Starting phenix.real_space_refine on Sun Aug 24 00:54:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eyk_28691/08_2025/8eyk_28691_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyk_28691/08_2025/8eyk_28691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eyk_28691/08_2025/8eyk_28691_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyk_28691/08_2025/8eyk_28691_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eyk_28691/08_2025/8eyk_28691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyk_28691/08_2025/8eyk_28691.map" } resolution = 2.7 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= 0.000 sd= 0.176 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 58 5.16 5 C 9777 2.51 5 N 2704 2.21 5 O 2835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s 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: 15386 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7179 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 47, 'TRANS': 918} Chain breaks: 2 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 6, 'ASP:plan': 10, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 151 Chain: "F" Number of atoms: 7949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 7949 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 54, 'TRANS': 1015} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 406 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 9, 'ASN:plan1': 5, 'GLN:plan1': 9, 'ARG:plan': 7, 'HIS:plan': 3, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 188 Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'NDP': 2, 'X5O': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'NDP': 2, 'X5O': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.71, per 1000 atoms: 0.24 Number of scatterers: 15386 At special positions: 0 Unit cell: (90.64, 195.7, 90.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 12 15.00 O 2835 8.00 N 2704 7.00 C 9777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 903.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3736 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 23 sheets defined 37.6% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'E' and resid 872 through 876 Processing helix chain 'E' and resid 887 through 903 Processing helix chain 'E' and resid 906 through 910 Processing helix chain 'E' and resid 965 through 970 removed outlier: 3.532A pdb=" N ASP E 970 " --> pdb=" O ARG E 967 " (cutoff:3.500A) Processing helix chain 'E' and resid 987 through 998 Processing helix chain 'E' and resid 1003 through 1006 Processing helix chain 'E' and resid 1025 through 1040 removed outlier: 4.134A pdb=" N GLY E1040 " --> pdb=" O MET E1036 " (cutoff:3.500A) Processing helix chain 'E' and resid 1058 through 1066 removed outlier: 3.589A pdb=" N GLN E1064 " --> pdb=" O ALA E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1423 through 1434 removed outlier: 4.314A pdb=" N SER E1427 " --> pdb=" O ARG E1423 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP E1434 " --> pdb=" O GLY E1430 " (cutoff:3.500A) Processing helix chain 'E' and resid 1453 through 1463 removed outlier: 3.839A pdb=" N ARG E1462 " --> pdb=" O ASN E1458 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E1463 " --> pdb=" O CYS E1459 " (cutoff:3.500A) Processing helix chain 'E' and resid 1465 through 1470 Processing helix chain 'E' and resid 1490 through 1500 removed outlier: 3.639A pdb=" N GLN E1494 " --> pdb=" O SER E1490 " (cutoff:3.500A) Processing helix chain 'E' and resid 1540 through 1542 No H-bonds generated for 'chain 'E' and resid 1540 through 1542' Processing helix chain 'E' and resid 1572 through 1580 Processing helix chain 'E' and resid 1584 through 1588 Processing helix chain 'E' and resid 1629 through 1631 No H-bonds generated for 'chain 'E' and resid 1629 through 1631' Processing helix chain 'E' and resid 1641 through 1646 Processing helix chain 'E' and resid 1647 through 1661 removed outlier: 4.288A pdb=" N VAL E1651 " --> pdb=" O SER E1647 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E1653 " --> pdb=" O PRO E1649 " (cutoff:3.500A) Processing helix chain 'E' and resid 1678 through 1691 Processing helix chain 'E' and resid 1701 through 1712 Processing helix chain 'E' and resid 1716 through 1718 No H-bonds generated for 'chain 'E' and resid 1716 through 1718' Processing helix chain 'E' and resid 1726 through 1736 removed outlier: 4.216A pdb=" N GLN E1730 " --> pdb=" O THR E1726 " (cutoff:3.500A) Processing helix chain 'E' and resid 1750 through 1759 removed outlier: 3.564A pdb=" N SER E1756 " --> pdb=" O LYS E1752 " (cutoff:3.500A) Processing helix chain 'E' and resid 1771 through 1776 Processing helix chain 'E' and resid 1783 through 1788 Processing helix chain 'E' and resid 1795 through 1797 No H-bonds generated for 'chain 'E' and resid 1795 through 1797' Processing helix chain 'E' and resid 1798 through 1803 removed outlier: 4.288A pdb=" N GLU E1802 " --> pdb=" O ALA E1798 " (cutoff:3.500A) Processing helix chain 'E' and resid 1804 through 1820 removed outlier: 3.678A pdb=" N VAL E1810 " --> pdb=" O ASP E1806 " (cutoff:3.500A) Processing helix chain 'E' and resid 1836 through 1846 removed outlier: 3.535A pdb=" N GLN E1845 " --> pdb=" O ARG E1841 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY E1846 " --> pdb=" O TYR E1842 " (cutoff:3.500A) Processing helix chain 'E' and resid 1894 through 1907 Processing helix chain 'E' and resid 1922 through 1936 Processing helix chain 'E' and resid 1948 through 1963 removed outlier: 3.586A pdb=" N LEU E1962 " --> pdb=" O GLU E1958 " (cutoff:3.500A) Processing helix chain 'E' and resid 1984 through 1993 Processing helix chain 'E' and resid 1995 through 2010 Processing helix chain 'E' and resid 2022 through 2026 Processing helix chain 'E' and resid 2031 through 2051 Processing helix chain 'E' and resid 2067 through 2072 removed outlier: 3.796A pdb=" N GLU E2071 " --> pdb=" O GLY E2067 " (cutoff:3.500A) Processing helix chain 'E' and resid 2087 through 2100 removed outlier: 3.777A pdb=" N ASN E2100 " --> pdb=" O ASP E2096 " (cutoff:3.500A) Processing helix chain 'F' and resid 873 through 876 Processing helix chain 'F' and resid 887 through 904 removed outlier: 3.552A pdb=" N TYR F 891 " --> pdb=" O PRO F 887 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU F 892 " --> pdb=" O ALA F 888 " (cutoff:3.500A) Processing helix chain 'F' and resid 906 through 910 Processing helix chain 'F' and resid 987 through 997 Processing helix chain 'F' and resid 1003 through 1006 Processing helix chain 'F' and resid 1025 through 1040 removed outlier: 3.571A pdb=" N PHE F1029 " --> pdb=" O ASN F1025 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET F1030 " --> pdb=" O TRP F1026 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY F1040 " --> pdb=" O MET F1036 " (cutoff:3.500A) Processing helix chain 'F' and resid 1058 through 1065 removed outlier: 3.687A pdb=" N GLN F1064 " --> pdb=" O ALA F1060 " (cutoff:3.500A) Processing helix chain 'F' and resid 1221 through 1234 removed outlier: 3.913A pdb=" N LYS F1225 " --> pdb=" O SER F1221 " (cutoff:3.500A) Processing helix chain 'F' and resid 1251 through 1254 removed outlier: 4.029A pdb=" N SER F1254 " --> pdb=" O HIS F1251 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1251 through 1254' Processing helix chain 'F' and resid 1255 through 1261 Processing helix chain 'F' and resid 1326 through 1336 Processing helix chain 'F' and resid 1376 through 1384 Processing helix chain 'F' and resid 1423 through 1433 removed outlier: 4.130A pdb=" N SER F1427 " --> pdb=" O ARG F1423 " (cutoff:3.500A) Processing helix chain 'F' and resid 1452 through 1462 removed outlier: 4.268A pdb=" N ARG F1462 " --> pdb=" O ASN F1458 " (cutoff:3.500A) Processing helix chain 'F' and resid 1490 through 1500 Processing helix chain 'F' and resid 1540 through 1542 No H-bonds generated for 'chain 'F' and resid 1540 through 1542' Processing helix chain 'F' and resid 1572 through 1580 Processing helix chain 'F' and resid 1584 through 1588 Processing helix chain 'F' and resid 1629 through 1631 No H-bonds generated for 'chain 'F' and resid 1629 through 1631' Processing helix chain 'F' and resid 1643 through 1646 Processing helix chain 'F' and resid 1647 through 1660 removed outlier: 4.214A pdb=" N VAL F1651 " --> pdb=" O SER F1647 " (cutoff:3.500A) Processing helix chain 'F' and resid 1678 through 1691 Processing helix chain 'F' and resid 1701 through 1712 Processing helix chain 'F' and resid 1716 through 1718 No H-bonds generated for 'chain 'F' and resid 1716 through 1718' Processing helix chain 'F' and resid 1727 through 1736 Processing helix chain 'F' and resid 1750 through 1759 Processing helix chain 'F' and resid 1771 through 1776 Processing helix chain 'F' and resid 1783 through 1788 Processing helix chain 'F' and resid 1797 through 1801 Processing helix chain 'F' and resid 1806 through 1820 removed outlier: 4.124A pdb=" N VAL F1810 " --> pdb=" O ASP F1806 " (cutoff:3.500A) Processing helix chain 'F' and resid 1835 through 1844 Processing helix chain 'F' and resid 1894 through 1907 removed outlier: 3.543A pdb=" N GLU F1899 " --> pdb=" O GLY F1895 " (cutoff:3.500A) Processing helix chain 'F' and resid 1922 through 1935 Processing helix chain 'F' and resid 1948 through 1963 removed outlier: 3.629A pdb=" N LEU F1962 " --> pdb=" O GLU F1958 " (cutoff:3.500A) Processing helix chain 'F' and resid 1979 through 1983 Processing helix chain 'F' and resid 1984 through 2010 Proline residue: F1994 - end of helix removed outlier: 4.124A pdb=" N SER F1997 " --> pdb=" O LYS F1993 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY F1998 " --> pdb=" O PRO F1994 " (cutoff:3.500A) Processing helix chain 'F' and resid 2022 through 2026 Processing helix chain 'F' and resid 2031 through 2051 removed outlier: 3.671A pdb=" N GLY F2035 " --> pdb=" O GLN F2031 " (cutoff:3.500A) Processing helix chain 'F' and resid 2068 through 2073 Processing helix chain 'F' and resid 2087 through 2099 Processing sheet with id=AA1, first strand: chain 'E' and resid 860 through 864 removed outlier: 6.848A pdb=" N PHE E 944 " --> pdb=" O SER E 955 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER E 955 " --> pdb=" O PHE E 944 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL E 946 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL E 953 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU E 919 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER E 955 " --> pdb=" O VAL E 917 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL E 917 " --> pdb=" O SER E 955 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL E 913 " --> pdb=" O HIS E1056 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N HIS E1056 " --> pdb=" O VAL E 913 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU E 915 " --> pdb=" O ALA E1054 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA E1054 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR E1050 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU E1100 " --> pdb=" O PRO E1049 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY E1096 " --> pdb=" O THR E1053 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE E1055 " --> pdb=" O ILE E1094 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE E1094 " --> pdb=" O ILE E1055 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E1057 " --> pdb=" O VAL E1092 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL E1092 " --> pdb=" O ILE E1057 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU E1010 " --> pdb=" O ARG E1019 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU E1021 " --> pdb=" O ILE E1008 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE E1008 " --> pdb=" O LEU E1021 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 860 through 864 removed outlier: 6.848A pdb=" N PHE E 944 " --> pdb=" O SER E 955 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER E 955 " --> pdb=" O PHE E 944 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL E 946 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL E 953 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU E 919 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER E 955 " --> pdb=" O VAL E 917 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL E 917 " --> pdb=" O SER E 955 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL E 913 " --> pdb=" O HIS E1056 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N HIS E1056 " --> pdb=" O VAL E 913 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU E 915 " --> pdb=" O ALA E1054 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA E1054 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR E1050 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU E1100 " --> pdb=" O PRO E1049 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY E1096 " --> pdb=" O THR E1053 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE E1055 " --> pdb=" O ILE E1094 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE E1094 " --> pdb=" O ILE E1055 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E1057 " --> pdb=" O VAL E1092 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL E1092 " --> pdb=" O ILE E1057 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 883 through 884 removed outlier: 3.604A pdb=" N THR E 879 " --> pdb=" O ASP E1000 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 1413 through 1416 removed outlier: 5.979A pdb=" N ILE E1413 " --> pdb=" O TRP E1442 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS E1444 " --> pdb=" O ILE E1413 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU E1415 " --> pdb=" O LYS E1444 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU E1473 " --> pdb=" O ASN E1504 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR E1506 " --> pdb=" O LEU E1473 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER E1475 " --> pdb=" O TYR E1506 