Starting phenix.real_space_refine on Tue Aug 26 18:12:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vg4_43199/08_2025/8vg4_43199_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vg4_43199/08_2025/8vg4_43199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vg4_43199/08_2025/8vg4_43199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vg4_43199/08_2025/8vg4_43199.map" model { file = "/net/cci-nas-00/data/ceres_data/8vg4_43199/08_2025/8vg4_43199_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vg4_43199/08_2025/8vg4_43199_trim.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 S 80 5.16 5 C 12302 2.51 5 N 3422 2.21 5 O 3657 1.98 5 H 19313 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38787 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1216, 18704 Classifications: {'peptide': 1216} Link IDs: {'PTRANS': 66, 'TRANS': 1149} Chain breaks: 2 Chain: "B" Number of atoms: 19891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1289, 19891 Classifications: {'peptide': 1289} Link IDs: {'PTRANS': 66, 'TRANS': 1222} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NDP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NDP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.87, per 1000 atoms: 0.18 Number of scatterers: 38787 At special positions: 0 Unit cell: (110.107, 119.728, 202.041, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 13 15.00 O 3657 8.00 N 3422 7.00 C 12302 6.00 H 19313 1.00 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: 3.51 Conformation dependent library (CDL) restraints added in 925.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4610 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 22 sheets defined 42.8% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 870 through 877 removed outlier: 4.538A pdb=" N TYR A 874 " --> pdb=" O PRO A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 904 removed outlier: 3.715A pdb=" N TYR A 891 " --> pdb=" O PRO A 887 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 892 " --> pdb=" O ALA A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 965 through 970 Processing helix chain 'A' and resid 987 through 998 Processing helix chain 'A' and resid 1002 through 1006 Processing helix chain 'A' and resid 1025 through 1040 removed outlier: 3.818A pdb=" N GLY A1040 " --> pdb=" O MET A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1126 through 1131 removed outlier: 4.040A pdb=" N GLU A1130 " --> pdb=" O CYS A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1146 Processing helix chain 'A' and resid 1176 through 1188 Processing helix chain 'A' and resid 1194 through 1200 Processing helix chain 'A' and resid 1208 through 1212 Processing helix chain 'A' and resid 1216 through 1221 Processing helix chain 'A' and resid 1222 through 1234 Processing helix chain 'A' and resid 1246 through 1251 Processing helix chain 'A' and resid 1252 through 1254 No H-bonds generated for 'chain 'A' and resid 1252 through 1254' Processing helix chain 'A' and resid 1255 through 1260 removed outlier: 3.774A pdb=" N LEU A1259 " --> pdb=" O ARG A1255 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A1260 " --> pdb=" O ILE A1256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1255 through 1260' Processing helix chain 'A' and resid 1283 through 1290 removed outlier: 3.665A pdb=" N LEU A1287 " --> pdb=" O ALA A1283 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS A1290 " --> pdb=" O GLU A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1335 Processing helix chain 'A' and resid 1351 through 1360 Processing helix chain 'A' and resid 1364 through 1370 Processing helix chain 'A' and resid 1373 through 1384 Processing helix chain 'A' and resid 1419 through 1422 removed outlier: 4.142A pdb=" N PHE A1422 " --> pdb=" O ASP A1419 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1419 through 1422' Processing helix chain 'A' and resid 1423 through 1434 removed outlier: 4.227A pdb=" N SER A1427 " --> pdb=" O ARG A1423 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP A1434 " --> pdb=" O GLY A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1462 removed outlier: 3.631A pdb=" N ASN A1458 " --> pdb=" O VAL A1454 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS A1459 " --> pdb=" O GLY A1455 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A1462 " --> pdb=" O ASN A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1467 No H-bonds generated for 'chain 'A' and resid 1465 through 1467' Processing helix chain 'A' and resid 1490 through 1500 Processing helix chain 'A' and resid 1540 through 1542 No H-bonds generated for 'chain 'A' and resid 1540 through 1542' Processing helix chain 'A' and resid 1550 through 1553 removed outlier: 3.660A pdb=" N HIS A1553 " --> pdb=" O SER A1550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1550 through 1553' Processing helix chain 'A' and resid 1572 through 1580 Processing helix chain 'A' and resid 1584 through 1588 Processing helix chain 'A' and resid 1629 through 1631 No H-bonds generated for 'chain 'A' and resid 1629 through 1631' Processing helix chain 'A' and resid 1641 through 1646 Processing helix chain 'A' and resid 1648 through 1661 Processing helix chain 'A' and resid 1678 through 1692 Processing helix chain 'A' and resid 1701 through 1712 Processing helix chain 'A' and resid 1716 through 1718 No H-bonds generated for 'chain 'A' and resid 1716 through 1718' Processing helix chain 'A' and resid 1727 through 1736 Processing helix chain 'A' and resid 1749 through 1758 removed outlier: 3.507A pdb=" N ARG A1758 " --> pdb=" O GLN A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1771 through 1777 Processing helix chain 'A' and resid 1781 through 1788 removed outlier: 3.599A pdb=" N ILE A1784 " --> pdb=" O GLY A1781 " (cutoff:3.500A) Processing helix chain 'A' and resid 1797 through 1802 removed outlier: 3.781A pdb=" N ASN A1801 " --> pdb=" O ASP A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1820 removed outlier: 3.688A pdb=" N ARG A1808 " --> pdb=" O SER A1804 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU A1809 " --> pdb=" O ALA A1805 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A1810 " --> pdb=" O ASP A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1846 removed outlier: 3.584A pdb=" N GLY A1846 " --> pdb=" O TYR A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1894 through 1906 removed outlier: 3.760A pdb=" N GLU A1899 " --> pdb=" O GLY A1895 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1936 Processing helix chain 'A' and resid 1948 through 1963 removed outlier: 3.881A pdb=" N LEU A1962 " --> pdb=" O GLU A1958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 