Starting phenix.real_space_refine on Tue Aug 26 18:15:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vf7_43187/08_2025/8vf7_43187_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vf7_43187/08_2025/8vf7_43187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vf7_43187/08_2025/8vf7_43187_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vf7_43187/08_2025/8vf7_43187_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vf7_43187/08_2025/8vf7_43187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vf7_43187/08_2025/8vf7_43187.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 S 80 5.16 5 C 12302 2.51 5 N 3422 2.21 5 O 3657 1.98 5 H 19312 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 38786 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1216, 18703 Classifications: {'peptide': 1216} Link IDs: {'PTRANS': 66, 'TRANS': 1149} Chain breaks: 2 Chain: "B" Number of atoms: 19891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1289, 19891 Classifications: {'peptide': 1289} Link IDs: {'PTRANS': 66, 'TRANS': 1222} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NDP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NDP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.69, per 1000 atoms: 0.17 Number of scatterers: 38786 At special positions: 0 Unit cell: (109.038, 119.728, 203.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 13 15.00 O 3657 8.00 N 3422 7.00 C 12302 6.00 H 19312 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: 2.91 Conformation dependent library (CDL) restraints added in 961.3 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: 107 helices and 22 sheets defined 42.0% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 870 through 877 removed outlier: 4.290A pdb=" N TYR A 874 " --> pdb=" O PRO A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 904 removed outlier: 3.750A pdb=" N TYR A 891 " --> pdb=" O PRO A 887 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 892 " --> pdb=" O ALA A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 910 removed outlier: 3.709A pdb=" N LEU A 910 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 970 Processing helix chain 'A' and resid 987 through 998 Processing helix chain 'A' and resid 1025 through 1040 removed outlier: 4.049A pdb=" N GLY A1040 " --> pdb=" O MET A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1126 through 1130 removed outlier: 4.491A pdb=" N GLU A1130 " --> pdb=" O CYS A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1145 removed outlier: 3.677A pdb=" N GLN A1135 " --> pdb=" O ARG A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1189 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 1221 through 1233 removed outlier: 4.214A pdb=" N LYS A1225 " --> pdb=" O SER A1221 " (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 Processing helix chain 'A' and resid 1283 through 1290 removed outlier: 3.550A pdb=" N LEU A1287 " --> pdb=" O ALA A1283 " (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 1369 Processing helix chain 'A' and resid 1373 through 1384 Processing helix chain 'A' and resid 1419 through 1422 removed outlier: 3.791A 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 1432 removed outlier: 3.764A pdb=" N SER A1427 " --> pdb=" O ARG A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1461 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 1691 removed outlier: 3.627A 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 1726 through 1736 removed outlier: 4.287A pdb=" N GLN A1730 " --> pdb=" O THR A1726 " (cutoff:3.500A) 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 1788 Processing helix chain 'A' and resid 1797 through 1802 removed outlier: 4.045A pdb=" N ASN A1801 " --> pdb=" O ASP A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1820 removed outlier: 3.781A pdb=" N ARG A1808 " --> pdb=" O SER A1804 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU A1809 " --> pdb=" O ALA A1805 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A1810 " --> pdb=" O ASP A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1832 through 1834 No H-bonds generated for 'chain 'A' and resid 1832 through 1834' Processing helix chain 'A' and resid 1835 through 1845 Processing helix chain 'A' and resid 1894 through 1907 Processing helix chain 'A' and resid 1922 through 1935 Processing helix chain 'A' and resid 1948 through 1963 removed outlier: 3.913A 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: 3.686A pdb=" N SER A1997 " --> pdb=" O LYS A1993 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A1998 " --> pdb=" O PRO A1994 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A2008 " --> pdb=" O ARG A2004 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2027 Processing helix chain 'A' and resid 2031 through 2051 Processing helix chain 'A' and resid 2087 through 2099 removed outlier: 3.541A pdb=" N LEU A2097 " --> pdb=" O GLU A2093 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 Processing helix chain 'B' and resid 887 through 904 removed outlier: 3.592A pdb=" N TYR B 891 " --> pdb=" O PRO B 887 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 892 " --> pdb=" O ALA B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 910 removed outlier: 3.842A pdb=" N LEU B 910 " --> pdb=" O VAL B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 970 Processing helix chain 'B' and resid 986 through 998 removed outlier: 3.536A pdb=" N TYR B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1040 removed outlier: 3.771A 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 1150 removed outlier: 3.551A 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 removed outlier: 4.171A pdb=" N LEU B1194 " --> pdb=" O ASN B1191 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1191 through 1194' Processing helix chain 'B' and resid 1195 through 1203 Processing helix chain 'B' and resid 1208 through 1211 Processing helix chain 'B' and resid 1212 through 1221 removed outlier: 5.783A pdb=" N LEU B1218 " --> pdb=" O LEU B1214 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU B1219 " --> pdb=" O LEU B1215 " (cutoff:3.500A) Processing helix chain 'B' and resid 1221 through 1234 removed outlier: 4.265A pdb=" N LYS B1225 " --> pdb=" O SER B1221 " (cutoff:3.500A) removed outlier: 3.511A 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 1276 through 1283 removed outlier: 4.126A pdb=" N LEU B1280 " --> pdb=" O HIS B1276 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1288 removed outlier: 3.569A pdb=" N LEU B1287 " --> pdb=" O ALA B1283 " (cutoff:3.500A) Processing helix chain 'B' and resid 1324 through 1335 Processing helix chain 'B' and resid 1351 through 1361 Processing helix chain 'B' and resid 1366 through 1371 removed outlier: 3.515A pdb=" N ILE B1371 " --> pdb=" O TYR B1367 " (cutoff:3.500A) Processing helix chain 'B' and resid 1373 through 1384 Processing helix chain 'B' and resid 1423 through 1435 removed outlier: 3.853A pdb=" N SER B1427 " --> pdb=" O ARG B1423 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU B1435 " --> pdb=" O ILE B1431 " (cutoff:3.500A) Processing helix chain 'B' and resid 1452 through 1461 removed outlier: 3.830A pdb=" N LEU B1456 " --> pdb=" O GLY B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1465 through 1467 No H-bonds generated for 'chain 'B' and resid 1465 through 1467' Processing helix chain 'B' and resid 1490 through 1500 removed outlier: 3.654A pdb=" N GLY B1499 " --> pdb=" O LYS B1495 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B1500 " --> pdb=" O VAL B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1550 through 1553 Processing helix chain 'B' and resid 1572 through 1581 Processing helix chain 'B' and resid 1629 through 1631 No H-bonds generated for 'chain 'B' and resid 1629 through 1631' Processing helix chain 'B' and resid 1641 through 1646 Processing helix chain 'B' and resid 1648 through 1660 Processing helix chain 'B' and resid 1678 through 1691 removed outlier: 3.702A 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: 3.653A pdb=" N GLN B1754 " --> pdb=" O GLU B1750 " (cutoff:3.500A) Processing helix chain 'B' and resid 1771 through 1777 Processing helix chain 'B' and resid 1783 through 1787 Processing helix chain 'B' and resid 1795 through 1799 Processing helix chain 'B' and resid 1804 through 1821 removed outlier: 3.810A pdb=" N GLU B1809 " --> pdb=" O ALA B1805 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B1810 " --> pdb=" O ASP B1806 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1846 removed outlier: 3.753A pdb=" N GLY B1846 " --> pdb=" O TYR B1842 " (cutoff:3.500A) Processing helix chain 'B' and resid 1894 through 1906 Processing helix chain 'B' and resid 1922 through 1935 Processing helix chain 'B' and resid 1948 through 1963 removed outlier: 3.595A 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: 3.688A pdb=" N SER B1997 " --> pdb=" O LYS B1993 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B1998 " --> pdb=" O PRO B1994 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B2008 " --> pdb=" O ARG B2004 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2027 Processing helix chain 'B' and resid 2031 through 2051 removed outlier: 3.615A pdb=" N GLU B2051 " --> pdb=" O LYS B2047 " (cutoff:3.500A) Processing helix chain 'B' and resid 2087 through 2100 removed outlier: 4.071A pdb=" N ASN B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) Processing helix chain 'B' and resid 2126 through 2136 Processing helix chain 'B' and resid 2148 through 2153 Processing helix chain 'B' and resid 2155 through 2171 Processing helix chain 'B' and resid 2175 through 2182 Processing helix chain 'B' and resid 2183 through 2193 Processing sheet with id=AA1, first strand: chain 'A' and resid 860 through 864 removed outlier: 3.575A pdb=" N VAL A 931 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 956 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLU A 948 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 952 " --> pdb=" O GLU A 948 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL A 953 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU A 919 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 955 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 917 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A1053 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 918 " --> pdb=" O ARG A1051 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A1051 " --> pdb=" O VAL A 918 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS A1098 " --> pdb=" O THR A1050 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL A1052 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY A1096 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA A1054 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE A1094 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS A1056 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A1092 " --> pdb=" O HIS A1056 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLN A1074 " --> pdb=" O TRP A1022 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER A1017 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A1011 " --> pdb=" O SER A1017 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG A1019 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 860 through 864 removed outlier: 3.575A pdb=" N VAL A 931 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 956 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLU A 948 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 952 " --> pdb=" O GLU A 948 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL A 953 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU A 919 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 955 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 917 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A1053 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 918 " --> pdb=" O ARG A1051 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A1051 " --> pdb=" O VAL A 918 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS A1098 " --> pdb=" O THR A1050 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL A1052 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY A1096 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA A1054 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE A1094 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS A1056 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A1092 " --> pdb=" O HIS A1056 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 879 through 880 Processing sheet with id=AA4, first strand: chain 'A' and resid 1413 through 1416 removed outlier: 6.462A pdb=" N ILE A1413 " --> pdb=" O TRP A1442 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LYS A1444 " --> pdb=" O ILE A1413 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A1415 " --> pdb=" O LYS A1444 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N TYR A1506 " --> pdb=" O CYS A1471 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A1473 " --> pdb=" O TYR A1506 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A2109 " --> pdb=" O ILE A1113 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL A2105 " --> pdb=" O PHE A1117 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N SER A1886 " --> pdb=" O GLY A1966 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A1968 " --> pdb=" O SER A1886 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A1888 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASN A1970 " --> pdb=" O ILE A1888 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA A1890 " --> pdb=" O ASN A1970 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR A1887 " --> pdb=" O VAL A1913 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N THR A1915 " --> pdb=" O TYR A1887 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE A1889 " --> pdb=" O THR A1915 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1413 through 1416 removed outlier: 6.462A pdb=" N ILE A1413 " --> pdb=" O TRP A1442 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LYS A1444 " --> pdb=" O ILE A1413 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A1415 " --> pdb=" O LYS A1444 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N TYR A1506 " --> pdb=" O CYS A1471 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A1473 " --> pdb=" O TYR A1506 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A2109 " --> pdb=" O ILE A1113 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL A2105 " --> pdb=" O PHE A1117 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL A2110 " --> pdb=" O LEU A2084 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1123 through 1124 removed outlier: 6.299A pdb=" N GLU A1124 " --> pdb=" O LYS A1393 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A1402 " --> pdb=" O VAL A1389 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU A1391 " --> pdb=" O LEU A1400 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A1400 " --> pdb=" O LEU A1391 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A1346 " --> pdb=" O THR A1399 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU A1313 " --> pdb=" O LEU A1343 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N HIS A1345 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS A1241 " --> pdb=" O LEU A1312 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL A1314 " --> pdb=" O LYS A1241 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A1243 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1525 through 1528 Processing sheet with id=AA8, first strand: chain 'A' and resid 1531 through 1535 Processing sheet with id=AA9, first strand: chain 'A' and resid 1625 through 1628 removed outlier: 6.615A pdb=" N SER A1604 " --> pdb=" O TYR A1567 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ALA A1569 " --> pdb=" O GLU A1602 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLU A1602 " --> pdb=" O ALA A1569 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A1603 " --> pdb=" O GLY A1615 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1625 through 1628 removed outlier: 5.339A pdb=" N THR A1829 " --> pdb=" O VAL A1853 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN A1855 " --> pdb=" O THR A1829 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE A1831 " --> pdb=" O GLN A1855 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1720 through 1722 removed outlier: 6.648A pdb=" N THR A1670 " --> pdb=" O LEU A1743 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU A1745 " --> pdb=" O THR A1670 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A1672 " --> pdb=" O LEU A1745 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP A1742 " --> pdb=" O ARG A1765 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU A1767 " --> pdb=" O ASP A1742 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL A1744 " --> pdb=" O LEU A1767 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N THR A1790 " --> pdb=" O THR A1762 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY A1764 " --> pdb=" O THR A1790 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS A1792 " --> pdb=" O GLY A1764 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE A1766 " --> pdb=" O HIS A1792 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B1789 " --> pdb=" O GLY A1793 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N THR B1790 " --> pdb=" O THR B1762 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY B1764 " --> pdb=" O THR B1790 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N HIS B1792 " --> pdb=" O GLY B1764 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE B1766 " --> pdb=" O HIS B1792 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B1742 " --> pdb=" O ARG B1765 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU B1767 " --> pdb=" O ASP B1742 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B1744 " --> pdb=" O LEU B1767 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR B1670 " --> pdb=" O VAL B1741 " (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 'B' and resid 860 through 865 removed outlier: 3.618A pdb=" N ALA B 860 " --> pdb=" O VAL B 935 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B 944 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER B 955 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 946 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL B 953 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B 919 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER B 955 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL B 917 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL B 913 " --> pdb=" O HIS B1056 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N HIS B1056 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU B 915 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA B1054 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N THR B1050 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B1048 " --> pdb=" O SER B1101 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER B1101 " --> pdb=" O LEU B1048 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR B1050 " --> pdb=" O THR B1099 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR B1099 " --> pdb=" O THR B1050 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B1052 " --> pdb=" O LEU B1097 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B1097 " --> pdb=" O VAL B1052 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B1054 " --> pdb=" O SER B1095 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B1019 " --> pdb=" O LEU B1009 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 860 through 865 removed outlier: 3.618A pdb=" N ALA B 860 " --> pdb=" O VAL B 935 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B 944 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER B 955 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 946 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL B 953 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B 919 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER B 955 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL B 917 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL B 913 " --> pdb=" O HIS B1056 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N HIS B1056 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU B 915 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA B1054 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N THR B1050 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B1048 " --> pdb=" O SER B1101 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER B1101 " --> pdb=" O LEU B1048 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR B1050 " --> pdb=" O THR B1099 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR B1099 " --> pdb=" O THR B1050 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B1052 " --> pdb=" O LEU B1097 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B1097 " --> pdb=" O VAL B1052 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B1054 " --> pdb=" O SER B1095 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 883 through 884 removed outlier: 4.164A pdb=" N THR B 879 " --> pdb=" O ASP B1000 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1413 through 1416 removed outlier: 6.400A pdb=" N ILE B1413 " --> pdb=" O TRP B1442 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS B1444 " --> pdb=" O ILE B1413 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU B1415 " --> pdb=" O LYS B1444 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR B1506 " --> pdb=" O CYS B1471 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU B1473 " --> pdb=" O TYR B1506 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B1517 " --> pdb=" O LYS B1116 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B1113 " --> pdb=" O PHE B2109 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B2109 " --> pdb=" O ILE B1113 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B2105 " --> pdb=" O PHE B1117 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N SER B1886 " --> pdb=" O GLY B1966 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL B1968 " --> pdb=" O SER B1886 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B1888 " --> pdb=" O VAL B1968 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASN B1970 " --> pdb=" O ILE B1888 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA B1890 " --> pdb=" O ASN B1970 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B1912 " --> pdb=" O GLN B1940 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N SER B1942 " --> pdb=" O LEU B1912 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B1914 " --> pdb=" O SER B1942 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1123 through 1125 removed outlier: 6.879A pdb=" N LEU B1402 " --> pdb=" O VAL B1389 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU B1391 " --> pdb=" O LEU B1400 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B1400 " --> pdb=" O LEU B1391 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP B1311 " --> pdb=" O PHE B1341 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU B1343 " --> pdb=" O ASP B1311 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B1313 " --> pdb=" O LEU B1343 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N HIS B1345 " --> pdb=" O LEU B1313 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LYS B1241 " --> pdb=" O ALA B1310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1525 through 1528 Processing sheet with id=AC1, first strand: chain 'B' and resid 1531 through 1535 Processing sheet with id=AC2, first strand: chain 'B' and resid 1625 through 1628 removed outlier: 6.602A pdb=" N SER B1604 " --> pdb=" O TYR B1567 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA B1569 " --> pdb=" O GLU B1602 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLU B1602 " --> pdb=" O ALA B1569 