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET E1503 " --> pdb=" O PHE E1514 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE E1514 " --> pdb=" O MET E1503 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG E1515 " --> pdb=" O CYS E1118 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS E1118 " --> pdb=" O ARG E1515 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL E2105 " --> pdb=" O PHE E1117 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER E1886 " --> pdb=" O VAL E1965 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY E1967 " --> pdb=" O SER E1886 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU E1912 " --> pdb=" O GLN E1940 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER E1942 " --> pdb=" O LEU E1912 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU E1914 " --> pdb=" O SER E1942 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 1413 through 1416 removed outlier: 5.979A pdb=" N ILE E1413 " --> pdb=" O TRP E1442 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS E1444 " --> pdb=" O ILE E1413 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU E1415 " --> pdb=" O LYS E1444 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU E1473 " --> pdb=" O ASN E1504 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR E1506 " --> pdb=" O LEU E1473 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER E1475 " --> pdb=" O TYR E1506 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET E1503 " --> pdb=" O PHE E1514 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE E1514 " --> pdb=" O MET E1503 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG E1515 " --> pdb=" O CYS E1118 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS E1118 " --> pdb=" O ARG E1515 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL E2105 " --> pdb=" O PHE E1117 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL E2110 " --> pdb=" O LEU E2084 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 1525 through 1528 Processing sheet with id=AA7, first strand: chain 'E' and resid 1531 through 1535 Processing sheet with id=AA8, first strand: chain 'E' and resid 1625 through 1628 removed outlier: 6.755A pdb=" N SER E1604 " --> pdb=" O TYR E1567 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA E1569 " --> pdb=" O GLU E1602 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU E1602 " --> pdb=" O ALA E1569 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 1625 through 1628 removed outlier: 4.527A pdb=" N VAL E1852 " --> pdb=" O LEU E1571 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N THR E1829 " --> pdb=" O VAL E1853 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN E1855 " --> pdb=" O THR E1829 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE E1831 " --> pdb=" O GLN E1855 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 1720 through 1722 removed outlier: 7.802A pdb=" N ALA E1721 " --> pdb=" O VAL E1695 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR E1697 " --> pdb=" O ALA E1721 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP E1742 " --> pdb=" O ARG E1765 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU E1767 " --> pdb=" O ASP E1742 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL E1744 " --> pdb=" O LEU E1767 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR E1790 " --> pdb=" O THR E1762 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY E1764 " --> pdb=" O THR E1790 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N HIS E1792 " --> pdb=" O GLY E1764 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE E1766 " --> pdb=" O HIS E1792 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR F1790 " --> pdb=" O THR F1762 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY F1764 " --> pdb=" O THR F1790 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N HIS F1792 " --> pdb=" O GLY F1764 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE F1766 " --> pdb=" O HIS F1792 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP F1742 " --> pdb=" O ARG F1765 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU F1767 " --> pdb=" O ASP F1742 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL F1744 " --> pdb=" O LEU F1767 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR F1670 " --> pdb=" O LEU F1743 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LEU F1745 " --> pdb=" O THR F1670 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU F1672 " --> pdb=" O LEU F1745 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU F1671 " --> pdb=" O PHE F1696 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR F1698 " --> pdb=" O LEU F1671 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE F1673 " --> pdb=" O THR F1698 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ALA F1721 " --> pdb=" O VAL F1695 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR F1697 " --> pdb=" O ALA F1721 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 1779 through 1781 Processing sheet with id=AB3, first strand: chain 'F' and resid 860 through 864 removed outlier: 6.787A pdb=" N PHE F 944 " --> pdb=" O SER F 955 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N SER F 955 " --> pdb=" O PHE F 944 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL F 946 " --> pdb=" O VAL F 953 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL F 953 " --> pdb=" O LEU F 919 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU F 919 " --> pdb=" O VAL F 953 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER F 955 " --> pdb=" O VAL F 917 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL F 917 " --> pdb=" O SER F 955 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL F 913 " --> pdb=" O HIS F1056 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS F1056 " --> pdb=" O VAL F 913 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU F 915 " --> pdb=" O ALA F1054 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA F1054 " --> pdb=" O GLU F 915 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N THR F1050 " --> pdb=" O LEU F 919 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 985 through 986 removed outlier: 6.233A pdb=" N ILE F1008 " --> pdb=" O LEU F1021 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU F1021 " --> pdb=" O ILE F1008 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU F1010 " --> pdb=" O ARG F1019 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLU F1100 " --> pdb=" O PRO F1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 883 through 884 removed outlier: 3.749A pdb=" N THR F 879 " --> pdb=" O ASP F1000 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 1475 through 1476 removed outlier: 6.711A pdb=" N SER F1475 " --> pdb=" O TYR F1506 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F1510 " --> pdb=" O ARG F1507 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL F2105 " --> pdb=" O PHE F1117 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY F1966 " --> pdb=" O TYR F2015 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL F2017 " --> pdb=" O GLY F1966 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL F1968 " --> pdb=" O VAL F2017 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE F2019 " --> pdb=" O VAL F1968 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASN F1970 " --> pdb=" O PHE F2019 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N SER F2021 " --> pdb=" O ASN F1970 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER F1886 " --> pdb=" O VAL F1965 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY F1967 " --> pdb=" O SER F1886 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU F1912 " --> pdb=" O GLN F1940 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N SER F1942 " --> pdb=" O LEU F1912 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU F1914 " --> pdb=" O SER F1942 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 1475 through 1476 removed outlier: 6.711A pdb=" N SER F1475 " --> pdb=" O TYR F1506 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F1510 " --> pdb=" O ARG F1507 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL F2105 " --> pdb=" O PHE F1117 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL F2110 " --> pdb=" O LEU F2084 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 1123 through 1124 removed outlier: 6.872A pdb=" N LEU F1402 " --> pdb=" O VAL F1389 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU F1313 " --> pdb=" O LEU F1343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 1239 through 1243 removed outlier: 6.117A pdb=" N MET F1240 " --> pdb=" O SER F1269 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR F1271 " --> pdb=" O MET F1240 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL F1242 " --> pdb=" O THR F1271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 1413 through 1416 removed outlier: 5.787A pdb=" N ILE F1413 " --> pdb=" O TRP F1442 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS F1444 " --> pdb=" O ILE F1413 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU F1415 " --> pdb=" O LYS F1444 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 1525 through 1528 Processing sheet with id=AC3, first strand: chain 'F' and resid 1531 through 1535 Processing sheet with id=AC4, first strand: chain 'F' and resid 1625 through 1627 removed outlier: 3.663A pdb=" N SER F1570 " --> pdb=" O GLU F1602 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU F1602 " --> pdb=" O SER F1570 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET F1614 " --> pdb=" O TRP F1634 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 1625 through 1627 removed outlier: 4.590A pdb=" N VAL F1852 " --> pdb=" O LEU F1571 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N THR F1829 " --> pdb=" O VAL F1853 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN F1855 " --> pdb=" O THR F1829 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE F1831 " --> pdb=" O GLN F1855 " (cutoff:3.500A) 743 hydrogen bonds defined for protein. 2013 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: 4.22 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2509 1.27 - 1.41: 3953 1.41 - 1.55: 9149 1.55 - 1.68: 50 1.68 - 1.82: 84 Bond restraints: 15745 Sorted by residual: bond pdb=" C1B NDP F2603 " pdb=" C2B NDP F2603 " ideal model delta sigma weight residual 1.575 1.252 0.323 3.70e-02 7.30e+02 7.64e+01 bond pdb=" C1B NDP E2602 " pdb=" C2B NDP E2602 " ideal model delta sigma weight residual 1.575 1.252 0.323 3.70e-02 7.30e+02 7.64e+01 bond pdb=" C2D NDP F2602 " pdb=" C3D NDP F2602 " ideal model delta sigma weight residual 1.545 1.233 0.312 3.60e-02 7.72e+02 7.50e+01 bond pdb=" C1B NDP F2602 " pdb=" C2B NDP F2602 " ideal model delta sigma weight residual 1.575 1.258 0.317 3.70e-02 7.30e+02 7.36e+01 bond pdb=" C2D NDP F2603 " pdb=" C3D NDP F2603 " ideal model delta sigma weight residual 1.545 1.237 0.308 3.60e-02 7.72e+02 7.32e+01 ... (remaining 15740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.34: 21410 6.34 - 12.69: 70 12.69 - 19.03: 17 19.03 - 25.37: 3 25.37 - 31.72: 2 Bond angle restraints: 21502 Sorted by residual: angle pdb=" PA NDP F2602 " pdb=" O3 NDP F2602 " pdb=" PN NDP F2602 " ideal model delta sigma weight residual 107.74 130.81 -23.07 1.95e+00 2.62e-01 1.39e+02 angle pdb=" C12 X5O E2601 " pdb=" C13 X5O E2601 " pdb=" C16 X5O E2601 " ideal model delta sigma weight residual 112.89 81.17 31.72 3.00e+00 1.11e-01 1.12e+02 angle pdb=" C12 X5O F2601 " pdb=" C13 X5O F2601 " pdb=" C16 X5O F2601 " ideal model delta sigma weight residual 112.89 82.95 29.94 3.00e+00 1.11e-01 9.96e+01 angle pdb=" PA NDP E2602 " pdb=" O3 NDP E2602 " pdb=" PN NDP E2602 " ideal model delta sigma weight residual 107.74 125.10 -17.36 1.95e+00 2.62e-01 7.89e+01 angle pdb=" C14 X5O F2601 " pdb=" C13 X5O F2601 " pdb=" C16 X5O F2601 " ideal model delta sigma weight residual 112.13 135.00 -22.87 3.00e+00 1.11e-01 5.81e+01 ... (remaining 21497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 8921 35.56 - 71.12: 271 71.12 - 106.68: 19 106.68 - 142.24: 1 142.24 - 177.80: 3 Dihedral angle restraints: 9215 sinusoidal: 3409 harmonic: 5806 Sorted by residual: dihedral pdb=" C5B NDP F2602 " pdb=" O5B NDP F2602 " pdb=" PA NDP F2602 " pdb=" O3 NDP F2602 " ideal model delta sinusoidal sigma weight residual 175.04 -2.76 177.80 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C5B NDP E2602 " pdb=" O5B NDP E2602 " pdb=" PA NDP E2602 " pdb=" O3 NDP E2602 " ideal model delta sinusoidal sigma weight residual 175.04 -26.89 -158.07 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C5B NDP F2603 " pdb=" O5B NDP F2603 " pdb=" PA NDP F2603 " pdb=" O3 NDP F2603 " ideal model delta sinusoidal sigma weight residual 175.04 23.03 152.01 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 9212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 2447 0.144 - 0.288: 16 0.288 - 0.431: 4 0.431 - 0.575: 1 0.575 - 0.719: 2 Chirality restraints: 2470 Sorted by residual: chirality pdb=" C1B NDP E2602 " pdb=" C2B NDP E2602 " pdb=" N9A NDP E2602 " pdb=" O4B NDP E2602 " both_signs ideal model delta sigma weight residual False 2.59 1.87 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C1B NDP F2602 " pdb=" C2B NDP F2602 " pdb=" N9A NDP F2602 " pdb=" O4B NDP F2602 " both_signs ideal model delta sigma weight residual False 2.59 2.00 0.59 2.00e-01 2.50e+01 8.78e+00 chirality pdb=" C3D NDP E2603 " pdb=" C2D NDP E2603 " pdb=" C4D NDP E2603 " pdb=" O3D NDP E2603 " both_signs ideal model delta sigma weight residual False -2.71 -2.27 -0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 2467 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F1558 " 0.065 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO F1559 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO F1559 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO F1559 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F1405 " 0.034 