2010 Proline residue: A1994 - end of helix removed outlier: 3.813A pdb=" N SER A1997 " --> pdb=" O LYS A1993 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A1998 " --> pdb=" O PRO A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2027 Processing helix chain 'A' and resid 2031 through 2051 removed outlier: 3.574A pdb=" N ILE A2044 " --> pdb=" O ALA A2040 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A2051 " --> pdb=" O LYS A2047 " (cutoff:3.500A) Processing helix chain 'A' and resid 2087 through 2101 removed outlier: 3.669A pdb=" N ASN A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 876 removed outlier: 4.467A pdb=" N TYR B 874 " --> pdb=" O PRO B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 904 removed outlier: 3.604A pdb=" N TYR B 891 " --> pdb=" O PRO B 887 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 892 " --> pdb=" O ALA B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 965 through 970 Processing helix chain 'B' and resid 987 through 998 Processing helix chain 'B' and resid 1003 through 1006 Processing helix chain 'B' and resid 1025 through 1040 removed outlier: 3.943A pdb=" N GLY B1040 " --> pdb=" O MET B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1066 Processing helix chain 'B' and resid 1131 through 1149 removed outlier: 3.511A pdb=" N GLN B1135 " --> pdb=" O ARG B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1188 Processing helix chain 'B' and resid 1191 through 1194 Processing helix chain 'B' and resid 1195 through 1204 removed outlier: 3.558A pdb=" N GLN B1204 " --> pdb=" O GLN B1200 " (cutoff:3.500A) Processing helix chain 'B' and resid 1208 through 1212 Processing helix chain 'B' and resid 1217 through 1220 Processing helix chain 'B' and resid 1221 through 1234 removed outlier: 4.173A pdb=" N LYS B1225 " --> pdb=" O SER B1221 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B1234 " --> pdb=" O THR B1230 " (cutoff:3.500A) Processing helix chain 'B' and resid 1246 through 1251 Processing helix chain 'B' and resid 1251 through 1260 removed outlier: 4.365A pdb=" N ARG B1255 " --> pdb=" O HIS B1251 " (cutoff:3.500A) Proline residue: B1257 - end of helix Processing helix chain 'B' and resid 1277 through 1288 removed outlier: 3.676A pdb=" N GLU B1281 " --> pdb=" O PRO B1277 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B1282 " --> pdb=" O GLN B1278 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B1283 " --> pdb=" O ALA B1279 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA B1285 " --> pdb=" O GLU B1281 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLU B1286 " --> pdb=" O ALA B1282 " (cutoff:3.500A) Processing helix chain 'B' and resid 1324 through 1335 Processing helix chain 'B' and resid 1351 through 1361 removed outlier: 3.522A pdb=" N ILE B1356 " --> pdb=" O PRO B1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 1363 through 1367 Processing helix chain 'B' and resid 1373 through 1384 Processing helix chain 'B' and resid 1423 through 1434 removed outlier: 4.002A pdb=" N SER B1427 " --> pdb=" O ARG B1423 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP B1434 " --> pdb=" O GLY B1430 " (cutoff:3.500A) Processing helix chain 'B' and resid 1452 through 1463 removed outlier: 4.036A pdb=" N ARG B1462 " --> pdb=" O ASN B1458 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B1463 " --> pdb=" O CYS B1459 " (cutoff:3.500A) Processing helix chain 'B' and resid 1465 through 1467 No H-bonds generated for 'chain 'B' and resid 1465 through 1467' Processing helix chain 'B' and resid 1490 through 1500 removed outlier: 3.666A pdb=" N GLY B1499 " --> pdb=" O LYS B1495 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B1500 " --> pdb=" O VAL B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1542 No H-bonds generated for 'chain 'B' and resid 1540 through 1542' Processing helix chain 'B' and resid 1550 through 1553 Processing helix chain 'B' and resid 1572 through 1580 Processing helix chain 'B' and resid 1584 through 1588 Processing helix chain 'B' and resid 1629 through 1631 No H-bonds generated for 'chain 'B' and resid 1629 through 1631' Processing helix chain 'B' and resid 1641 through 1646 Processing helix chain 'B' and resid 1647 through 1661 removed outlier: 4.426A pdb=" N VAL B1651 " --> pdb=" O SER B1647 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1691 removed outlier: 3.607A pdb=" N LEU B1691 " --> pdb=" O ILE B1687 " (cutoff:3.500A) Processing helix chain 'B' and resid 1701 through 1712 Processing helix chain 'B' and resid 1716 through 1718 No H-bonds generated for 'chain 'B' and resid 1716 through 1718' Processing helix chain 'B' and resid 1727 through 1736 Processing helix chain 'B' and resid 1749 through 1758 removed outlier: 3.597A pdb=" N GLN B1754 " --> pdb=" O GLU B1750 " (cutoff:3.500A) Processing helix chain 'B' and resid 1771 through 1777 Processing helix chain 'B' and resid 1781 through 1787 removed outlier: 3.856A pdb=" N ILE B1784 " --> pdb=" O GLY B1781 " (cutoff:3.500A) Processing helix chain 'B' and resid 1797 through 1802 removed outlier: 3.704A pdb=" N ASN B1801 " --> pdb=" O ASP B1797 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU B1802 " --> pdb=" O ALA B1798 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1797 through 1802' Processing helix chain 'B' and resid 1805 through 1820 removed outlier: 3.850A pdb=" N GLU B1809 " --> pdb=" O ALA B1805 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B1810 " --> pdb=" O ASP B1806 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1846 removed outlier: 3.664A pdb=" N GLY B1846 " --> pdb=" O TYR B1842 " (cutoff:3.500A) Processing helix chain 'B' and resid 1894 through 1907 removed outlier: 3.821A pdb=" N GLU B1899 " --> pdb=" O GLY B1895 " (cutoff:3.500A) Processing helix chain 'B' and resid 1922 through 1936 Processing helix chain 'B' and resid 1948 through 1963 removed outlier: 3.529A pdb=" N GLN B1961 " --> pdb=" O ALA B1957 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B1962 " --> pdb=" O GLU B1958 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) Processing helix chain 'B' and resid 1979 through 1983 Processing helix chain 'B' and resid 1984 through 2010 Proline residue: B1994 - end of helix removed outlier: 3.580A pdb=" N SER B1997 " --> pdb=" O LYS B1993 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B1998 " --> pdb=" O PRO B1994 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B2008 " --> pdb=" O ARG B2004 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2026 Processing helix chain 'B' and resid 2031 through 2051 removed outlier: 3.854A pdb=" N ILE B2044 " --> pdb=" O ALA B2040 