Starting phenix.real_space_refine on Tue Aug 26 17:13:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vmd_43356/08_2025/8vmd_43356_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vmd_43356/08_2025/8vmd_43356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vmd_43356/08_2025/8vmd_43356_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vmd_43356/08_2025/8vmd_43356_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vmd_43356/08_2025/8vmd_43356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vmd_43356/08_2025/8vmd_43356.map" } resolution = 3.46 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= 0.004 sd= 0.040 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 7 5.49 5 S 80 5.16 5 C 12238 2.51 5 N 3404 2.21 5 O 3615 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 29 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: 38657 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 6.70, per 1000 atoms: 0.17 Number of scatterers: 38657 At special positions: 0 Unit cell: (107.969, 103.693, 205.248, 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 7 15.00 O 3615 8.00 N 3404 7.00 C 12238 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: 2.88 Conformation dependent library (CDL) restraints added in 928.2 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: 110 helices and 23 sheets defined 42.5% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 870 through 876 removed outlier: 4.451A pdb=" N TYR A 874 " --> pdb=" O PRO A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 904 removed outlier: 3.796A pdb=" N TYR A 891 " --> pdb=" O PRO A 887 " (cutoff:3.500A) removed outlier: 4.084A 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 1003 through 1006 Processing helix chain 'A' and resid 1025 through 1041 removed outlier: 3.756A pdb=" N GLY A1040 " --> pdb=" O MET A1036 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1127 through 1131 removed outlier: 4.174A 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 1189 removed outlier: 3.834A pdb=" N GLN A1189 " --> pdb=" O ALA A1185 " (cutoff:3.500A) 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 removed outlier: 3.502A pdb=" N ASN A1234 " --> pdb=" O THR A1230 " (cutoff:3.500A) 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: 3.851A pdb=" N LEU A1259 " --> pdb=" O ARG A1255 " (cutoff:3.500A) removed outlier: 3.733A 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: 3.760A 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: 4.125A 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: 4.149A pdb=" N SER A1427 " --> pdb=" O ARG A1423 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP A1434 " --> pdb=" O GLY A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1461 removed outlier: 3.564A pdb=" N ASN A1458 " --> pdb=" O VAL A1454 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS A1459 " --> pdb=" O GLY A1455 " (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 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 removed outlier: 3.604A pdb=" N LEU A1691 " --> pdb=" O ILE A1687 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 1771 through 1777 Processing helix chain 'A' and resid 1783 through 1787 Processing helix chain 'A' and resid 1796 through 1802 removed outlier: 4.184A pdb=" N PHE A1800 " --> pdb=" O LEU A1796 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A1801 " --> pdb=" O ASP A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1820 removed outlier: 4.348A pdb=" N GLU A1809 " --> pdb=" O ALA A1805 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A1810 " --> pdb=" O ASP A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1846 removed outlier: 3.683A pdb=" N GLY A1846 " --> pdb=" O TYR A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1894 through 1907 removed outlier: 3.506A pdb=" N ARG A1907 " --> pdb=" O TRP A1903 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1935 Processing helix chain 'A' and resid 1948 through 1963 removed outlier: 3.911A 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: 3.817A pdb=" N SER A1997 " --> pdb=" O LYS A1993 " (cutoff:3.500A) removed outlier: 3.741A 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: 3.930A pdb=" N GLU A2051 " --> pdb=" O LYS A2047 " (cutoff:3.500A) Processing helix chain 'A' and resid 2087 through 2101 removed outlier: 4.092A pdb=" N ASN A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 Processing helix chain 'B' and resid 887 through 904 removed outlier: 3.735A pdb=" N TYR B 891 " --> pdb=" O PRO B 887 " (cutoff:3.500A) removed outlier: 3.962A 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: 3.845A 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: 3.565A 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: 3.630A 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: 4.191A pdb=" N LYS B1225 " --> pdb=" O SER B1221 " (cutoff:3.500A) removed outlier: 3.889A 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 1252 through 1254 No H-bonds generated for 'chain 'B' and resid 1252 through 1254' Processing helix chain 'B' and resid 1255 through 1260 Processing helix chain 'B' and resid 1277 through 1288 removed outlier: 3.797A pdb=" N GLU B1281 " --> pdb=" O PRO B1277 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B1282 " --> pdb=" O GLN B1278 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA B1285 " --> pdb=" O GLU B1281 " (cutoff:3.500A) removed outlier: 5.821A 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: 3.744A pdb=" N ILE B1356 " --> pdb=" O PRO B1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing helix chain 'B' and resid 1366 through 1371 Processing helix chain 'B' and resid 1373 through 1384 Processing helix chain 'B' and resid 1423 through 1434 removed outlier: 4.267A pdb=" N SER B1427 " --> pdb=" O ARG B1423 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B1434 " --> pdb=" O GLY B1430 " (cutoff:3.500A) Processing helix chain 'B' and resid 1452 through 1461 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: 