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO F1406 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO F1406 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F1406 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR E1657 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.63e+00 pdb=" C TYR E1657 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR E1657 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA E1658 " -0.011 2.00e-02 2.50e+03 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 719 2.72 - 3.26: 15374 3.26 - 3.81: 27793 3.81 - 4.35: 34031 4.35 - 4.90: 57158 Nonbonded interactions: 135075 Sorted by model distance: nonbonded pdb=" N GLU F1950 " pdb=" OE1 GLU F1950 " model vdw 2.171 3.120 nonbonded pdb=" O GLU F1233 " pdb=" NH1 ARG F1461 " model vdw 2.181 3.120 nonbonded pdb=" OD1 ASP F1716 " pdb=" N SER F1717 " model vdw 2.181 3.120 nonbonded pdb=" OH TYR E 891 " pdb=" OG1 THR E 923 " model vdw 2.213 3.040 nonbonded pdb=" O VAL F1732 " pdb=" OG1 THR F1736 " model vdw 2.214 3.040 ... (remaining 135070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 858 through 871 or (resid 872 and (name N or name CA or na \ me C or name O or name CB )) or resid 873 through 947 or (resid 948 and (name N \ or name CA or name C or name O or name CB )) or resid 949 through 962 or (resid \ 963 and (name N or name CA or name C or name O or name CB )) or resid 964 throug \ h 1067 or (resid 1068 and (name N or name CA or name C or name O or name CB )) o \ r resid 1069 or (resid 1070 and (name N or name CA or name C or name O or name C \ B )) or resid 1071 through 1104 or (resid 1105 through 1109 and (name N or name \ CA or name C or name O or name CB )) or resid 1110 through 1418 or (resid 1419 t \ hrough 1421 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 22 through 1503 or (resid 1504 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1505 through 1522 or (resid 1523 and (name N or name CA or name \ C or name O or name CB )) or resid 1524 through 1554 or (resid 1555 and (name N \ or name CA or name C or name O or name CB )) or resid 1556 or (resid 1557 throu \ gh 1558 and (name N or name CA or name C or name O or name CB )) or resid 1559 t \ hrough 1802 or resid 1805 through 1866 or resid 1871 through 1933 or (resid 1934 \ and (name N or name CA or name C or name O or name CB )) or resid 1935 through \ 1960 or (resid 1961 and (name N or name CA or name C or name O or name CB )) or \ resid 1962 through 2080 or (resid 2081 and (name N or name CA or name C or name \ O or name CB )) or resid 2082 through 2603)) selection = (chain 'F' and (resid 858 through 866 or (resid 867 through 869 and (name N or n \ ame CA or name C or name O or name CB )) or resid 870 through 926 or (resid 927 \ through 928 and (name N or name CA or name C or name O or name CB )) or resid 92 \ 9 through 966 or (resid 967 and (name N or name CA or name C or name O or name C \ B )) or resid 968 through 969 or (resid 970 and (name N or name CA or name C or \ name O or name CB )) or resid 971 through 975 or (resid 976 and (name N or name \ CA or name C or name O or name CB )) or resid 977 through 980 or (resid 981 and \ (name N or name CA or name C or name O or name CB )) or resid 982 or (resid 983 \ and (name N or name CA or name C or name O or name CB )) or resid 984 through 10 \ 42 or (resid 1043 through 1044 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1045 through 1105 or (resid 1106 through 1109 and (name N or na \ me CA or name C or name O or name CB )) or resid 1110 or (resid 1111 and (name N \ or name CA or name C or name O or name CB )) or resid 1112 through 1122 or (res \ id 1410 through 1411 and (name N or name CA or name C or name O or name CB )) or \ resid 1412 or (resid 1413 and (name N or name CA or name C or name O or name CB \ )) or resid 1414 or (resid 1415 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1416 through 1427 or (resid 1428 through 1429 and (name N or \ name CA or name C or name O or name CB )) or resid 1430 or (resid 1431 through 1 \ 439 and (name N or name CA or name C or name O or name CB )) or resid 1440 throu \ gh 1443 or (resid 1444 through 1445 and (name N or name CA or name C or name O o \ r name CB )) or resid 1446 through 1459 or (resid 1460 through 1461 and (name N \ or name CA or name C or name O or name CB )) or resid 1462 through 1466 or (resi \ d 1467 through 1471 and (name N or name CA or name C or name O or name CB )) or \ resid 1472 through 1482 or (resid 1483 and (name N or name CA or name C or name \ O or name CB )) or resid 1484 through 1492 or (resid 1493 through 1498 and (name \ N or name CA or name C or name O or name CB )) or (resid 1499 through 1504 and \ (name N or name CA or name C or name O or name CB )) or resid 1505 through 1519 \ or (resid 1520 through 1523 and (name N or name CA or name C or name O or name C \ B )) or resid 1524 through 1557 or (resid 1558 and (name N or name CA or name C \ or name O or name CB )) or resid 1559 through 1585 or (resid 1586 through 1587 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1588 through 15 \ 92 or (resid 1593 and (name N or name CA or name C or name O or name CB )) or re \ sid 1594 or (resid 1595 and (name N or name CA or name C or name O or name CB )) \ or resid 1596 through 1861 or (resid 1862 through 1864 and (name N or name CA o \ r name C or name O or name CB )) or resid 1865 through 1980 or (resid 1981 and ( \ name N or name CA or name C or name O or name CB )) or resid 1982 through 2070 o \ r (resid 2071 and (name N or name CA or name C or name O or name CB )) or resid \ 2072 through 2074 or resid 2077 through 2603)) } 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: 1.590 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.050 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.013 0.323 15745 Z= 0.441 Angle : 1.000 31.716 21502 Z= 0.461 Chirality : 0.051 0.719 2470 Planarity : 0.004 0.096 2754 Dihedral : 16.758 177.797 5479 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.25 % Allowed : 23.16 % Favored : 75.59 % 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: 0.16 (0.20), residues: 2012 helix: 0.72 (0.21), residues: 698 sheet: -0.47 (0.27), residues: 392 loop : 0.07 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F1461 TYR 0.024 0.001 TYR F 991 PHE 0.009 0.001 PHE E1728 TRP 0.024 0.001 TRP E1442 HIS 0.003 0.001 HIS E1735 Details of bonding type rmsd covalent geometry : bond 0.01308 (15745) covalent geometry : angle 1.00019 (21502) hydrogen bonds : bond 0.16134 ( 660) hydrogen bonds : angle 7.14602 ( 2013) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9081 (t0) cc_final: 0.8754 (t0) REVERT: E 1458 ASN cc_start: 0.8831 (m-40) cc_final: 0.8348 (m110) outliers start: 19 outliers final: 17 residues processed: 136 average time/residue: 0.6294 time to fit residues: 95.2593 Evaluate side-chains 133 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1473 