored : 92.73 % Rotamer: Outliers : 6.46 % Allowed : 30.04 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.20), residues: 1719 helix: 0.06 (0.25), residues: 456 sheet: -0.67 (0.39), residues: 153 loop : -0.88 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 887 TYR 0.012 0.001 TYR B1377 PHE 0.016 0.001 PHE B1256 TRP 0.015 0.001 TRP A1511 HIS 0.003 0.001 HIS A1073 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (13493) covalent geometry : angle 0.59804 / 0.30 (18461) hydrogen bonds : bond 0.03484 / 2.31 ( 355) hydrogen bonds : angle 4.79035 / 3.26 ( 975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 163 time to evaluate : 0.517 Fit side-chains REVERT: A 926 ARG cc_start: 0.7944 (ttm110) cc_final: 0.6613 (mmt-90) REVERT: A 969 MET cc_start: 0.8654 (mpp) cc_final: 0.8366 (mmp) REVERT: A 1124 THR cc_start: 0.8365 (m) cc_final: 0.7804 (p) REVERT: A 1323 MET cc_start: 0.8087 (mmp) cc_final: 0.7624 (mmp) REVERT: A 1395 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.6871 (tppp) REVERT: A 1455 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: B 811 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.6120 (m-30) REVERT: B 880 ILE cc_start: 0.8033 (mm) cc_final: 0.7741 (mt) REVERT: B 926 ARG cc_start: 0.5165 (ttp-110) cc_final: 0.4437 (ptt180) REVERT: B 969 MET cc_start: 0.8043 (mmt) cc_final: 0.7660 (mmt) REVERT: B 1083 THR cc_start: 0.7920 (p) cc_final: 0.7286 (t) REVERT: B 1119 ILE cc_start: 0.7398 (mp) cc_final: 0.6833 (tt) REVERT: B 1240 ASP cc_start: 0.8007 (t0) cc_final: 0.7704 (t70) REVERT: B 1503 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8090 (mtt) REVERT: B 1536 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7846 (mm-30) outliers start: 91 outliers final: 61 residues processed: 232 average time/residue: 0.3802 time to fit residues: 101.4094 Evaluate side-chains 220 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 154 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1424 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1569 ASP Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 896 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1133 CYS Chi-restraints excluded: chain B residue 1168 GLU Chi-restraints excluded: chain B residue 1169 TRP Chi-restraints excluded: chain B residue 1198 VAL Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1283 LEU Chi-restraints excluded: chain B residue 1301 VAL Chi-restraints excluded: chain B residue 1307 SER Chi-restraints excluded: chain B residue 1354 THR Chi-restraints excluded: chain B residue 1358 THR Chi-restraints excluded: chain B residue 1382 HIS Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1416 SER Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain B residue 1435 CYS Chi-restraints excluded: chain B residue 1463 SER Chi-restraints excluded: chain B residue 1503 MET Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1536 GLU Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1553 ILE Chi-restraints excluded: chain B residue 1556 THR Chi-restraints excluded: chain B residue 1563 VAL Chi-restraints excluded: chain B residue 1575 THR Chi-restraints excluded: chain B residue 1598 SER Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1624 THR Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1644 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 142 optimal weight: 4.9990 chunk 21 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 ASN B 889 GLN ** B 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108949 restraints weight = 18575.267| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.61 r_work: 0.3250 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13493 Z= 0.163 Angle : 0.637 11.532 18461 Z= 0.321 Chirality : 0.045 0.167 2111 Planarity : 0.006 0.156 2417 Dihedral : 6.449 59.803 1880 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.21 % Favored : 92.15 % Rotamer: Outliers : 6.61 % Allowed : 30.26 % Favored : 63.