3.623A 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 removed outlier: 3.580A pdb=" N ALA B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) Processing helix chain 'B' and resid 1647 through 1661 removed outlier: 4.528A pdb=" N VAL B1651 " --> pdb=" O SER B1647 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1691 removed outlier: 3.722A 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 1759 removed outlier: 3.780A pdb=" N GLN B1754 " --> pdb=" O GLU B1750 " (cutoff:3.500A) Processing helix chain 'B' and resid 1771 through 1777 removed outlier: 3.575A pdb=" N SER B1775 " --> pdb=" O LYS B1771 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1786 Processing helix chain 'B' and resid 1797 through 1802 removed outlier: 3.880A pdb=" N ASN B1801 " --> pdb=" O ASP B1797 " (cutoff:3.500A) removed outlier: 3.720A 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: 3.975A pdb=" N GLU B1809 " --> pdb=" O ALA B1805 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B1810 " --> pdb=" O ASP B1806 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1846 removed outlier: 3.670A pdb=" N GLY B1846 " --> pdb=" O TYR B1842 " (cutoff:3.500A) Processing helix chain 'B' and resid 1894 through 1907 removed outlier: 3.826A 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: 3.968A pdb=" N LEU B1962 " --> pdb=" O GLU B1958 " (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: 3.552A pdb=" N SER B1997 " --> pdb=" O LYS B1993 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B1998 " --> pdb=" O PRO B1994 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B2008 " --> pdb=" O ARG B2004 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS B2010 " --> pdb=" O THR B2006 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2026 Processing helix chain 'B' and resid 2031 through 2051 removed outlier: 3.530A pdb=" N ARG B2043 " --> pdb=" O SER B2039 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B2044 " --> pdb=" O ALA B2040 " (cutoff:3.500A) Processing helix chain 'B' and resid 2087 through 2101 removed outlier: 4.167A pdb=" N ASN B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B2101 " --> pdb=" O LEU B2097 " (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: 3.530A 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 865 removed outlier: 3.663A pdb=" N VAL A 931 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLU A 948 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU A 952 " --> pdb=" O GLU A 948 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS A 957 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASP A 916 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 959 " --> pdb=" O PHE A 914 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE A 914 " --> pdb=" O TYR A 959 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 913 " --> pdb=" O HIS A1056 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N HIS A1056 " --> pdb=" O VAL A 913 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU A 915 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA A1054 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR A1050 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 985 through 986 removed outlier: 6.659A pdb=" N ARG A1019 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA A1011 " --> pdb=" O SER A1017 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER A1017 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A1078 " --> pdb=" O GLY A1018 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N HIS A1098 " --> pdb=" O THR A1050 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 883 through 884 removed outlier: 4.011A pdb=" N THR A 879 " --> pdb=" O ASP A1000 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1413 through 1416 removed outlier: 6.018A pdb=" N ILE A1413 " --> pdb=" O TRP A1442 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A1444 " --> pdb=" O ILE A1413 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A1415 " --> pdb=" O LYS A1444 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N TYR A1506 " --> pdb=" O CYS A1471 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A1473 " --> pdb=" O TYR A1506 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A1513 " --> pdb=" O THR A1120 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL A2105 " --> pdb=" O PHE A1117 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA A2057 " --> pdb=" O LEU A2106 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N SER A2108 " --> pdb=" O ALA A2057 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLN A2059 " --> pdb=" O SER A2108 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP A2060 " --> pdb=" O SER A2020 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A2019 " --> pdb=" O ASN A1970 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N SER A1886 " --> pdb=" O GLY A1966 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL A1968 " --> pdb=" O SER A1886 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A1888 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASN A1970 " --> pdb=" O ILE A1888 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA A1890 " --> pdb=" O ASN A1970 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1123 through 1125 removed outlier: 6.278A pdb=" N GLU A1124 " --> pdb=" O LYS A1393 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU A1402 " --> pdb=" O VAL A1389 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU A1391 " --> pdb=" O LEU A1400 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A1400 " --> pdb=" O LEU A1391 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS A1393 " --> pdb=" O SER A1398 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER A1398 " --> pdb=" O LYS A1393 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A1346 " --> pdb=" O THR A1399 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP A1311 " --> pdb=" O PHE A1341 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU A1343 " --> pdb=" O ASP A1311 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU A1313 " --> pdb=" O LEU A1343 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N HIS A1345 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASP A1311 " --> pdb=" O LYS A1239 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS A1241 " --> pdb=" O ASP A1311 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU A1313 " --> pdb=" O LYS A1241 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A1243 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N MET A1240 " --> pdb=" O SER A1269 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR A1271 " --> pdb=" O MET A1240 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A1242 " --> pdb=" O THR A1271 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR A1273 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLU A1244 " --> pdb=" O THR A1273 " (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 removed outlier: 3.596A pdb=" N LEU A1628 " --> pdb=" O GLN A1562 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1568 through 1571 removed outlier: 4.687A pdb=" N VAL A1852 " --> pdb=" O LEU A1571 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N THR A1829 " --> pdb=" O VAL A1853 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLN A1855 " --> pdb=" O THR A1829 " (cutoff:3.500A) removed outlier: 6.774A 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: 4.046A 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: 6.702A pdb=" N THR A1670 " --> pdb=" O LEU A1743 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N LEU A1745 " --> pdb=" O THR A1670 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A1672 " --> pdb=" O LEU A1745 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP A1742 " --> pdb=" O ARG A1765 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU A1767 " --> pdb=" O ASP A1742 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL A1744 " --> pdb=" O LEU A1767 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR A1790 " --> pdb=" O THR A1762 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A1764 " --> pdb=" O THR A1790 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N HIS A1792 " --> pdb=" O GLY A1764 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE A1766 " --> pdb=" O HIS A1792 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A1789 " --> pdb=" O GLY B1793 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B1789 " --> pdb=" O GLY A1793 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR B1790 " --> pdb=" O THR B1762 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY B1764 " --> pdb=" O THR B1790 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N HIS B1792 " --> pdb=" O GLY B1764 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B1766 " --> pdb=" O HIS B1792 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP B1742 " --> pdb=" O ARG B1765 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B1767 " --> pdb=" O ASP B1742 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL B1744 " --> pdb=" O LEU B1767 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR B1670 " --> pdb=" O ASP B1742 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B1744 " --> pdb=" O THR B1670 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B1672 " --> pdb=" O VAL B1744 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASN B1746 " --> pdb=" O LEU B1672 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N HIS B1674 " --> pdb=" O ASN B1746 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1779 through 1781 Processing sheet with id=AB4, first strand: chain 'A' and resid 2083 through 2084 removed outlier: 4.461A pdb=" N VAL A2110 " --> pdb=" O LEU A2084 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 860 through 865 removed outlier: 3.610A pdb=" N ALA B 860 " --> pdb=" O VAL B 935 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 931 " --> pdb=" O ILE B 864 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE B 944 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER B 955 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 946 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS B 957 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP B 916 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR B 959 " --> pdb=" O PHE B 914 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE B 914 " --> pdb=" O TYR B 959 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL B 913 " --> pdb=" O HIS B1056 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N HIS B1056 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU B 915 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B1054 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N THR B1050 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N HIS B1098 " --> pdb=" O THR B1050 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL B1052 " --> pdb=" O GLY B1096 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLY B1096 " --> pdb=" O VAL B1052 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA B1054 " --> pdb=" O ILE B1094 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE B1094 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HIS B1056 " --> pdb=" O VAL B1092 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B1092 " --> pdb=" O HIS B1056 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER B1017 " --> pdb=" O ALA B1011 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA B1011 " --> pdb=" O SER B1017 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG B1019 " --> pdb=" O LEU B1009 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 860 through 865 removed outlier: 3.610A pdb=" N ALA B 860 " --> pdb=" O VAL B 935 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 931 " --> pdb=" O ILE B 864 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE B 944 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER B 955 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 