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS B2045 " --> pdb=" O MET B2041 " (cutoff:3.500A) Processing helix chain 'B' and resid 2087 through 2100 removed outlier: 3.994A pdb=" N ASN B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) Processing helix chain 'B' and resid 2126 through 2136 Processing helix chain 'B' and resid 2148 through 2153 Processing helix chain 'B' and resid 2155 through 2171 removed outlier: 3.541A pdb=" N VAL B2160 " --> pdb=" O 4HH B2156 " (cutoff:3.500A) Processing helix chain 'B' and resid 2175 through 2182 Processing helix chain 'B' and resid 2183 through 2193 Processing sheet with id=AA1, first strand: chain 'A' and resid 860 through 864 removed outlier: 3.627A pdb=" N VAL A 931 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU A 948 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU A 952 " --> pdb=" O GLU A 948 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS A 957 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASP A 916 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR A 959 " --> pdb=" O PHE A 914 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N PHE A 914 " --> pdb=" O TYR A 959 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A1053 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 918 " --> pdb=" O ARG A1051 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG A1051 " --> pdb=" O VAL A 918 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS A1098 " --> pdb=" O THR A1050 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A1052 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY A1096 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ALA A1054 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A1094 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS A1056 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A1092 " --> pdb=" O HIS A1056 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N SER A1017 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA A1011 " --> pdb=" O SER A1017 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG A1019 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 860 through 864 removed outlier: 3.627A pdb=" N VAL A 931 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU A 948 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU A 952 " --> pdb=" O GLU A 948 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS A 957 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASP A 916 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR A 959 " --> pdb=" O PHE A 914 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N PHE A 914 " --> pdb=" O TYR A 959 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A1053 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 918 " --> pdb=" O ARG A1051 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG A1051 " --> pdb=" O VAL A 918 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS A1098 " --> pdb=" O THR A1050 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A1052 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY A1096 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ALA A1054 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A1094 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS A1056 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A1092 " --> pdb=" O HIS A1056 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 879 through 880 Processing sheet with id=AA4, first strand: chain 'A' and resid 1413 through 1416 removed outlier: 5.739A pdb=" N ILE A1413 " --> pdb=" O TRP A1442 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS A1444 " --> pdb=" O ILE A1413 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU A1415 " --> pdb=" O LYS A1444 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N ASN A1504 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N CYS A1471 " --> pdb=" O ASN A1504 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR A1506 " --> pdb=" O CYS A1471 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A1473 " --> pdb=" O TYR A1506 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N MET A1503 " --> pdb=" O PHE A1514 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE A1514 " --> pdb=" O MET A1503 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL A2105 " --> pdb=" O PHE A1117 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE A2016 " --> pdb=" O LEU A2056 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A2058 " --> pdb=" O PHE A2016 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A2018 " --> pdb=" O VAL A2058 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TRP A2060 " --> pdb=" O VAL A2018 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N SER A2020 " --> pdb=" O TRP A2060 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A2019 " --> pdb=" O ASN A1970 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N SER A1886 " --> pdb=" O GLY A1966 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL A1968 " --> pdb=" O SER A1886 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A1888 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ASN A1970 " --> pdb=" O ILE A1888 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA A1890 " --> pdb=" O ASN A1970 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1123 through 1124 removed outlier: 5.541A pdb=" N LEU A1388 " --> pdb=" O ARG A1404 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A1404 " --> pdb=" O LEU A1388 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP A1311 " --> pdb=" O PHE A1341 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU A1343 " --> pdb=" O ASP A1311 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU A1313 " --> pdb=" O LEU A1343 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N HIS A1345 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP A1311 " --> pdb=" O LYS A1239 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS A1241 " --> pdb=" O ASP A1311 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU A1313 " --> pdb=" O LYS A1241 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1243 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1525 through 1528 Processing sheet with id=AA7, first strand: chain 'A' and resid 1531 through 1535 Processing sheet with id=AA8, first strand: chain 'A' and resid 1562 through 1565 Processing sheet with id=AA9, first strand: chain 'A' and resid 1568 through 1571 removed outlier: 4.669A pdb=" N VAL A1852 " --> pdb=" O LEU A1571 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR A1829 " --> pdb=" O VAL A1853 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLN A1855 " --> pdb=" O THR A1829 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE A1831 " --> pdb=" O GLN A1855 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1602 through 1606 removed outlier: 3.773A pdb=" N PHE A1603 " --> pdb=" O GLY A1615 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1720 through 1722 removed outlier: 6.165A pdb=" N LEU A1671 " --> pdb=" O PHE A1696 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N THR A1698 " --> pdb=" O LEU A1671 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE A1673 " --> pdb=" O THR A1698 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR A1670 " --> pdb=" O LEU A1743 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU A1745 " --> pdb=" O THR A1670 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU A1672 " --> pdb=" O LEU A1745 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP A1742 " --> pdb=" O ARG A1765 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU A1767 " --> pdb=" O ASP A1742 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL A1744 " --> pdb=" O LEU A1767 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B1789 " --> pdb=" O GLY A1793 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP B1742 " --> pdb=" O ARG B1765 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU B1767 " --> pdb=" O ASP B1742 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL B1744 " --> pdb=" O LEU B1767 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR B1670 " --> pdb=" O LEU B1743 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N LEU B1745 " --> pdb=" O THR B1670 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU B1672 " --> pdb=" O LEU B1745 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA B1721 " --> pdb=" O VAL B1695 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR B1697 " --> pdb=" O ALA B1721 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2083 through 2084 removed outlier: 4.469A pdb=" N VAL A2110 " --> pdb=" O LEU A2084 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 860 through 864 removed outlier: 3.508A pdb=" N ALA B 860 " --> pdb=" O VAL B 935 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 931 " --> pdb=" O ILE B 864 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE B 944 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER B 955 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 946 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL B 953 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU B 919 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER B 955 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 917 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B1053 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 918 " --> pdb=" O ARG B1051 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG B1051 " --> pdb=" O VAL B 918 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS B1098 " --> pdb=" O THR B1050 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B1052 " --> pdb=" O GLY B1096 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY B1096 " --> pdb=" O VAL B1052 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA B1054 " --> pdb=" O ILE B1094 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE B1094 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS B1056 " --> pdb=" O VAL B1092 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B1092 " --> pdb=" O HIS B1056 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER B1017 " --> pdb=" O SER B1012 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B1010 " --> pdb=" O ARG B1019 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B1021 " --> pdb=" O ILE B1008 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B1008 " --> pdb=" O LEU B1021 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 860 through 864 removed outlier: 3.508A pdb=" N ALA B 860 " --> pdb=" O VAL B 935 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 931 " --> pdb=" O ILE B 864 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE B 944 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER B 955 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 946 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL B 953 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU B 919 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER B 955 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 917 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B1053 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 918 " --> pdb=" O ARG B1051 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG B1051 " --> pdb=" O VAL B 918 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS B1098 " --> pdb=" O THR B1050 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B1052 " --> pdb=" O GLY B1096 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY B1096 " --> pdb=" O VAL B1052 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA B1054 " --> pdb=" O ILE B1094 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE B1094 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS B1056 " --> pdb=" O VAL B1092 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B1092 " --> pdb=" O HIS B1056 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 883 through 884 removed outlier: 4.181A pdb=" N THR B 879 " --> pdb=" O ASP B1000 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1413 through 1416 removed outlier: 6.091A pdb=" N ILE B1413 " --> pdb=" O TRP B1442 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS B1444 " --> pdb=" O ILE B1413 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B1415 " --> pdb=" O LYS B1444 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN B1504 " --> pdb=" O LEU B1469 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N CYS B1471 " --> pdb=" O ASN B1504 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR B1506 " --> pdb=" O CYS B1471 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B1473 " --> pdb=" O TYR B1506 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N MET B1503 " --> pdb=" O PHE B1514 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE B1514 " --> pdb=" O MET B1503 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B1510 " --> pdb=" O ARG B1507 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B1513 " --> pdb=" O THR B1120 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B2109 " --> pdb=" O ILE B1113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B1115 " --> pdb=" O SER B2107 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL B2105 " --> pdb=" O PHE B1117 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY B1966 " --> pdb=" O TYR B2015 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N VAL B2017 " --> pdb=" O GLY B1966 