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.20), residues: 1719 helix: -0.14 (0.24), residues: 469 sheet: -0.63 (0.39), residues: 153 loop : -0.96 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 926 TYR 0.016 0.002 TYR B1377 PHE 0.020 0.002 PHE B1256 TRP 0.014 0.002 TRP A1511 HIS 0.004 0.001 HIS B1029 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.16 (13493) covalent geometry : angle 0.63732 / 0.32 (18461) hydrogen bonds : bond 0.03835 / 2.50 ( 355) hydrogen bonds : angle 4.88575 / 3.32 ( 975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 157 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 926 ARG cc_start: 0.7938 (ttm110) cc_final: 0.6623 (mmt-90) REVERT: A 969 MET cc_start: 0.8684 (mpp) cc_final: 0.8363 (mmp) REVERT: A 1118 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: A 1293 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7300 (mm110) REVERT: A 1323 MET cc_start: 0.7982 (mmp) cc_final: 0.7553 (mmp) REVERT: A 1395 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.6817 (tppp) REVERT: A 1455 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: B 803 PHE cc_start: 0.6973 (t80) cc_final: 0.6439 (t80) REVERT: B 811 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6064 (m-30) REVERT: B 880 ILE cc_start: 0.8040 (mm) cc_final: 0.7737 (mt) REVERT: B 889 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7193 (mm-40) REVERT: B 926 ARG cc_start: 0.5171 (ttp-110) cc_final: 0.4369 (ptt180) REVERT: B 969 MET cc_start: 0.8028 (mmt) cc_final: 0.7755 (mmt) REVERT: B 1119 ILE cc_start: 0.7424 (mp) cc_final: 0.6850 (tt) REVERT: B 1240 ASP cc_start: 0.8001 (t0) cc_final: 0.7679 (t70) REVERT: B 1503 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8126 (mtt) REVERT: B 1536 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7946 (mm-30) outliers start: 93 outliers final: 64 residues processed: 231 average time/residue: 0.3767 time to fit residues: 100.2514 Evaluate side-chains 224 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 152 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1239 SER Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1293 GLN Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1424 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1569 ASP Chi-restraints excluded: chain A residue 1579 THR Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 889 GLN Chi-restraints excluded: chain B residue 896 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1198 VAL Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1283 LEU Chi-restraints excluded: chain B residue 1301 VAL Chi-restraints excluded: chain B residue 1307 SER Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1354 THR Chi-restraints excluded: chain B residue 1358 THR Chi-restraints excluded: chain B residue 1382 HIS Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1416 SER Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain B residue 1435 CYS Chi-restraints excluded: chain B residue 1463 SER Chi-restraints excluded: chain B residue 1503 MET Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1536 GLU Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1553 ILE Chi-restraints excluded: chain B residue 1556 THR Chi-restraints excluded: chain B residue 1563 VAL Chi-restraints excluded: chain B residue 1575 THR Chi-restraints excluded: chain B residue 1598 SER Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1624 THR Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1644 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 145 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 59 optimal weight: 0.0470 chunk 112 optimal weight: 9.9990 chunk 8 optimal weight: 0.0980 chunk 108 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 overall best weight: 2.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 ASN ** B 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109005 restraints weight = 18761.012| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.63 r_work: 0.3252 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 13493 Z= 0.152 Angle : 0.631 11.323 18461 Z= 0.318 Chirality : 0.044 0.170 2111 Planarity : 0.006 0.155 2417 Dihedral : 6.288 59.946 1877 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.98 % Favored : 92.38 % Rotamer: Outliers : 6.25 % Allowed : 30.47 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.20), residues: 1719 helix: -0.03 (0.25), residues: 458 sheet: -0.63 (0.39), residues: 152 loop : -0.92 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 926 TYR 0.015 0.001 TYR B1377 PHE 0.019 0.002 PHE B1256 TRP 0.017 0.001 TRP A1511 HIS 0.003 0.001 HIS B1029 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.15 (13493) covalent geometry : angle 0.63065 / 0.32 (18461) hydrogen bonds : bond 0.03743 / 2.45 ( 355) hydrogen bonds : angle 4.85318 / 3.30 ( 975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 