LEU Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1789 VAL Chi-restraints excluded: chain E residue 1974 VAL Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1065 LYS Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1650 VAL Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1915 THR Chi-restraints excluded: chain F residue 2070 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2031 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.085578 restraints weight = 24029.567| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.45 r_work: 0.2933 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15745 Z= 0.147 Angle : 0.552 7.568 21502 Z= 0.278 Chirality : 0.042 0.169 2470 Planarity : 0.004 0.055 2754 Dihedral : 8.772 159.963 2299 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.55 % Allowed : 19.47 % Favored : 76.97 % 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: 0.15 (0.20), residues: 2012 helix: 0.77 (0.21), residues: 712 sheet: -0.73 (0.27), residues: 398 loop : 0.14 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F1461 TYR 0.022 0.001 TYR F 991 PHE 0.011 0.001 PHE F1791 TRP 0.013 0.001 TRP E1442 HIS 0.006 0.001 HIS E1674 Details of bonding type rmsd covalent geometry : bond 0.00352 (15745) covalent geometry : angle 0.55210 (21502) hydrogen bonds : bond 0.03729 ( 660) hydrogen bonds : angle 5.01048 ( 2013) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 140 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: E 915 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8670 (mt-10) REVERT: E 1071 ASP cc_start: 0.9174 (t0) cc_final: 0.8807 (t0) REVERT: E 1458 ASN cc_start: 0.8856 (m-40) cc_final: 0.8590 (m-40) REVERT: E 1596 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: E 1614 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.7108 (pp-130) REVERT: E 2012 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8386 (mp0) REVERT: F 862 TYR cc_start: 0.8902 (m-80) cc_final: 0.8619 (m-80) REVERT: F 915 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8940 (mt-10) REVERT: F 1023 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8594 (mtmm) REVERT: F 1989 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7306 (mp10) outliers start: 54 outliers final: 15 residues processed: 180 average time/residue: 0.6172 time to fit residues: 123.6048 Evaluate side-chains 138 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1583 LEU Chi-restraints excluded: chain E residue 1596 ASP Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1739 LYS Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1974 VAL Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1601 MET Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1872 LEU Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 14 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 125 optimal weight: 0.0050 chunk 64 optimal weight: 2.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2031 GLN F2059 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.082795 restraints weight = 24049.754| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.46 r_work: 0.2871 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15745 Z= 0.217 Angle : 0.575 10.142 21502 Z= 0.288 Chirality : 0.044 0.308 2470 Planarity : 0.004 0.049 2754 Dihedral : 8.092 153.030 2280 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.01 % Allowed : 19.34 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.19), residues: 2012 helix: 0.73 (0.20), residues: 711 sheet: -0.82 (0.26), residues: 422 loop : 0.15 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F1461 TYR 0.027 0.002 TYR E 991 PHE 0.012 0.001 PHE F1791 TRP 0.016 0.001 TRP F1442 HIS 0.005 0.001 HIS E1674 Details of bonding type rmsd covalent geometry : bond 0.00518 (15745) covalent geometry : angle 0.57490 (21502) hydrogen bonds : bond 0.03670 ( 660) hydrogen bonds : angle 4.87805 ( 2013) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 130 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9237 (t0) cc_final: 0.8866 (t0) REVERT: E 1458 ASN cc_start: 0.8888 (m-40) cc_final: 0.8590 (m110) REVERT: E 1614 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.7175 (pp-130) REVERT: E 1725 ASP cc_start: 0.7940 (t70) cc_final: 0.7672 (m-30) REVERT: E 1797 ASP cc_start: 0.8847 (p0) cc_final: 0.8634 (p0) REVERT: E 2012 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8380 (mp0) REVERT: F 1023 LYS cc_start: 0.8946 (mtmt) cc_final: 0.8624 (mtmm) REVERT: F 1666 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7732 (mmp80) REVERT: F 1835 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7238 (mt0) REVERT: F 1989 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7157 (mp10) REVERT: F 2008 GLU cc_start: 0.7876 (pp20) cc_final: 0.7601 (pp20) outliers start: 61 outliers final: 21 residues processed: 174 average time/residue: 0.6611 time to fit residues: 127.0592 Evaluate side-chains 146 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1505 VAL Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1974 VAL Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1726 THR Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1824 ARG Chi-restraints excluded: chain F residue 1853 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1886 SER Chi-restraints excluded: chain F residue 1974 VAL Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Chi-restraints excluded: chain F residue 2070 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 190 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2031 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.085093 restraints weight = 23948.833| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.47 r_work: 0.2922 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15745 Z= 0.138 Angle : 0.533 9.140 21502 Z= 0.266 Chirality : 0.042 0.196 2470 Planarity : 0.003 0.049 2754 Dihedral : 7.740 154.617 2280 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.62 % Allowed : 20.26 % Favored : 76.12 % 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: 0.12 (0.19), residues: 2012 helix: 0.81 (0.20), residues: 711 sheet: -0.87 (0.26), residues: 413 loop : 0.15 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F1515 TYR 0.023 0.001 TYR E 991 PHE 0.010 0.001 PHE F1791 TRP 0.018 0.001 TRP F1442 HIS 0.006 0.001 HIS E1674 Details of bonding type rmsd covalent geometry : bond 0.00334 (15745) covalent geometry : angle 0.53252 (21502) hydrogen bonds : bond 0.03155 ( 660) hydrogen bonds : angle 4.62089 ( 2013) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 136 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9227 (t0) cc_final: 0.8879 (t0) REVERT: E 1458 ASN cc_start: 0.8931 (m-40) cc_final: 0.8627 (m110) REVERT: E 1518 LEU cc_start: 0.9050 (mt) cc_final: 0.8620 (tm) REVERT: E 1596 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8401 (m-30) REVERT: E 1614 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.7105 (pp-130) REVERT: E 1725 ASP