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B1603 " --> pdb=" O GLY B1615 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1625 through 1628 removed outlier: 5.539A pdb=" N THR B1829 " --> pdb=" O VAL B1853 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN B1855 " --> pdb=" O THR B1829 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE B1831 " --> pdb=" O GLN B1855 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 2062 through 2063 removed outlier: 6.764A pdb=" N ALA B2062 " --> pdb=" O GLN B2086 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 932 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.29 Time building geometry restraints manager: 3.94 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: 19266 1.03 - 1.23: 52 1.23 - 1.42: 8214 1.42 - 1.62: 11569 1.62 - 1.81: 113 Bond restraints: 39214 Sorted by residual: bond pdb=" O2B NDP B2601 " pdb=" P2B NDP B2601 " ideal model delta sigma weight residual 1.833 1.611 0.222 3.80e-02 6.93e+02 3.41e+01 bond pdb=" O2B NDP A2601 " pdb=" P2B NDP A2601 " ideal model delta sigma weight residual 1.833 1.611 0.222 3.80e-02 6.93e+02 3.41e+01 bond pdb=" O2B NDP B2602 " pdb=" P2B NDP B2602 " ideal model delta sigma weight residual 1.833 1.613 0.220 3.80e-02 6.93e+02 3.35e+01 bond pdb=" O2B NDP A2602 " pdb=" P2B NDP A2602 " ideal model delta sigma weight residual 1.833 1.614 0.219 3.80e-02 6.93e+02 3.33e+01 bond pdb=" O5D NDP A2601 " pdb=" PN NDP A2601 " ideal model delta sigma weight residual 1.757 1.600 0.157 3.50e-02 8.16e+02 2.01e+01 ... (remaining 39209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.99: 70852 4.99 - 9.99: 61 9.99 - 14.98: 11 14.98 - 19.97: 2 19.97 - 24.97: 3 Bond angle restraints: 70929 Sorted by residual: angle pdb=" PA NDP B2601 " pdb=" O3 NDP B2601 " pdb=" PN NDP B2601 " ideal model delta sigma weight residual 107.74 132.71 -24.97 1.95e+00 2.62e-01 1.63e+02 angle pdb=" PA NDP A2602 " pdb=" O3 NDP A2602 " pdb=" PN NDP A2602 " ideal model delta sigma weight residual 107.74 131.95 -24.21 1.95e+00 2.62e-01 1.54e+02 angle pdb=" PA NDP A2601 " pdb=" O3 NDP A2601 " pdb=" PN NDP A2601 " ideal model delta sigma weight residual 107.74 130.76 -23.02 1.95e+00 2.62e-01 1.39e+02 angle pdb=" PA NDP B2602 " pdb=" O3 NDP B2602 " pdb=" PN NDP B2602 " ideal model delta sigma weight residual 107.74 125.91 -18.17 1.95e+00 2.62e-01 8.65e+01 angle pdb=" C5B NDP B2602 " pdb=" O5B NDP B2602 " pdb=" PA NDP B2602 " ideal model delta sigma weight residual 103.84 119.73 -15.89 1.91e+00 2.73e-01 6.88e+01 ... (remaining 70924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.39: 17923 34.39 - 68.77: 427 68.77 - 103.16: 17 103.16 - 137.54: 0 137.54 - 171.93: 1 Dihedral angle restraints: 18368 sinusoidal: 10109 harmonic: 8259 Sorted by residual: dihedral pdb=" NR 4HH B2156 " pdb=" CS 4HH B2156 " pdb=" CT 4HH B2156 " pdb=" SU 4HH B2156 " ideal model delta sinusoidal sigma weight residual 173.45 -14.62 -171.93 1 3.00e+01 1.11e-03 2.12e+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 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" C5B NDP B2602 " pdb=" O5B NDP B2602 " pdb=" PA NDP B2602 " pdb=" O3 NDP B2602 " ideal model delta sinusoidal sigma weight residual 175.04 -89.27 -95.69 1 3.00e+01 1.11e-03 1.17e+01 ... (remaining 18365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2502 0.045 - 0.089: 361 0.089 - 0.134: 207 0.134 - 0.178: 3 0.178 - 0.223: 8 Chirality restraints: 3081 Sorted by residual: chirality pdb=" C4D NDP A2601 " pdb=" C3D NDP A2601 " pdb=" C5D NDP A2601 " pdb=" O4D NDP A2601 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C4D NDP A2602 " pdb=" C3D NDP A2602 " pdb=" C5D NDP A2602 " pdb=" O4D NDP A2602 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C4D NDP B2601 " pdb=" C3D NDP B2601 " pdb=" C5D NDP B2601 " pdb=" O4D NDP B2601 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3078 not shown) Planarity restraints: 5861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CL3 4HH B2156 " -0.081 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" CM 4HH B2156 " 0.076 2.00e-02 2.50e+03 pdb=" CO 4HH B2156 " 0.341 2.00e-02 2.50e+03 pdb=" NN 4HH B2156 " -0.522 2.00e-02 2.50e+03 pdb=" ON 4HH B2156 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP B2602 " -0.307 2.00e-02 2.50e+03 1.90e-01 4.53e+02 pdb=" C3N NDP B2602 " -0.070 2.00e-02 2.50e+03 pdb=" C4N NDP B2602 " -0.020 2.00e-02 2.50e+03 pdb=" C7N NDP B2602 " 0.159 2.00e-02 2.50e+03 pdb=" N1N NDP B2602 " 0.238 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CP 4HH B2156 " 0.031 2.00e-02 2.50e+03 1.89e-01 4.46e+02 pdb=" CQ 4HH B2156 " 0.052 2.00e-02 2.50e+03 pdb=" CS 4HH B2156 " -0.221 2.00e-02 2.50e+03 pdb=" NR 4HH B2156 " 0.311 2.00e-02 2.50e+03 pdb=" OR 4HH B2156 " -0.172 2.00e-02 2.50e+03 ... (remaining 5858 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1455 2.16 - 2.77: 77271 2.77 - 3.38: 110342 3.38 - 3.99: 141996 3.99 - 4.60: 223421 Nonbonded interactions: 554485 Sorted by model distance: nonbonded pdb=" OE1 GLU B1837 " pdb=" H GLU B1837 " model vdw 1.554 2.450 nonbonded pdb=" HG SER A1723 " pdb=" O3X NDP A2601 " model vdw 1.558 2.450 nonbonded pdb=" OE1 GLN A1595 " pdb=" HE ARG A1907 " model vdw 1.579 2.450 nonbonded pdb=" O THR B1230 " pdb="HD22 ASN B1234 " model vdw 1.586 2.450 nonbonded pdb=" HE1 TRP A1297 " pdb=" O ASP A1301 " model vdw 1.589 2.450 ... (remaining 554480 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' selection = (chain 'B' and (resid 859 through 1097 or (resid 1098 and (name N or name CA or \ name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or na \ me NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or n \ ame HE2)) or resid 1099 through 1148 or resid 1173 through 1289 or (resid 1290 a \ nd (name N or name CA or name C or name O or name CB or name CG or name ND1 or n \ ame CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or \ name HD2 or name HE1 or name HE2)) or resid 1291 through 2112 or resid 2601 thro \ ugh 2602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.230 