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL B1968 " --> pdb=" O VAL B2017 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE B2019 " --> pdb=" O VAL B1968 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASN B1970 " --> pdb=" O PHE B2019 " (cutoff:3.500A) removed outlier: 9.504A pdb=" N SER B2021 " --> pdb=" O ASN B1970 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER B1886 " --> pdb=" O GLY B1966 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL B1968 " --> pdb=" O SER B1886 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B1888 " --> pdb=" O VAL B1968 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASN B1970 " --> pdb=" O ILE B1888 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA B1890 " --> pdb=" O ASN B1970 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B1912 " --> pdb=" O GLN B1940 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N SER B1942 " --> pdb=" O LEU B1912 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B1914 " --> pdb=" O SER B1942 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1413 through 1416 removed outlier: 6.091A pdb=" N ILE B1413 " --> pdb=" O TRP B1442 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS B1444 " --> pdb=" O ILE B1413 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B1415 " --> pdb=" O LYS B1444 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN B1504 " --> pdb=" O LEU B1469 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N CYS B1471 " --> pdb=" O ASN B1504 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR B1506 " --> pdb=" O CYS B1471 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B1473 " --> pdb=" O TYR B1506 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N MET B1503 " --> pdb=" O PHE B1514 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE B1514 " --> pdb=" O MET B1503 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B1510 " --> pdb=" O ARG B1507 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B1513 " --> pdb=" O THR B1120 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B2109 " --> pdb=" O ILE B1113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B1115 " --> pdb=" O SER B2107 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL B2105 " --> pdb=" O PHE B1117 " (cutoff:3.500A) removed outlier: 11.552A pdb=" N SER B2108 " --> pdb=" O GLN B2086 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLN B2086 " --> pdb=" O SER B2108 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B2110 " --> pdb=" O LEU B2084 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA B2062 " --> pdb=" O GLN B2086 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1123 through 1125 removed outlier: 6.386A pdb=" N LEU B1402 " --> pdb=" O VAL B1389 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU B1391 " --> pdb=" O LEU B1400 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B1400 " --> pdb=" O LEU B1391 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B1346 " --> pdb=" O THR B1399 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP B1311 " --> pdb=" O PHE B1341 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU B1343 " --> pdb=" O ASP B1311 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU B1313 " --> pdb=" O LEU B1343 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N HIS B1345 " --> pdb=" O LEU B1313 " (cutoff:3.500A) removed outlier: 11.420A pdb=" N LYS B1239 " --> pdb=" O ALA B1310 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU B1312 " --> pdb=" O LYS B1239 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS B1241 " --> pdb=" O LEU B1312 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL B1314 " --> pdb=" O LYS B1241 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B1243 " --> pdb=" O VAL B1314 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ALA B1293 " --> pdb=" O LEU B1268 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR B1270 " --> pdb=" O ALA B1293 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLY B1295 " --> pdb=" O TYR B1270 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA B1272 " --> pdb=" O GLY B1295 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1525 through 1528 Processing sheet with id=AC2, first strand: chain 'B' and resid 1531 through 1535 Processing sheet with id=AC3, first strand: chain 'B' and resid 1625 through 1628 removed outlier: 6.584A pdb=" N SER B1604 " --> pdb=" O TYR B1567 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ALA B1569 " --> pdb=" O GLU B1602 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLU B1602 " --> pdb=" O ALA B1569 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B1603 " --> pdb=" O GLY B1615 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B1615 " --> pdb=" O PHE B1603 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1625 through 1628 removed outlier: 4.666A pdb=" N VAL B1852 " --> pdb=" O LEU B1571 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N THR B1829 " --> pdb=" O VAL B1853 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLN B1855 " --> pdb=" O THR B1829 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE B1831 " --> pdb=" O GLN B1855 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2514 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: 10.78 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19267 1.03 - 1.23: 61 1.23 - 1.42: 8204 1.42 - 1.62: 11569 1.62 - 1.81: 114 Bond restraints: 39215 Sorted by residual: bond pdb=" O2B NDP B2602 " pdb=" P2B NDP B2602 " ideal model delta sigma weight residual 1.833 1.613 0.220 3.80e-02 6.93e+02 3.36e+01 bond pdb=" O2B NDP B2601 " pdb=" P2B NDP B2601 " ideal model delta sigma weight residual 1.833 1.615 0.218 3.80e-02 6.93e+02 3.31e+01 bond pdb=" O2B NDP A2601 " pdb=" P2B NDP A2601 " ideal model delta sigma weight residual 1.833 1.616 0.217 3.80e-02 6.93e+02 3.27e+01 bond pdb=" O2B NDP A2602 " pdb=" P2B NDP A2602 " ideal model delta sigma weight residual 1.833 1.617 0.216 3.80e-02 6.93e+02 3.22e+01 bond pdb=" O5D NDP A2602 " pdb=" PN NDP A2602 " ideal model delta sigma weight residual 1.757 1.602 0.155 3.50e-02 8.16e+02 1.97e+01 ... (remaining 39210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 70825 4.84 - 9.68: 86 9.68 - 14.52: 14 14.52 - 19.36: 2 19.36 - 24.19: 4 Bond angle restraints: 70931 Sorted by residual: angle pdb=" PA NDP A2602 " pdb=" O3 NDP A2602 " pdb=" PN NDP A2602 " ideal model delta sigma weight residual 107.74 131.93 -24.19 1.95e+00 2.62e-01 1.53e+02 angle pdb=" PA NDP B2601 " pdb=" O3 NDP B2601 " pdb=" PN NDP B2601 " ideal model delta sigma weight residual 107.74 131.81 -24.07 1.95e+00 2.62e-01 1.52e+02 angle pdb=" PA NDP B2602 " pdb=" O3 NDP B2602 " pdb=" PN NDP B2602 " ideal model delta sigma weight residual 107.74 129.05 -21.31 1.95e+00 2.62e-01 1.19e+02 angle pdb=" PA NDP A2601 " pdb=" O3 NDP A2601 " pdb=" PN NDP A2601 " ideal model delta sigma weight residual 107.74 128.90 -21.16 1.95e+00 2.62e-01 1.17e+02 angle pdb=" C5B NDP B2602 " pdb=" O5B NDP B2602 " pdb=" PA NDP B2602 " ideal model delta sigma weight residual 103.84 120.43 -16.59 1.91e+00 2.73e-01 7.51e+01 ... (remaining 70926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.52: 17796 29.52 - 59.04: 539 59.04 - 88.56: 30 88.56 - 118.09: 3 118.09 - 147.61: 1 Dihedral angle restraints: 18369 sinusoidal: 10109 harmonic: 8260 Sorted by residual: dihedral pdb=" C5B NDP B2602 " pdb=" O5B NDP B2602 " pdb=" PA NDP B2602 " pdb=" O3 NDP B2602 " ideal model delta sinusoidal sigma weight residual 175.04 -37.35 -147.61 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C5B NDP A2602 " pdb=" O5B NDP A2602 " pdb=" PA NDP A2602 " pdb=" O3 NDP A2602 " ideal model delta sinusoidal sigma weight residual 175.04 65.66 109.38 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C5B NDP B2601 " pdb=" O5B NDP B2601 " pdb=" PA NDP B2601 " pdb=" O3 NDP B2601 " ideal model delta sinusoidal sigma weight residual 175.04 72.39 102.65 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 18366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2547 0.050 - 0.100: 369 0.100 - 0.150: 138 0.150 - 0.200: 13 0.200 - 0.250: 14 Chirality restraints: 3081 Sorted by residual: chirality pdb=" C4D NDP A2602 " pdb=" C3D NDP A2602 " pdb=" C5D NDP A2602 " pdb=" O4D NDP A2602 " both_signs ideal model delta sigma weight residual False -2.71 -2.46 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA VAL B2131 " pdb=" N VAL B2131 " pdb=" C VAL B2131 " pdb=" CB VAL B2131 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C4D NDP A2601 " pdb=" C3D NDP A2601 " pdb=" C5D NDP A2601 " pdb=" O4D NDP A2601 " both_signs ideal model delta sigma weight residual False -2.71 -2.47 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3078 not shown) Planarity restraints: 5861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B2138 " 0.070 9.50e-02 1.11e+02 3.47e-01 2.70e+03 pdb=" NE ARG B2138 " 0.257 2.00e-02 2.50e+03 pdb=" CZ ARG B2138 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG B2138 " -0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG B2138 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG B2138 " -0.751 2.00e-02 2.50e+03 pdb="HH12 ARG B2138 " 0.620 2.00e-02 2.50e+03 pdb="HH21 ARG B2138 " 0.070 2.00e-02 2.50e+03 pdb="HH22 ARG B2138 " -0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A2101 " 0.239 2.00e-02 2.50e+03 3.86e-01 2.23e+03 pdb=" CD GLN A2101 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN A2101 " -0.228 2.00e-02 2.50e+03 pdb=" NE2 GLN A2101 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN A2101 " 0.631 2.00e-02 2.50e+03 pdb="HE22 GLN A2101 " -0.620 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2007 " -0.336 9.50e-02 1.11e+02 3.02e-01 1.78e+03 pdb=" NE ARG A2007 " -0.260 2.00e-02 2.50e+03 pdb=" CZ ARG A2007 " -0.067 2.00e-02 2.50e+03 pdb=" NH1 ARG A2007 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A2007 " 0.052 2.00e-02 2.50e+03 pdb="HH11 ARG A2007 " 0.591 2.00e-02 2.50e+03 pdb="HH12 ARG A2007 " -0.496 2.00e-02 2.50e+03 pdb="HH21 ARG A2007 " 0.191 2.00e-02 2.50e+03 pdb="HH22 ARG A2007 " -0.013 2.00e-02 2.50e+03 ... (remaining 5858 not shown) Histogram of nonbonded interaction distances: 1.28 - 1.94: 239 1.94 - 2.61: 44740 2.61 - 3.27: 121271 3.27 - 3.94: 151839 3.94 - 4.60: 238538 Nonbonded interactions: 556627 Sorted by model distance: nonbonded pdb="HH22 ARG B 883 " pdb="HD12 LEU B2157 " model vdw 1.278 2.270 nonbonded pdb=" OE1 GLU B2012 " pdb=" H GLU B2012 " model vdw 1.523 2.450 nonbonded pdb=" OE1 GLU B1521 " pdb=" H GLU B1521 " model vdw 1.586 2.450 nonbonded pdb=" OE1 GLU B1492 " pdb=" H GLU B1492 " model vdw 1.594 2.450 nonbonded pdb=" O ILE B1413 " pdb=" H TRP B1442 " model vdw 1.597 2.450 ... (remaining 556622 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 859 through 1847 or (resid 1848 and (name N or name CA or \ name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or na \ me NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or n \ ame HE2)) or resid 1849 through 2602)) selection = (chain 'B' and (resid 859 through 1097 or (resid 1098 and (name N or name CA or \ name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or na \ me NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or n \ ame HE2)) or resid 1099 through 1148 or resid 1173 through 1289 or (resid 1290 a \ nd (name N or name CA or name C or name O or name CB or name CG or name ND1 or n \ ame CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or \ name HD2 or name HE1 or name HE2)) or resid 1291 through 2112 or resid 2601 thro \ ugh 2602)) } 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: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.500 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.230 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 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 : 0.006 0.220 19902 Z= 0.262 Angle : 0.787 24.195 27087 Z= 0.429 Chirality : 0.044 0.250 3081 Planarity : 0.010 0.299 3494 Dihedral : 10.493 147.607 7231 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.18), residues: 2488 helix: 0.93 (0.18), residues: 897 sheet: -0.71 (0.25), residues: 501 loop : 0.25 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B2138 TYR 0.037 0.001 TYR B 991 PHE 0.007 0.001 PHE A1117 TRP 0.009 0.001 TRP B1807 HIS 0.006 0.001 HIS A2103 Details of bonding type rmsd covalent geometry : bond 0.00639 (19902) covalent geometry : angle 0.78712 (27087) hydrogen bonds : bond 0.19312 ( 834) hydrogen bonds : angle 7.62667 ( 2514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1240 MET cc_start: 0.9005 (mtp) cc_final: 0.8663 (mtp) outliers start: 3 outliers final: 1 residues processed: 69 average time/residue: 0.4411 time to fit residues: 42.2363 Evaluate side-chains 44 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2140 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1193 ASN A1296 GLN A1504 ASN B 978 ASN B1504 ASN B1709 GLN B1983 GLN B2001 ASN B2086 GLN B2188 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.051875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.037225 restraints weight = 261335.769| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.11 r_work: 0.2710 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19902 Z= 0.162 Angle : 0.525 5.312 27087 Z= 0.275 Chirality : 0.040 0.143 3081 Planarity : 0.004 0.043 3494 Dihedral : 7.517 179.704 2744 