946 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS B 957 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP B 916 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR B 959 " --> pdb=" O PHE B 914 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE B 914 " --> pdb=" O TYR B 959 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL B 913 " --> pdb=" O HIS B1056 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N HIS B1056 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU B 915 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B1054 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N THR B1050 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N HIS B1098 " --> pdb=" O THR B1050 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL B1052 " --> pdb=" O GLY B1096 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLY B1096 " --> pdb=" O VAL B1052 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA B1054 " --> pdb=" O ILE B1094 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE B1094 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HIS B1056 " --> pdb=" O VAL B1092 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B1092 " --> pdb=" O HIS B1056 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 883 through 884 removed outlier: 3.947A pdb=" N THR B 879 " --> pdb=" O ASP B1000 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1413 through 1416 removed outlier: 5.876A pdb=" N ILE B1413 " --> pdb=" O TRP B1442 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LYS B1444 " --> pdb=" O ILE B1413 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B1415 " --> pdb=" O LYS B1444 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B1474 " --> pdb=" O ALA B1445 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N TYR B1506 " --> pdb=" O CYS B1471 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B1473 " --> pdb=" O TYR B1506 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B1113 " --> pdb=" O PHE B2109 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B2109 " --> pdb=" O ILE B1113 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1115 " --> pdb=" O SER B2107 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL B2105 " --> pdb=" O PHE B1117 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B2057 " --> pdb=" O LEU B2106 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N SER B2108 " --> pdb=" O ALA B2057 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN B2059 " --> pdb=" O SER B2108 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N VAL B2110 " --> pdb=" O GLN B2059 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY B1966 " --> pdb=" O TYR B2015 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N VAL B2017 " --> pdb=" O GLY B1966 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B1968 " --> pdb=" O VAL B2017 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N PHE B2019 " --> pdb=" O VAL B1968 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASN B1970 " --> pdb=" O PHE B2019 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N SER B2021 " --> pdb=" O ASN B1970 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER B1886 " --> pdb=" O GLY B1966 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL B1968 " --> pdb=" O SER B1886 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B1888 " --> pdb=" O VAL B1968 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASN B1970 " --> pdb=" O ILE B1888 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B1890 " --> pdb=" O ASN B1970 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR B1887 " --> pdb=" O VAL B1913 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR B1915 " --> pdb=" O TYR B1887 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE B1889 " --> pdb=" O THR B1915 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B1912 " --> pdb=" O GLN B1940 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N SER B1942 " --> pdb=" O LEU B1912 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B1914 " --> pdb=" O SER B1942 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1413 through 1416 removed outlier: 5.876A pdb=" N ILE B1413 " --> pdb=" O TRP B1442 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LYS B1444 " --> pdb=" O ILE B1413 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B1415 " --> pdb=" O LYS B1444 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B1474 " --> pdb=" O ALA B1445 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N TYR B1506 " --> pdb=" O CYS B1471 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B1473 " --> pdb=" O TYR B1506 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B1113 " --> pdb=" O PHE B2109 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B2109 " --> pdb=" O ILE B1113 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1115 " --> pdb=" O SER B2107 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL B2105 " --> pdb=" O PHE B1117 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B2110 " --> pdb=" O LEU B2084 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1123 through 1125 removed outlier: 6.603A pdb=" N LEU B1402 " --> pdb=" O VAL B1389 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU B1391 " --> pdb=" O LEU B1400 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B1400 " --> pdb=" O LEU B1391 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP B1311 " --> pdb=" O PHE B1341 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU B1343 " --> pdb=" O ASP B1311 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU B1313 " --> pdb=" O LEU B1343 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N HIS B1345 " --> pdb=" O LEU B1313 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N ALA B1310 " --> pdb=" O LYS B1239 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS B1241 " --> pdb=" O ALA B1310 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ALA B1293 " --> pdb=" O LEU B1268 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR B1270 " --> pdb=" O ALA B1293 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N GLY B1295 " --> pdb=" O TYR B1270 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA B1272 " --> pdb=" O GLY B1295 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1525 through 1528 Processing sheet with id=AC3, first strand: chain 'B' and resid 1531 through 1535 Processing sheet with id=AC4, first strand: chain 'B' and resid 1626 through 1628 removed outlier: 6.573A pdb=" N SER B1604 " --> pdb=" O TYR B1567 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA B1569 " --> pdb=" O GLU B1602 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLU B1602 " --> pdb=" O ALA B1569 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B1603 " --> pdb=" O GLY B1615 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B1615 " --> pdb=" O PHE B1603 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1626 through 1628 removed outlier: 4.818A pdb=" N VAL B1852 " --> pdb=" O LEU B1571 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N THR B1829 " --> pdb=" O VAL B1853 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLN B1855 " --> pdb=" O THR B1829 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE B1831 " --> pdb=" O GLN B1855 " (cutoff:3.500A) 872 hydrogen bonds defined for protein. 2400 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: 9.97 Time building geometry restraints manager: 3.86 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: 68 1.23 - 1.42: 8137 1.42 - 1.62: 11488 1.62 - 1.81: 113 Bond restraints: 39073 Sorted by residual: bond pdb=" O2B NAP A2601 " pdb=" P2B NAP A2601 " ideal model delta sigma weight residual 1.736 1.609 0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" O2B NAP B2601 " pdb=" P2B NAP B2601 " ideal model delta sigma weight residual 1.736 1.615 0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" N PRO A1559 " pdb=" CD PRO A1559 " ideal model delta sigma weight residual 1.473 1.405 0.068 1.40e-02 5.10e+03 2.37e+01 bond pdb=" CE1 HIS A1553 " pdb=" NE2 HIS A1553 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.61e+01 bond pdb=" CE1 HIS A1792 " pdb=" NE2 HIS A1792 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.51e+01 ... (remaining 39068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 70222 2.55 - 5.10: 441 5.10 - 7.65: 38 7.65 - 10.20: 11 10.20 - 12.75: 3 Bond angle restraints: 70715 Sorted by residual: angle pdb=" N VAL B1496 " pdb=" CA VAL B1496 " pdb=" C VAL B1496 " ideal model delta sigma weight residual 111.00 102.58 8.42 1.09e+00 8.42e-01 5.97e+01 angle pdb=" N LEU A2002 " pdb=" CA LEU A2002 " pdb=" C LEU A2002 " ideal model delta sigma weight residual 111.36 103.27 8.09 1.09e+00 8.42e-01 5.51e+01 angle pdb=" N LYS A1787 " pdb=" CA LYS A1787 " pdb=" C LYS A1787 " ideal model delta sigma weight residual 110.28 100.17 10.11 1.48e+00 4.57e-01 4.67e+01 angle pdb=" N LEU B2152 " pdb=" CA LEU B2152 " pdb=" C LEU B2152 " ideal model delta sigma weight residual 111.28 103.83 7.45 1.09e+00 8.42e-01 4.67e+01 angle pdb=" N LEU A1900 " pdb=" CA LEU A1900 " pdb=" C LEU A1900 " ideal model delta sigma weight residual 111.36 104.12 7.24 1.09e+00 8.42e-01 4.41e+01 ... (remaining 70710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 17170 17.81 - 35.61: 797 35.61 - 53.42: 316 53.42 - 71.23: 101 71.23 - 89.03: 19 Dihedral angle restraints: 18403 sinusoidal: 10143 harmonic: 8260 Sorted by residual: dihedral pdb=" N GLU A1802 " pdb=" C GLU A1802 " pdb=" CA GLU A1802 " pdb=" CB GLU A1802 " ideal model delta harmonic sigma weight residual 122.80 133.38 -10.58 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" CA VAL B1648 " pdb=" C VAL B1648 " pdb=" N PRO B1649 " pdb=" CA PRO B1649 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" N CYS A1558 " pdb=" C CYS A1558 " pdb=" CA CYS A1558 " pdb=" CB CYS A1558 " ideal model delta harmonic sigma weight residual 122.80 131.92 -9.12 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 18400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2771 0.079 - 0.157: 265 0.157 - 0.236: 16 0.236 - 0.315: 3 0.315 - 0.393: 2 Chirality restraints: 3057 Sorted by residual: chirality pdb=" CA GLU A1802 " pdb=" N GLU A1802 " pdb=" C GLU A1802 " pdb=" CB GLU A1802 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA CYS A1558 " pdb=" N CYS A1558 " pdb=" C CYS A1558 " pdb=" CB CYS A1558 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA LEU B2152 " pdb=" N LEU B2152 " pdb=" C LEU B2152 " pdb=" CB LEU B2152 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 3054 not shown) Planarity restraints: 5843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1788 " 0.156 2.00e-02 2.50e+03 4.26e-01 2.72e+03 pdb=" CG ASN A1788 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A1788 " -0.153 2.00e-02 2.50e+03 pdb=" ND2 ASN A1788 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A1788 " 0.726 2.00e-02 2.50e+03 pdb="HD22 ASN A1788 " -0.718 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B1498 " 0.229 2.00e-02 2.50e+03 3.95e-01 2.34e+03 pdb=" CD GLN B1498 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN B1498 " -0.223 2.00e-02 2.50e+03 pdb=" NE2 GLN B1498 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B1498 " 0.650 2.00e-02 2.50e+03 pdb="HE22 GLN B1498 " -0.641 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A1204 " 0.251 2.00e-02 2.50e+03 3.64e-01 1.99e+03 pdb=" CD GLN A1204 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A1204 " -0.241 2.00e-02 2.50e+03 pdb=" NE2 GLN A1204 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A1204 " -0.574 2.00e-02 2.50e+03 pdb="HE22 GLN A1204 " 0.587 2.00e-02 2.50e+03 ... (remaining 5840 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 545 2.07 - 2.71: 64208 2.71 - 3.34: 113394 3.34 - 3.97: 142159 3.97 - 4.60: 224217 Nonbonded interactions: 544523 Sorted by model distance: nonbonded pdb=" O ASN A1788 " pdb="HG23 VAL A1789 " model vdw 1.443 2.620 nonbonded pdb=" OD1 ASN A1234 " pdb=" H VAL A1502 " model vdw 1.565 2.450 nonbonded pdb=" OD2 ASP A1418 " pdb=" H ILE A1446 " model vdw 1.587 2.450 nonbonded pdb=" OE1 GLU B1492 " pdb=" H GLU B1492 " model vdw 1.590 2.450 nonbonded pdb=" O SER A1886 " pdb=" H GLY A1966 " model vdw 1.602 2.450 ... (remaining 544518 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 2601)) 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)) } 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: 2.860 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: 0.180 Extract box with map and model: 0.420 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 33.070 Find NCS groups from input model: 0.620 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: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 19760 Z= 0.253 Angle : 0.678 10.115 26871 Z= 0.430 Chirality : 0.045 0.393 3057 Planarity : 0.006 0.214 3476 Dihedral : 10.468 89.035 7265 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.10 % Allowed : 2.93 % Favored : 96.97 % Cbeta Deviations : 0.04 % 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: 1.13 (0.18), residues: 917 sheet: -0.64 (0.24), residues: 515 loop : 0.00 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1538 TYR 0.015 0.001 TYR A 991 PHE 0.028 0.001 PHE A1896 TRP 0.007 0.001 TRP B1903 HIS 0.005 0.001 HIS A1792 Details of bonding type rmsd covalent geometry : bond 0.00444 (19760) covalent geometry : angle 0.67763 (26871) hydrogen bonds : bond 0.20395 ( 813) hydrogen bonds : angle 7.22413 ( 2400) *********************** 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 54 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1843 MET cc_start: 0.8780 (mmm) cc_final: 0.8336 (tpt) outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.2965 time to fit residues: 25.6595 Evaluate side-chains 39 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1193 ASN A1296 GLN A1316 ASN A1351 HIS A1504 ASN A1530 HIS A1553 HIS A1763 HIS A2100 ASN B1110 GLN B1278 GLN B1369 GLN B1504 ASN B1709 GLN B1763 HIS B1845 GLN B1983 GLN B2086 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.051908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.036116 restraints weight = 346778.199| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.51 r_work: 0.2874 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19760 Z= 0.145 Angle : 0.520 5.031 26871 Z= 0.274 Chirality : 0.039 0.143 3057 Planarity : 0.004 0.040 3476 Dihedral : 6.798 83.074 2776 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.34 % Allowed : 3.65 % 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: 0.32 (0.18), residues: 2488 helix: 1.13 (0.18), residues: 936 sheet: -0.69 (0.23), residues: 552 loop : 0.05 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 901 TYR 0.016 0.001 TYR A 991 PHE 0.009 0.001 PHE A1785 TRP 0.010 0.001 TRP B1903 HIS 0.005 0.001 HIS A1093 Details of bonding type rmsd covalent geometry : bond 0.00307 (19760) covalent geometry : angle 0.51999 (26871) hydrogen bonds : bond 0.04857 ( 813) hydrogen bonds : angle 5.51304 ( 2400) *********************** 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 45 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1843 MET cc_start: 0.9371 (mmm) cc_final: 0.8883 (tpt) outliers start: 7 outliers final: 4 residues processed: 42 average time/residue: 0.2455 time to fit residues: 18.0101 Evaluate side-chains 39 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain B residue 1504 ASN Chi-restraints excluded: chain B residue 2041 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1107 GLN B1110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.050715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.035616 restraints weight = 347248.323| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.31 r_work: 0.2841 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19760 Z= 0.169 Angle : 0.498 5.467 26871 Z= 0.260 Chirality : 0.039 0.136 3057 Planarity : 0.003 0.036 3476 Dihedral : 6.392 83.783 2776 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.29 % Allowed : 3.79 % Favored : 95.92 % 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: 1.23 (0.18), residues: 938 sheet: -0.82 (0.23), residues: 536 loop : 0.03 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2007 TYR 0.015 0.001 TYR A 991 PHE 0.014 0.001 PHE A1573 TRP 0.007 0.001 TRP B1903 HIS 0.006 0.001 HIS A1093 Details of bonding type rmsd covalent geometry : bond 0.00366 (19760) covalent geometry : angle 0.49779 (26871) hydrogen bonds : bond 0.04135 ( 813) hydrogen bonds : angle 5.07856 ( 2400) *********************** 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 42 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1332 MET cc_start: 0.9089 (mtt) cc_final: 0.8799 (mtt) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 0.2688 time to fit residues: 17.9654 Evaluate side-chains 41 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain A residue 2104 MET Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain B residue 1504 ASN Chi-restraints excluded: chain B residue 2041 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 243 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.051132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035310 restraints weight = 349857.201| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 4.48 r_work: 0.2854 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19760 Z= 0.152 Angle : 0.474 4.548 26871 Z= 0.244 Chirality : 0.039 0.140 3057 Planarity : 0.003 0.040 3476 Dihedral : 6.066 82.972 2776 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.38 % Allowed : 3.70 % Favored : 95.92 % 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: 0.39 (0.18), residues: 2488 helix: 1.35 (0.18), residues: 942 sheet: -0.93 (0.23), residues: 523 loop : 0.06 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 995 TYR 0.015 0.001 TYR A 991 PHE 0.010 0.001 PHE A1573 TRP 0.006 0.001 TRP B1903 HIS 0.005 0.001 HIS A1093 Details of bonding type rmsd covalent geometry : bond 0.00329 (19760) covalent geometry : angle 0.47424 (26871) hydrogen bonds : bond 0.03396 ( 813) hydrogen bonds : angle 4.78803 ( 2400) *********************** 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 44 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1332 MET cc_start: 0.9156 (mtt) cc_final: 0.8827 (mtt) REVERT: A 1503 MET cc_start: 0.8659 (mmm) cc_final: 0.8169 (mmm) outliers start: 8 outliers final: 3 residues processed: 40 average time/residue: 0.2513 time to fit residues: 17.7107 Evaluate side-chains 38 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain A residue 2104 MET Chi-restraints excluded: chain B residue 2041 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 138 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.050132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.035238 restraints weight = 344314.450| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.25 r_work: 0.2852 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19760 Z= 0.146 Angle : 0.466 6.047 26871 Z= 0.238 Chirality : 0.039 0.135 3057 Planarity : 0.003 0.040 3476 Dihedral : 5.899 82.122 2776 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.38 % Allowed : 3.84 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.18), residues: 2488 helix: 1.45 (0.18), residues: 943 sheet: -0.95 (0.23), residues: 518 loop : 0.06 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1574 TYR 0.014 0.001 TYR A 991 PHE 0.013 0.001 PHE B1573 TRP 0.005 0.001 TRP B1903 HIS 0.004 0.001 HIS B2133 Details of bonding type rmsd covalent geometry : bond 0.00319 (19760) covalent geometry : angle 0.46624 (26871) hydrogen bonds : bond 0.03207 ( 813) hydrogen bonds : angle 4.61490 ( 2400) *********************** 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 44 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1332 MET cc_start: 0.9177 (mtt) cc_final: 0.8827 (mtt) REVERT: A 1503 MET cc_start: 0.8622 (mmm) cc_final: 0.8150 (mmm) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.2376 time to fit residues: 16.5353 Evaluate side-chains 40 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain A residue 2104 MET Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain B residue 1504 ASN Chi-restraints excluded: chain B residue 2041 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 162 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1351 HIS B1504 ASN B2100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.049369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.034371 restraints weight = 350197.599| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 4.26 r_work: 0.2827 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 19760 Z= 0.235 Angle : 0.513 4.561 26871 Z= 0.266 Chirality : 0.039 0.143 3057 Planarity : 0.003 0.040 3476 Dihedral : 5.681 77.978 2776 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.34 % Allowed : 3.99 % Favored : 95.68 % 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: 0.24 (0.18), residues: 2488 helix: 1.27 (0.18), residues: 942 sheet: -1.04 (0.23), residues: 516 loop : -0.07 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B2180 TYR 0.014 0.001 TYR A 991 PHE 0.009 0.001 PHE A1896 TRP 0.008 0.001 TRP B1592 HIS 0.005 0.001 HIS B2133 Details of bonding type rmsd covalent geometry : bond 0.00512 (19760) covalent geometry : angle 0.51334 (26871) hydrogen bonds : bond 0.03408 ( 813) hydrogen bonds : angle 4.78789 ( 2400) *********************** 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 43 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1332 MET cc_start: 0.9196 (mtt) cc_final: 0.8831 (mtt) REVERT: A 1503 MET cc_start: 0.8585 (mmm) cc_final: 0.8121 (mmm) REVERT: A 1628 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9191 (pp) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.2974 time to fit residues: 20.7446 Evaluate side-chains 40 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1628 LEU Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain A residue 2104 MET Chi-restraints excluded: chain B residue 1504 ASN Chi-restraints excluded: chain B residue 2041 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.049747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.034684 restraints weight = 346608.518| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.32 r_work: 0.2843 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19760 Z= 0.111 Angle : 0.455 4.725 26871 Z= 0.233 Chirality : 0.039 0.130 3057 Planarity : 0.003 0.041 3476 Dihedral : 5.224 79.373 2776 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.29 % Allowed : 4.13 % 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: 0.44 (0.18), residues: 2488 helix: 1.46 (0.18), residues: 945 sheet: -1.02 (0.23), residues: 513 loop : 0.04 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B2180 TYR 0.014 0.001 TYR A 991 PHE 0.009 0.001 PHE A1117 TRP 0.005 0.001 TRP B1592 HIS 0.004 0.001 HIS B2133 Details of bonding type rmsd covalent geometry : bond 0.00244 (19760) covalent geometry : angle 0.45527 (26871) hydrogen bonds : bond 0.03098 ( 813) hydrogen bonds : angle 4.53329 ( 2400) *********************** 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 41 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1332 MET cc_start: 0.9212 (mtt) cc_final: 0.8847 (mtt) REVERT: A 1503 MET cc_start: 0.8614 (mmm) cc_final: 0.8144 (mmm) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.2817 time to fit residues: 18.1865 Evaluate side-chains 39 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain A residue 2104 MET Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain B residue 2041 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 215 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.049513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.034564 restraints weight = 347921.567| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 4.27 r_work: 0.2843 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19760 