Extract box with map and model: 0.490 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 34.360 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.222 19902 Z= 0.199 Angle : 0.710 24.967 27087 Z= 0.350 Chirality : 0.041 0.223 3081 Planarity : 0.008 0.295 3494 Dihedral : 10.451 171.930 7231 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.19 % Allowed : 3.75 % Favored : 96.06 % 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: 0.97 (0.18), residues: 2488 helix: 1.56 (0.19), residues: 885 sheet: -0.10 (0.25), residues: 498 loop : 0.41 (0.20), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1612 TYR 0.014 0.001 TYR A 991 PHE 0.025 0.001 PHE A1896 TRP 0.007 0.001 TRP B1807 HIS 0.003 0.001 HIS B1735 Details of bonding type rmsd covalent geometry : bond 0.00565 (19902) covalent geometry : angle 0.71045 (27087) hydrogen bonds : bond 0.19305 ( 841) hydrogen bonds : angle 7.61589 ( 2574) *********************** 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 61 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 915 GLU cc_start: 0.8895 (tt0) cc_final: 0.8629 (mt-10) REVERT: A 1577 MET cc_start: 0.9185 (mmm) cc_final: 0.8874 (mmp) REVERT: B 1332 MET cc_start: 0.9477 (mtt) cc_final: 0.9131 (mtt) REVERT: B 1768 GLU cc_start: 0.8549 (tp30) cc_final: 0.8334 (tp30) outliers start: 4 outliers final: 0 residues processed: 61 average time/residue: 0.3469 time to fit residues: 32.4597 Evaluate side-chains 38 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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: 5.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1035 GLN A1276 HIS A1845 GLN A1906 GLN A1961 GLN B 863 ASN B1006 GLN B1139 GLN B1200 GLN B1639 ASN B1709 GLN B1845 GLN B1855 GLN B2100 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.050942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.036211 restraints weight = 266034.564| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.17 r_work: 0.2686 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19902 Z= 0.172 Angle : 0.523 5.129 27087 Z= 0.275 Chirality : 0.040 0.141 3081 Planarity : 0.004 0.049 3494 Dihedral : 6.463 136.637 2742 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.29 % Allowed : 4.47 % Favored : 95.24 % 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: 1.23 (0.18), residues: 920 sheet: -0.34 (0.24), residues: 500 loop : 0.14 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1105 TYR 0.017 0.001 TYR A 991 PHE 0.009 0.001 PHE A 914 TRP 0.008 0.001 TRP A1903 HIS 0.005 0.001 HIS B1093 Details of bonding type rmsd covalent geometry : bond 0.00387 (19902) covalent geometry : angle 0.52334 (27087) hydrogen bonds : bond 0.04961 ( 841) hydrogen bonds : angle 5.68789 ( 2574) *********************** 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 44 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 1577 MET cc_start: 0.9196 (mmm) cc_final: 0.8856 (mmm) REVERT: B 1332 MET cc_start: 0.9481 (mtt) cc_final: 0.9168 (mtt) outliers start: 6 outliers final: 2 residues processed: 44 average time/residue: 0.2453 time to fit residues: 18.9904 Evaluate side-chains 37 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain B residue 1670 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 155 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1530 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.050450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.035498 restraints weight = 268174.252| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.20 r_work: 0.2682 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19902 Z= 0.156 Angle : 0.491 5.023 27087 Z= 0.253 Chirality : 0.039 0.135 3081 Planarity : 0.004 0.046 3494 Dihedral : 6.296 120.309 2742 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.24 % Allowed : 4.85 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.17), residues: 2488 helix: 1.27 (0.18), residues: 920 sheet: -0.43 (0.24), residues: 499 loop : 0.09 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1574 TYR 0.018 0.001 TYR A 991 PHE 0.009 0.001 PHE A 914 TRP 0.008 0.001 TRP B1807 HIS 0.005 0.001 HIS B1093 Details of bonding type rmsd covalent geometry : bond 0.00357 (19902) covalent geometry : angle 0.49072 (27087) hydrogen bonds : bond 0.03984 ( 841) hydrogen bonds : angle 5.18843 ( 2574) *********************** 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 43 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.9183 (mmm) cc_final: 0.8937 (mmm) REVERT: B 1332 MET cc_start: 0.9485 (mtt) cc_final: 0.9163 (mtt) outliers start: 5 outliers final: 1 residues processed: 42 average time/residue: 0.2477 time to fit residues: 17.8678 Evaluate side-chains 38 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1670 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 213 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 248 optimal weight: 0.4980 chunk 202 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.049701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.035089 restraints weight = 267767.474| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.12 r_work: 0.2665 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19902 Z= 0.218 Angle : 0.506 5.010 27087 Z= 0.262 Chirality : 0.040 0.141 3081 Planarity : 0.004 0.048 3494 Dihedral : 6.287 104.211 2742 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.24 % Allowed : 5.33 % Favored : 94.43 % 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: 0.40 (0.17), residues: 2488 helix: 1.23 (0.18), residues: 921 sheet: -0.60 (0.23), residues: 513 loop : 0.01 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1337 TYR 0.020 0.001 TYR A 991 PHE 0.009 0.001 PHE A 914 TRP 0.008 0.001 TRP B1807 HIS 0.004 0.001 HIS A1553 Details of bonding type rmsd covalent geometry : bond 0.00497 (19902) covalent geometry : angle 0.50598 (27087) hydrogen bonds : bond 0.03767 ( 841) hydrogen bonds : angle 5.02744 ( 2574) *********************** 