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.14 % Allowed : 3.75 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.17), residues: 2488 helix: 0.84 (0.17), residues: 935 sheet: -0.84 (0.23), residues: 529 loop : 0.23 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B2138 TYR 0.021 0.001 TYR A 991 PHE 0.009 0.001 PHE A 914 TRP 0.010 0.001 TRP B1592 HIS 0.004 0.001 HIS B2050 Details of bonding type rmsd covalent geometry : bond 0.00362 (19902) covalent geometry : angle 0.52469 (27087) hydrogen bonds : bond 0.04803 ( 834) hydrogen bonds : angle 5.54824 ( 2514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1843 MET cc_start: 0.9389 (tpt) cc_final: 0.9085 (tpt) outliers start: 3 outliers final: 0 residues processed: 50 average time/residue: 0.3829 time to fit residues: 28.5766 Evaluate side-chains 43 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 207 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2028 ASN B1278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.051512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.036932 restraints weight = 261325.113| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.09 r_work: 0.2682 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19902 Z= 0.175 Angle : 0.493 5.278 27087 Z= 0.255 Chirality : 0.039 0.135 3081 Planarity : 0.003 0.036 3494 Dihedral : 7.069 174.421 2742 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.17), residues: 2488 helix: 0.85 (0.17), residues: 940 sheet: -1.01 (0.22), residues: 548 loop : 0.14 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2177 TYR 0.019 0.001 TYR A 991 PHE 0.007 0.001 PHE A1117 TRP 0.009 0.001 TRP B1903 HIS 0.005 0.001 HIS B1553 Details of bonding type rmsd covalent geometry : bond 0.00395 (19902) covalent geometry : angle 0.49313 (27087) hydrogen bonds : bond 0.03958 ( 834) hydrogen bonds : angle 5.07929 ( 2514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1843 MET cc_start: 0.9304 (tpt) cc_final: 0.9019 (tpt) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.3979 time to fit residues: 28.1249 Evaluate side-chains 43 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 172 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.051348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.036853 restraints weight = 260905.118| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.07 r_work: 0.2679 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19902 Z= 0.158 Angle : 0.478 5.232 27087 Z= 0.246 Chirality : 0.039 0.135 3081 Planarity : 0.003 0.037 3494 Dihedral : 6.825 165.021 2742 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.05 % Allowed : 4.42 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.17), residues: 2488 helix: 0.96 (0.17), residues: 940 sheet: -1.04 (0.22), residues: 542 loop : 0.13 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B2177 TYR 0.019 0.001 TYR A 991 PHE 0.008 0.001 PHE B1117 TRP 0.008 0.001 TRP B1903 HIS 0.005 0.001 HIS B1553 Details of bonding type rmsd covalent geometry : bond 0.00360 (19902) covalent geometry : angle 0.47814 (27087) hydrogen bonds : bond 0.03455 ( 834) hydrogen bonds : angle 4.80486 ( 2514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.4124 time to fit residues: 28.5888 Evaluate side-chains 44 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 73 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 225 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.051844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.037300 restraints weight = 258791.844| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.09 r_work: 0.2717 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19902 Z= 0.094 Angle : 0.454 4.721 27087 Z= 0.231 Chirality : 0.039 0.134 3081 Planarity : 0.003 0.039 3494 Dihedral : 6.558 160.873 2742 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.18), residues: 2488 helix: 1.19 (0.18), residues: 940 sheet: -0.94 (0.23), residues: 534 loop : 0.21 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B2177 TYR 0.017 0.001 TYR A 991 PHE 0.009 0.001 PHE B1117 TRP 0.007 0.001 TRP B1592 HIS 0.004 0.001 HIS B1553 Details of bonding type rmsd covalent geometry : bond 0.00218 (19902) covalent geometry : angle 0.45393 (27087) hydrogen bonds : bond 0.03049 ( 834) hydrogen bonds : angle 4.55551 ( 2514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1235 MET cc_start: 0.8036 (ptp) cc_final: 0.6389 (ptp) REVERT: A 1240 MET cc_start: 0.9011 (mtp) cc_final: 0.8257 (tpp) REVERT: A 1577 MET cc_start: 0.9245 (mmm) cc_final: 0.8887 (mmp) REVERT: B 1229 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: B 1235 MET cc_start: 0.8763 (mmp) cc_final: 0.8519 (mmt) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.3900 time to fit residues: 28.3511 Evaluate side-chains 47 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1229 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 116 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.051305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.036755 restraints weight = 261533.191| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.10 r_work: 0.2697 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19902 Z= 0.161 Angle : 0.464 4.639 27087 Z= 0.238 Chirality : 0.039 0.132 3081 Planarity : 0.003 0.038 3494 Dihedral : 6.357 154.868 2742 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.17), residues: 2488 helix: 1.16 (0.18), residues: 945 sheet: -0.99 (0.22), residues: 541 loop : 0.11 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 883 TYR 0.018 0.001 TYR A 991 PHE 0.007 0.001 PHE B1117 TRP 0.007 0.001 TRP B1903 HIS 0.004 0.001 HIS B1553 Details of bonding type rmsd covalent geometry : bond 0.00369 (19902) covalent geometry : angle 0.46427 (27087) hydrogen bonds : bond 0.03145 ( 834) hydrogen bonds : angle 4.53961 ( 2514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1240 MET cc_start: 0.9006 (mtp) cc_final: 0.8256 (tpp) REVERT: A 1409 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 1577 MET cc_start: 0.9275 (mmm) cc_final: 0.8954 (mmp) REVERT: B 1229 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8217 (m-30) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.3867 time to fit residues: 28.0156 Evaluate side-chains 47 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1229 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 164 optimal weight: 5.9990 chunk 96 optimal weight: 0.2980 chunk 161 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.051097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.036596 restraints weight = 259847.695| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.07 r_work: 0.2700 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19902 