cc_start: 0.7932 (t70) cc_final: 0.7672 (m-30) REVERT: E 2012 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8376 (mp0) REVERT: F 862 TYR cc_start: 0.8825 (m-80) cc_final: 0.8475 (m-80) REVERT: F 915 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8910 (mt-10) REVERT: F 1023 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8620 (mtmm) REVERT: F 1666 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7656 (mmp80) REVERT: F 1835 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7115 (mt0) REVERT: F 1989 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7162 (mp10) REVERT: F 2008 GLU cc_start: 0.7962 (pp20) cc_final: 0.7652 (pp20) outliers start: 55 outliers final: 23 residues processed: 176 average time/residue: 0.6746 time to fit residues: 131.2866 Evaluate side-chains 147 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1505 VAL Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1562 GLN Chi-restraints excluded: chain E residue 1596 ASP Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1940 GLN Chi-restraints excluded: chain E residue 1974 VAL Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1428 LEU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1872 LEU Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Chi-restraints excluded: chain F residue 2070 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 151 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 0.0570 chunk 10 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 114 optimal weight: 0.0980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2031 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087239 restraints weight = 24200.995| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.47 r_work: 0.2959 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15745 Z= 0.114 Angle : 0.527 12.607 21502 Z= 0.261 Chirality : 0.042 0.337 2470 Planarity : 0.003 0.050 2754 Dihedral : 7.431 156.465 2280 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.96 % Allowed : 20.99 % Favored : 76.05 % 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: 0.21 (0.20), residues: 2012 helix: 0.90 (0.21), residues: 711 sheet: -0.79 (0.26), residues: 417 loop : 0.17 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F1515 TYR 0.020 0.001 TYR F 991 PHE 0.009 0.001 PHE F1791 TRP 0.021 0.001 TRP F1442 HIS 0.006 0.001 HIS E1674 Details of bonding type rmsd covalent geometry : bond 0.00277 (15745) covalent geometry : angle 0.52666 (21502) hydrogen bonds : bond 0.02886 ( 660) hydrogen bonds : angle 4.42459 ( 2013) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9199 (t0) cc_final: 0.8905 (t0) REVERT: E 1458 ASN cc_start: 0.8954 (m-40) cc_final: 0.8650 (m110) REVERT: E 1518 LEU cc_start: 0.9119 (mt) cc_final: 0.8672 (tm) REVERT: E 1596 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8373 (m-30) REVERT: E 1614 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.7104 (pp-130) REVERT: E 1725 ASP cc_start: 0.7993 (t70) cc_final: 0.7731 (m-30) REVERT: E 1768 GLU cc_start: 0.8938 (tp30) cc_final: 0.8715 (tp30) REVERT: E 1797 ASP cc_start: 0.8820 (p0) cc_final: 0.8618 (p0) REVERT: E 1996 TYR cc_start: 0.8195 (t80) cc_final: 0.7930 (t80) REVERT: E 2012 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8377 (mp0) REVERT: F 862 TYR cc_start: 0.8878 (m-80) cc_final: 0.8373 (m-80) REVERT: F 915 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8847 (mt-10) REVERT: F 1023 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8597 (mtmm) REVERT: F 1432 LEU cc_start: 0.9316 (mm) cc_final: 0.9003 (mm) REVERT: F 1518 LEU cc_start: 0.9009 (tp) cc_final: 0.8740 (tm) REVERT: F 1835 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7154 (mt0) REVERT: F 1989 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7147 (mp10) REVERT: F 2071 GLU cc_start: 0.7795 (pp20) cc_final: 0.7552 (pp20) outliers start: 45 outliers final: 21 residues processed: 179 average time/residue: 0.5997 time to fit residues: 120.0038 Evaluate side-chains 157 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1557 THR Chi-restraints excluded: chain E residue 1562 GLN Chi-restraints excluded: chain E residue 1596 ASP Chi-restraints excluded: chain E residue 1602 GLU Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1826 LEU Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1940 GLN Chi-restraints excluded: chain F residue 945 GLU Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1789 VAL Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1795 LEU Chi-restraints excluded: chain F residue 1843 MET Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1974 VAL Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 26 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2031 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.083740 restraints weight = 23828.492| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.48 r_work: 0.2900 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15745 Z= 0.187 Angle : 0.555 10.053 21502 Z= 0.277 Chirality : 0.043 0.236 2470 Planarity : 0.003 0.051 2754 Dihedral : 7.458 155.352 2279 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.03 % Allowed : 21.45 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.20), residues: 2012 helix: 0.81 (0.20), residues: 713 sheet: -0.92 (0.26), residues: 416 loop : 0.18 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F1515 TYR 0.026 0.002 TYR E 991 PHE 0.014 0.001 PHE E2109 TRP 0.024 0.001 TRP F1442 HIS 0.005 0.001 HIS E1674 Details of bonding type rmsd covalent geometry : bond 0.00450 (15745) covalent geometry : angle 0.55499 (21502) hydrogen bonds : bond 0.03196 ( 660) hydrogen bonds : angle 4.54185 ( 2013) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9225 (t0) cc_final: 0.8930 (t0) REVERT: E 1458 ASN cc_start: 0.8957 (m-40) cc_final: 0.8649 (m110) REVERT: E 1518 LEU cc_start: 0.9101 (mt) cc_final: 0.8670 (tm) REVERT: E 1614 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.7149 (pp-130) REVERT: E 1725 ASP cc_start: 0.7981 (t70) cc_final: 0.7726 (m-30) REVERT: E 1835 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: E 1996 TYR cc_start: 0.8198 (t80) cc_final: 0.7990 (t80) REVERT: E 2012 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8400 (mp0) REVERT: F 1023 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8626 (mtmm) REVERT: F 1432 LEU cc_start: 0.9331 (mm) cc_final: 0.9033 (mm) REVERT: F 1520 GLU cc_start: 0.8755 (mp0) cc_final: 0.8536 (mp0) REVERT: F 1835 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7210 (mt0) REVERT: F 1989 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: F 2071 GLU cc_start: 0.7800 (pp20) cc_final: 0.7537 (pp20) outliers start: 46 outliers final: 25 residues processed: 165 average time/residue: 0.6053 time to fit residues: 111.2153 Evaluate side-chains 152 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 1505 VAL Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1557 THR Chi-restraints excluded: chain E residue 