158 time to evaluate : 0.539 Fit side-chains REVERT: A 926 ARG cc_start: 0.7933 (ttm110) cc_final: 0.6599 (mmt-90) REVERT: A 969 MET cc_start: 0.8666 (mpp) cc_final: 0.8355 (mmp) REVERT: A 1118 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8068 (pm20) REVERT: A 1124 THR cc_start: 0.8377 (m) cc_final: 0.7805 (p) REVERT: A 1134 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.5329 (tmt) REVERT: A 1293 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7291 (mm110) REVERT: A 1395 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.6804 (tppp) REVERT: A 1455 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: B 803 PHE cc_start: 0.6994 (t80) cc_final: 0.6488 (t80) REVERT: B 811 ASP cc_start: 0.6682 (OUTLIER) cc_final: 0.6068 (m-30) REVERT: B 880 ILE cc_start: 0.8029 (mm) cc_final: 0.7734 (mt) REVERT: B 926 ARG cc_start: 0.5204 (ttp-110) cc_final: 0.4445 (ptt180) REVERT: B 969 MET cc_start: 0.8050 (mmt) cc_final: 0.7645 (mmt) REVERT: B 1083 THR cc_start: 0.7908 (p) cc_final: 0.7290 (t) REVERT: B 1119 ILE cc_start: 0.7416 (mp) cc_final: 0.6852 (tt) REVERT: B 1240 ASP cc_start: 0.7975 (t0) cc_final: 0.7666 (t70) REVERT: B 1503 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8120 (mtt) REVERT: B 1536 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7969 (mm-30) REVERT: B 1627 ASN cc_start: 0.7415 (m-40) cc_final: 0.6907 (p0) outliers start: 88 outliers final: 72 residues processed: 229 average time/residue: 0.3818 time to fit residues: 100.6103 Evaluate side-chains 233 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 153 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1239 SER Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1293 GLN Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 GLU Chi-restraints excluded: chain A residue 1424 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1569 ASP Chi-restraints excluded: chain A residue 1579 THR Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 896 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 927 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1198 VAL Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1283 LEU Chi-restraints excluded: chain B residue 1295 MET Chi-restraints excluded: chain B residue 1301 VAL Chi-restraints excluded: chain B residue 1307 SER Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1354 THR Chi-restraints excluded: chain B residue 1358 THR Chi-restraints excluded: chain B residue 1382 HIS Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1416 SER Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain B residue 1435 CYS Chi-restraints excluded: chain B residue 1463 SER Chi-restraints excluded: chain B residue 1503 MET Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1516 ASN Chi-restraints excluded: chain B residue 1536 GLU Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1553 ILE Chi-restraints excluded: chain B residue 1556 THR Chi-restraints excluded: chain B residue 1563 VAL Chi-restraints excluded: chain B residue 1575 THR Chi-restraints excluded: chain B residue 1598 SER Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1624 THR Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1644 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 166 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 169 optimal weight: 0.0670 chunk 118 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 0.0570 chunk 122 optimal weight: 0.9980 overall best weight: 1.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 ASN A1208 HIS B 889 GLN ** B 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.126621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110571 restraints weight = 18763.529| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.65 r_work: 0.3272 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13493 Z= 0.117 Angle : 0.596 10.685 18461 Z= 0.299 Chirality : 0.043 0.202 2111 Planarity : 0.005 0.154 2417 Dihedral : 6.034 57.844 1877 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.69 % Favored : 92.73 % Rotamer: Outliers : 5.68 % Allowed : 31.04 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.20), residues: 1719 helix: 0.15 (0.25), residues: 461 sheet: -0.59 (0.39), residues: 152 loop : -0.81 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1108 TYR 0.011 0.001 TYR B1377 PHE 0.015 0.001 PHE B1256 TRP 0.020 0.001 TRP A1511 HIS 0.003 0.001 HIS A1073 