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 42 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.9164 (mmm) cc_final: 0.8925 (mmp) REVERT: B 1332 MET cc_start: 0.9490 (mtt) cc_final: 0.9188 (mtt) REVERT: B 2104 MET cc_start: 0.8702 (mtm) cc_final: 0.8466 (mtt) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 0.2885 time to fit residues: 19.7319 Evaluate side-chains 39 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain B residue 1670 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 155 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.049920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.034966 restraints weight = 269304.064| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.21 r_work: 0.2659 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19902 Z= 0.179 Angle : 0.485 4.933 27087 Z= 0.250 Chirality : 0.040 0.137 3081 Planarity : 0.004 0.049 3494 Dihedral : 6.164 103.612 2742 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.34 % Allowed : 5.72 % Favored : 93.95 % 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: 0.41 (0.17), residues: 2488 helix: 1.26 (0.18), residues: 923 sheet: -0.62 (0.23), residues: 490 loop : -0.01 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1574 TYR 0.018 0.001 TYR A 991 PHE 0.010 0.001 PHE A1117 TRP 0.008 0.001 TRP B1807 HIS 0.004 0.001 HIS B1093 Details of bonding type rmsd covalent geometry : bond 0.00409 (19902) covalent geometry : angle 0.48470 (27087) hydrogen bonds : bond 0.03485 ( 841) hydrogen bonds : angle 4.83967 ( 2574) *********************** 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 43 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.9173 (mmm) cc_final: 0.8964 (mmm) REVERT: B 1332 MET cc_start: 0.9507 (mtt) cc_final: 0.9200 (mtt) outliers start: 7 outliers final: 4 residues processed: 42 average time/residue: 0.2861 time to fit residues: 20.2105 Evaluate side-chains 40 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain B residue 1522 ASP Chi-restraints excluded: chain B residue 1670 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 169 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.049285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.034428 restraints weight = 271694.801| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.18 r_work: 0.2637 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 19902 Z= 0.265 Angle : 0.526 5.328 27087 Z= 0.273 Chirality : 0.040 0.142 3081 Planarity : 0.004 0.050 3494 Dihedral : 6.241 106.584 2742 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.38 % Allowed : 6.29 % Favored : 93.32 % 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: 0.26 (0.17), residues: 2488 helix: 1.17 (0.18), residues: 927 sheet: -0.71 (0.23), residues: 508 loop : -0.12 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1574 TYR 0.021 0.001 TYR A 991 PHE 0.010 0.001 PHE B1119 TRP 0.007 0.001 TRP A1903 HIS 0.004 0.001 HIS A1792 Details of bonding type rmsd covalent geometry : bond 0.00602 (19902) covalent geometry : angle 0.52560 (27087) hydrogen bonds : bond 0.03730 ( 841) hydrogen bonds : angle 4.91997 ( 2574) *********************** 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 44 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.9177 (mmm) cc_final: 0.8966 (mmp) REVERT: B 1332 MET cc_start: 0.9536 (mtt) cc_final: 0.9225 (mtt) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.3303 time to fit residues: 23.2628 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 : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1240 MET Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1670 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 135 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.049388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.034866 restraints weight = 268046.752| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.12 r_work: 0.2651 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19902 Z= 0.185 Angle : 0.487 5.294 27087 Z= 0.251 Chirality : 0.040 0.141 3081 Planarity : 0.004 0.050 3494 Dihedral : 6.109 104.272 2742 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.43 % Allowed : 6.44 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.17), residues: 2488 helix: 1.25 (0.18), residues: 928 sheet: -0.69 (0.23), residues: 492 loop : -0.08 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1574 TYR 0.019 0.001 TYR A 991 PHE 0.010 0.001 PHE A1117 TRP 0.008 0.001 TRP B1807 HIS 0.004 0.001 HIS B1093 Details of bonding type rmsd covalent geometry : bond 0.00425 (19902) covalent geometry : angle 0.48691 (27087) hydrogen bonds : bond 0.03436 ( 841) hydrogen bonds : angle 4.76447 ( 2574) *********************** 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 45 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.9163 (mmm) cc_final: 0.8960 (mmm) REVERT: B 1332 MET cc_start: 0.9534 (mtt) cc_final: 0.9227 (mtt) outliers start: 9 outliers final: 6 residues processed: 43 average time/residue: 0.3097 time to fit residues: 23.4304 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 : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1670 THR Chi-restraints excluded: chain B residue 2066 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 228 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 201 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.049758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.035279 restraints weight = 266331.103| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.11 r_work: 0.2667 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19902 Z= 0.125 Angle : 0.463 5.221 27087 Z= 0.237 Chirality : 0.039 0.136 3081 Planarity : 0.003 0.050 3494 Dihedral : 5.946 101.650 2742 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.34 % Allowed : 6.77 % Favored : 92.89 % 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: 0.48 (0.17), residues: 2488 helix: 1.39 (0.18), residues: 929 sheet: -0.69 (0.23), residues: 505 loop : 0.02 