Z= 0.163 Angle : 0.467 4.506 26871 Z= 0.239 Chirality : 0.038 0.136 3057 Planarity : 0.003 0.041 3476 Dihedral : 5.130 77.197 2776 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.24 % Allowed : 4.18 % 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: 0.39 (0.18), residues: 2488 helix: 1.45 (0.18), residues: 945 sheet: -1.05 (0.23), residues: 518 loop : 0.01 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B2180 TYR 0.014 0.001 TYR A 991 PHE 0.009 0.001 PHE A1117 TRP 0.006 0.001 TRP B1592 HIS 0.005 0.001 HIS B2133 Details of bonding type rmsd covalent geometry : bond 0.00354 (19760) covalent geometry : angle 0.46679 (26871) hydrogen bonds : bond 0.03096 ( 813) hydrogen bonds : angle 4.55079 ( 2400) *********************** 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 40 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1332 MET cc_start: 0.9159 (mtt) cc_final: 0.8781 (mtt) REVERT: A 1503 MET cc_start: 0.8574 (mmm) cc_final: 0.8115 (mmm) outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.2927 time to fit residues: 19.0077 Evaluate side-chains 39 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain A residue 2104 MET Chi-restraints excluded: chain B residue 1671 LEU Chi-restraints excluded: chain B residue 2041 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 176 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 225 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.049801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.034852 restraints weight = 348273.840| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.23 r_work: 0.2851 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19760 Z= 0.089 Angle : 0.439 4.882 26871 Z= 0.222 Chirality : 0.038 0.128 3057 Planarity : 0.003 0.041 3476 Dihedral : 4.971 78.642 2776 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.19 % Allowed : 4.27 % 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: 0.57 (0.18), residues: 2488 helix: 1.62 (0.18), residues: 945 sheet: -0.98 (0.23), residues: 517 loop : 0.10 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B2180 TYR 0.014 0.001 TYR A 991 PHE 0.010 0.001 PHE A1117 TRP 0.004 0.001 TRP B2060 HIS 0.005 0.001 HIS B2133 Details of bonding type rmsd covalent geometry : bond 0.00199 (19760) covalent geometry : angle 0.43945 (26871) hydrogen bonds : bond 0.02847 ( 813) hydrogen bonds : angle 4.35523 ( 2400) *********************** 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 39 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1332 MET cc_start: 0.9147 (mtt) cc_final: 0.8756 (mtt) REVERT: A 1503 MET cc_start: 0.8592 (mmm) cc_final: 0.8118 (mmm) outliers start: 4 outliers final: 4 residues processed: 36 average time/residue: 0.3052 time to fit residues: 19.4180 Evaluate side-chains 39 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain A residue 2104 MET Chi-restraints excluded: chain B residue 1671 LEU Chi-restraints excluded: chain B residue 2041 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 152 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1778 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.049392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.034496 restraints weight = 349358.213| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.22 r_work: 0.2831 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19760 Z= 0.181 Angle : 0.470 4.534 26871 Z= 0.241 Chirality : 0.038 0.141 3057 Planarity : 0.003 0.041 3476 Dihedral : 4.963 75.998 2776 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.19 % Allowed : 4.42 % Favored : 95.39 % 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: 0.42 (0.18), residues: 2488 helix: 1.50 (0.18), residues: 946 sheet: -1.06 (0.23), residues: 518 loop : 0.01 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B2180 TYR 0.013 0.001 TYR A 991 PHE 0.009 0.001 PHE A1728 TRP 0.006 0.001 TRP B1592 HIS 0.005 0.001 HIS B2133 Details of bonding type rmsd covalent geometry : bond 0.00394 (19760) covalent geometry : angle 0.47033 (26871) hydrogen bonds : bond 0.03034 ( 813) hydrogen bonds : angle 4.49274 ( 2400) ********************** 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 39 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1332 MET cc_start: 0.9162 (mtt) cc_final: 0.8783 (mtt) REVERT: A 1503 MET cc_start: 0.8578 (mmm) cc_final: 0.8122 (mmm) outliers start: 4 outliers final: 4 residues processed: 36 average time/residue: 0.3090 time to fit residues: 19.6280 Evaluate side-chains 39 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain A residue 2104 MET Chi-restraints excluded: chain B residue 1671 LEU Chi-restraints excluded: chain B residue 2041 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 118 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 247 optimal weight: 0.3980 chunk 179 optimal weight: 0.1980 chunk 244 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.049837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.034795 restraints weight = 346973.364| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.28 r_work: 0.2853 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19760 Z= 0.081 Angle : 0.435 4.631 26871 Z= 0.219 Chirality : 0.038 0.128 3057 Planarity : 0.003 0.040 3476 Dihedral : 4.805 78.139 2776 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.19 % Allowed : 4.47 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.18), residues: 2488 helix: 1.69 (0.18), residues: 945 sheet: -0.98 (0.23), residues: 517 loop : 0.13 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B2049 TYR 0.013 0.001 TYR A 991 PHE 0.011 0.001 PHE A1117 TRP 0.005 0.001 TRP B2060 HIS 0.005 0.001 HIS B2133 Details of bonding type rmsd covalent geometry : bond 0.00182 (19760) covalent geometry : angle 0.43453 (26871) hydrogen bonds : bond 0.02742 ( 813) hydrogen bonds : angle 4.25572 ( 2400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6611.04 seconds wall clock time: 113 minutes 16.64 seconds (6796.64 seconds total)