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (13493) covalent geometry : angle 0.59565 / 0.30 (18461) hydrogen bonds : bond 0.03387 / 2.23 ( 355) hydrogen bonds : angle 4.70904 / 3.21 ( 975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 161 time to evaluate : 0.513 Fit side-chains REVERT: A 926 ARG cc_start: 0.7965 (ttm110) cc_final: 0.6611 (mmt-90) REVERT: A 969 MET cc_start: 0.8629 (mpp) cc_final: 0.8377 (mmp) REVERT: A 1118 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: A 1124 THR cc_start: 0.8362 (m) cc_final: 0.7786 (p) REVERT: A 1134 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.5244 (tmt) REVERT: A 1323 MET cc_start: 0.8137 (mmp) cc_final: 0.7619 (mmp) REVERT: A 1395 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.6829 (tppp) REVERT: A 1455 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: B 803 PHE cc_start: 0.6911 (t80) cc_final: 0.6447 (t80) REVERT: B 811 ASP cc_start: 0.6667 (OUTLIER) cc_final: 0.6055 (m-30) REVERT: B 880 ILE cc_start: 0.8016 (mm) cc_final: 0.7718 (mt) REVERT: B 889 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7174 (mm-40) REVERT: B 926 ARG cc_start: 0.5165 (ttp-110) cc_final: 0.4440 (ptt180) REVERT: B 969 MET cc_start: 0.7976 (mmt) cc_final: 0.7635 (mmt) REVERT: B 1119 ILE cc_start: 0.7424 (mp) cc_final: 0.6850 (tt) REVERT: B 1240 ASP cc_start: 0.8029 (t0) cc_final: 0.7708 (t70) REVERT: B 1503 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8085 (mtt) REVERT: B 1536 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7876 (mm-30) outliers start: 80 outliers final: 60 residues processed: 223 average time/residue: 0.3847 time to fit residues: 98.8167 Evaluate side-chains 220 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 152 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1424 CYS Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1569 ASP Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 889 GLN Chi-restraints excluded: chain B residue 896 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1198 VAL Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1283 LEU Chi-restraints excluded: chain B residue 1295 MET Chi-restraints excluded: chain B residue 1301 VAL Chi-restraints excluded: chain B residue 1307 SER Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1354 THR Chi-restraints excluded: chain B residue 1358 THR Chi-restraints excluded: chain B residue 1382 HIS Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1416 SER Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain B residue 1435 CYS Chi-restraints excluded: chain B residue 1463 SER Chi-restraints excluded: chain B residue 1503 MET Chi-restraints excluded: chain B residue 1536 GLU Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1553 ILE Chi-restraints excluded: chain B residue 1556 THR Chi-restraints excluded: chain B residue 1563 VAL Chi-restraints excluded: chain B residue 1575 THR Chi-restraints excluded: chain B residue 1598 SER Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1624 THR Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1644 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 30 optimal weight: 10.0000 chunk 49 optimal weight: 0.3980 chunk 140 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 970 ASN ** B 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108498 restraints weight = 18636.710| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.64 r_work: 0.3235 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13493 Z= 0.177 Angle : 0.650 12.259 18461 Z= 0.327 Chirality : 0.046 0.167 2111 Planarity : 0.006 0.155 2417 Dihedral : 6.260 59.180 1877 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.92 % Favored : 92.50 % Rotamer: Outliers : 5.97 % Allowed : 31.11 % Favored : 62.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.20), residues: 1719 helix: -0.02 (0.24), residues: 461 sheet: -0.79 (0.38), residues: 158 loop : -0.90 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 887 TYR 0.012 0.002 TYR A1204 PHE 0.021 0.002 PHE B1256 TRP 0.027 0.002 TRP A1511 HIS 0.004 0.001 HIS B1208 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (13493) covalent geometry : angle 0.64963 / 0.33 (18461) hydrogen bonds : bond 0.03881 / 2.53 ( 355) hydrogen bonds : angle 4.83304 / 3.28 ( 975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4236.50 seconds wall clock time: 73 minutes 26.68 seconds (4406.68 seconds total)