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1574 TYR 0.017 0.001 TYR A 991 PHE 0.010 0.001 PHE A1117 TRP 0.009 0.001 TRP B1807 HIS 0.004 0.001 HIS B1093 Details of bonding type rmsd covalent geometry : bond 0.00289 (19902) covalent geometry : angle 0.46289 (27087) hydrogen bonds : bond 0.03118 ( 841) hydrogen bonds : angle 4.56920 ( 2574) *********************** 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 43 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1332 MET cc_start: 0.9513 (mtt) cc_final: 0.9197 (mtt) outliers start: 7 outliers final: 7 residues processed: 41 average time/residue: 0.2991 time to fit residues: 21.6663 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 : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1240 MET Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain B residue 1670 THR Chi-restraints excluded: chain B residue 1671 LEU Chi-restraints excluded: chain B residue 2066 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 74 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 120 optimal weight: 0.0980 chunk 196 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 152 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.049795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.035248 restraints weight = 267146.456| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.14 r_work: 0.2669 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19902 Z= 0.130 Angle : 0.461 5.320 27087 Z= 0.235 Chirality : 0.039 0.139 3081 Planarity : 0.003 0.050 3494 Dihedral : 5.852 101.167 2742 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.43 % Allowed : 6.68 % Favored : 92.89 % 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: 0.55 (0.17), residues: 2488 helix: 1.46 (0.18), residues: 929 sheet: -0.68 (0.23), residues: 505 loop : 0.06 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1574 TYR 0.017 0.001 TYR A 991 PHE 0.009 0.001 PHE A1117 TRP 0.008 0.001 TRP B1807 HIS 0.004 0.001 HIS B1093 Details of bonding type rmsd covalent geometry : bond 0.00300 (19902) covalent geometry : angle 0.46080 (27087) hydrogen bonds : bond 0.03054 ( 841) hydrogen bonds : angle 4.49556 ( 2574) *********************** 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 45 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1332 MET cc_start: 0.9499 (mtt) cc_final: 0.9181 (mtt) REVERT: B 1496 VAL cc_start: 0.9541 (OUTLIER) cc_final: 0.9242 (m) REVERT: B 1503 MET cc_start: 0.8784 (mmp) cc_final: 0.8560 (mmp) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 0.3041 time to fit residues: 23.0601 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 : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1240 MET Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1670 THR Chi-restraints excluded: chain B residue 2066 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 217 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.049291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.034763 restraints weight = 268264.782| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.13 r_work: 0.2643 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19902 Z= 0.226 Angle : 0.495 5.029 27087 Z= 0.255 Chirality : 0.040 0.145 3081 Planarity : 0.004 0.050 3494 Dihedral : 5.914 104.885 2742 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.43 % Allowed : 6.77 % Favored : 92.80 % 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 (0.17), residues: 2488 helix: 1.36 (0.18), residues: 928 sheet: -0.72 (0.23), residues: 506 loop : -0.04 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1574 TYR 0.019 0.001 TYR A 991 PHE 0.009 0.001 PHE A1117 TRP 0.006 0.001 TRP B1634 HIS 0.004 0.001 HIS A1792 Details of bonding type rmsd covalent geometry : bond 0.00513 (19902) covalent geometry : angle 0.49460 (27087) hydrogen bonds : bond 0.03350 ( 841) hydrogen bonds : angle 4.62186 ( 2574) ********************** 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 44 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1332 MET cc_start: 0.9527 (mtt) cc_final: 0.9218 (mtt) REVERT: B 1496 VAL cc_start: 0.9540 (OUTLIER) cc_final: 0.9232 (m) outliers start: 9 outliers final: 8 residues processed: 42 average time/residue: 0.3044 time to fit residues: 22.5498 Evaluate side-chains 44 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1240 MET Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1790 THR Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain B residue 1314 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1670 THR Chi-restraints excluded: chain B residue 2066 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 217 optimal weight: 0.2980 chunk 216 optimal weight: 2.9990 chunk 156 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 162 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 168 optimal weight: 0.0030 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.050339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035590 restraints weight = 266811.487| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.15 r_work: 0.2682 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19902 Z= 0.083 Angle : 0.453 5.951 27087 Z= 0.229 Chirality : 0.039 0.133 3081 Planarity : 0.003 0.051 3494 Dihedral : 5.685 98.781 2742 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.24 % Allowed : 7.06 % Favored : 92.70 % 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: 0.67 (0.18), residues: 2488 helix: 1.55 (0.18), residues: 923 sheet: -0.61 (0.23), residues: 505 loop : 0.15 (0.20), residues: 1060 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 0.011 0.001 PHE A1117 TRP 0.010 0.001 TRP B1807 HIS 0.004 0.001 HIS B1093 Details of bonding type rmsd covalent geometry : bond 0.00198 (19902) covalent geometry : angle 0.45309 (27087) hydrogen bonds : bond 0.02833 ( 841) hydrogen bonds : angle 4.35639 ( 2574) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6808.81 seconds wall clock time: 116 minutes 55.65 seconds (7015.65 seconds total)