Z= 0.164 Angle : 0.467 4.602 27087 Z= 0.240 Chirality : 0.039 0.133 3081 Planarity : 0.003 0.039 3494 Dihedral : 6.174 148.129 2742 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.14 % Allowed : 4.71 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.17), residues: 2488 helix: 1.15 (0.18), residues: 945 sheet: -1.01 (0.22), residues: 539 loop : 0.10 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 883 TYR 0.019 0.001 TYR A 991 PHE 0.007 0.001 PHE A1117 TRP 0.006 0.001 TRP B1903 HIS 0.004 0.001 HIS B1553 Details of bonding type rmsd covalent geometry : bond 0.00375 (19902) covalent geometry : angle 0.46667 (27087) hydrogen bonds : bond 0.03140 ( 834) hydrogen bonds : angle 4.51228 ( 2514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.9283 (mmm) cc_final: 0.8967 (mmp) REVERT: B 1229 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8317 (m-30) outliers start: 3 outliers final: 0 residues processed: 49 average time/residue: 0.3908 time to fit residues: 29.6691 Evaluate side-chains 47 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1229 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 131 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.051309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.036836 restraints weight = 259150.455| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.07 r_work: 0.2699 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19902 Z= 0.123 Angle : 0.454 4.666 27087 Z= 0.232 Chirality : 0.039 0.133 3081 Planarity : 0.003 0.039 3494 Dihedral : 6.041 143.042 2742 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.14 % Allowed : 4.71 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.17), residues: 2488 helix: 1.24 (0.18), residues: 945 sheet: -0.97 (0.22), residues: 530 loop : 0.14 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 883 TYR 0.017 0.001 TYR A 991 PHE 0.007 0.001 PHE B1117 TRP 0.006 0.001 TRP B1903 HIS 0.003 0.001 HIS B1553 Details of bonding type rmsd covalent geometry : bond 0.00285 (19902) covalent geometry : angle 0.45369 (27087) hydrogen bonds : bond 0.02969 ( 834) hydrogen bonds : angle 4.41490 ( 2514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1409 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7570 (tm-30) REVERT: A 1577 MET cc_start: 0.9306 (mmm) cc_final: 0.8999 (mmp) REVERT: B 1229 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8265 (m-30) outliers start: 3 outliers final: 0 residues processed: 49 average time/residue: 0.3880 time to fit residues: 29.4062 Evaluate side-chains 47 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1229 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 92 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.051178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.036719 restraints weight = 260525.550| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.06 r_work: 0.2695 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19902 Z= 0.143 Angle : 0.458 4.610 27087 Z= 0.234 Chirality : 0.039 0.132 3081 Planarity : 0.003 0.038 3494 Dihedral : 5.908 137.492 2742 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.17), residues: 2488 helix: 1.23 (0.18), residues: 945 sheet: -1.02 (0.22), residues: 542 loop : 0.14 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 883 TYR 0.018 0.001 TYR A 991 PHE 0.008 0.001 PHE A1117 TRP 0.007 0.001 TRP B1903 HIS 0.004 0.001 HIS B1553 Details of bonding type rmsd covalent geometry : bond 0.00328 (19902) covalent geometry : angle 0.45806 (27087) hydrogen bonds : bond 0.02981 ( 834) hydrogen bonds : angle 4.38794 ( 2514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1409 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 1577 MET cc_start: 0.9330 (mmm) cc_final: 0.9020 (mmp) REVERT: B 1229 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8273 (m-30) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.4320 time to fit residues: 31.7386 Evaluate side-chains 47 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1229 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 163 optimal weight: 7.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 951 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.050701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.036176 restraints weight = 261531.769| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.07 r_work: 0.2675 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19902 Z= 0.218 Angle : 0.489 5.072 27087 Z= 0.252 Chirality : 0.040 0.136 3081 Planarity : 0.003 0.037 3494 Dihedral : 5.892 133.443 2742 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.05 % Allowed : 4.95 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.17), residues: 2488 helix: 1.13 (0.18), residues: 943 sheet: -1.02 (0.22), residues: 543 loop : 0.03 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 883 TYR 0.019 0.001 TYR A 991 PHE 0.008 0.001 PHE A1728 TRP 0.007 0.001 TRP A1903 HIS 0.005 0.001 HIS B1553 Details of bonding type rmsd covalent geometry : bond 0.00499 (19902) covalent geometry : angle 0.48863 (27087) hydrogen bonds : bond 0.03235 ( 834) hydrogen bonds : angle 4.49719 ( 2514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.9325 (mmm) cc_final: 0.8967 (mmp) REVERT: B 1229 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8262 (m-30) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.4229 time to fit residues: 30.0170 Evaluate side-chains 46 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1229 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 152 optimal weight: 7.9990 chunk 239 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 214 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.051131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.036623 restraints weight = 259863.509| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.08 r_work: 0.2689 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19902 Z= 0.119 Angle : 0.459 4.697 27087 Z= 0.234 Chirality : 0.039 0.132 3081 Planarity : 0.003 0.039 3494 Dihedral : 5.824 132.435 2742 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.18), residues: 2488 helix: 1.25 (0.18), residues: 945 sheet: -1.01 (0.22), residues: 532 loop : 0.12 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 883 TYR 0.018 0.001 TYR A 991 PHE 0.008 0.001 PHE A1117 TRP 0.007 0.001 TRP B1807 HIS 0.003 0.001 HIS B1553 Details of bonding type rmsd covalent geometry : bond 0.00277 (19902) covalent geometry : angle 0.45884 (27087) hydrogen bonds : bond 0.02968 ( 834) hydrogen bonds : angle 4.37233 ( 2514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6704.80 seconds wall clock time: 115 minutes 0.06 seconds (6900.06 seconds total)