1562 GLN Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1940 GLN Chi-restraints excluded: chain E residue 1974 VAL Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1428 LEU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1782 MET Chi-restraints excluded: chain F residue 1789 VAL Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1872 LEU Chi-restraints excluded: chain F residue 1922 THR Chi-restraints excluded: chain F residue 1974 VAL Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 0.0670 chunk 143 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2031 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.085239 restraints weight = 23697.421| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.48 r_work: 0.2929 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15745 Z= 0.141 Angle : 0.542 9.755 21502 Z= 0.270 Chirality : 0.042 0.172 2470 Planarity : 0.003 0.051 2754 Dihedral : 7.387 158.040 2279 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.16 % Allowed : 21.38 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.19), residues: 2012 helix: 0.83 (0.21), residues: 713 sheet: -0.84 (0.26), residues: 401 loop : 0.12 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F1552 TYR 0.022 0.001 TYR E 991 PHE 0.011 0.001 PHE E2109 TRP 0.026 0.001 TRP F1442 HIS 0.007 0.001 HIS F1553 Details of bonding type rmsd covalent geometry : bond 0.00343 (15745) covalent geometry : angle 0.54235 (21502) hydrogen bonds : bond 0.02982 ( 660) hydrogen bonds : angle 4.44966 ( 2013) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9223 (t0) cc_final: 0.8935 (t0) REVERT: E 1458 ASN cc_start: 0.8948 (m-40) cc_final: 0.8628 (m110) REVERT: E 1515 ARG cc_start: 0.7900 (mmm-85) cc_final: 0.7646 (mmt-90) REVERT: E 1518 LEU cc_start: 0.9085 (mt) cc_final: 0.8652 (tm) REVERT: E 1596 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8394 (m-30) REVERT: E 1614 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.7126 (pp-130) REVERT: E 1725 ASP cc_start: 0.7980 (t70) cc_final: 0.7735 (m-30) REVERT: E 1797 ASP cc_start: 0.8816 (p0) cc_final: 0.8600 (p0) REVERT: E 1835 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: E 1996 TYR cc_start: 0.8108 (t80) cc_final: 0.7888 (t80) REVERT: E 2012 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8391 (mp0) REVERT: F 862 TYR cc_start: 0.8747 (m-80) cc_final: 0.8404 (m-80) REVERT: F 1023 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8617 (mtmm) REVERT: F 1071 ASP cc_start: 0.8683 (t0) cc_final: 0.8232 (t0) REVERT: F 1432 LEU cc_start: 0.9331 (mm) cc_final: 0.9039 (mm) REVERT: F 1520 GLU cc_start: 0.8738 (mp0) cc_final: 0.8508 (mp0) REVERT: F 1666 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7698 (mmp80) REVERT: F 1835 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7171 (mt0) REVERT: F 1989 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7058 (mp10) REVERT: F 2071 GLU cc_start: 0.7772 (pp20) cc_final: 0.7479 (pp20) outliers start: 48 outliers final: 29 residues processed: 173 average time/residue: 0.6241 time to fit residues: 120.2093 Evaluate side-chains 167 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 1505 VAL Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1557 THR Chi-restraints excluded: chain E residue 1562 GLN Chi-restraints excluded: chain E residue 1596 ASP Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1940 GLN Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1048 LEU Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1428 LEU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1789 VAL Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1843 MET Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1872 LEU Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1886 SER Chi-restraints excluded: chain F residue 1974 VAL Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 183 optimal weight: 0.0020 chunk 143 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2031 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.086832 restraints weight = 23913.778| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.49 r_work: 0.2947 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15745 Z= 0.120 Angle : 0.536 9.415 21502 Z= 0.268 Chirality : 0.042 0.194 2470 Planarity : 0.003 0.052 2754 Dihedral : 7.320 162.526 2279 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.63 % Allowed : 22.04 % Favored : 75.33 % 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: 0.18 (0.20), residues: 2012 helix: 0.87 (0.21), residues: 710 sheet: -0.75 (0.26), residues: 405 loop : 0.10 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F1552 TYR 0.021 0.001 TYR E 991 PHE 0.021 0.001 PHE E2109 TRP 0.031 0.001 TRP F1442 HIS 0.005 0.001 HIS E1674 Details of bonding type rmsd covalent geometry : bond 0.00294 (15745) covalent geometry : angle 0.53649 (21502) hydrogen bonds : bond 0.02923 ( 660) hydrogen bonds : angle 4.37607 ( 2013) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9216 (t0) cc_final: 0.8948 (t0) REVERT: E 1458 ASN cc_start: 0.8956 (m-40) cc_final: 0.8631 (m110) REVERT: E 1515 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7617 (mmt-90) REVERT: E 1517 PHE cc_start: 0.8267 (m-80) cc_final: 0.8028 (m-80) REVERT: E 1518 LEU cc_start: 0.9061 (mt) cc_final: 0.8637 (tm) REVERT: E 1596 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8364 (m-30) REVERT: E 1614 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.7153 (pp-130) REVERT: E 1725 ASP cc_start: 0.7987 (t70) cc_final: 0.7721 (m-30) REVERT: E 1797 ASP cc_start: 0.8808 (p0) cc_final: 0.8591 (p0) REVERT: E 1835 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: E 1996 TYR cc_start: 0.7996 (t80) cc_final: 0.7636 (t80) REVERT: E 2012 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8386 (mp0) REVERT: F 862 TYR cc_start: 0.8740 (m-80) cc_final: 0.8339 (m-80) REVERT: F 915 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8887 (mt-10) REVERT: F 1023 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8613 (mtmm) REVERT: F 1071 ASP cc_start: 0.8703 (t0) cc_final: 0.8290 (t0) REVERT: F 1432 LEU cc_start: 0.9322 (mm) cc_final: 0.9057 (mm) REVERT: F 1520 GLU cc_start: 0.8721 (mp0) cc_final: 0.8487 (mp0) REVERT: F 1666 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7689 (mmp80) REVERT: F 1835 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7082 (mt0) REVERT: F 1989 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7069 (mp10) REVERT: F 1993 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8049 (mmmt) REVERT: F 2071 GLU cc_start: 0.7723 (pp20) cc_final: 0.7416 (pp20) outliers start: 40 outliers final: 27 residues processed: 173 average time/residue: 0.6356 time to fit residues: 122.3565 Evaluate side-chains 163 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 1505 VAL Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1557 THR Chi-restraints excluded: chain E residue 1562 GLN Chi-restraints excluded: chain E residue 1596 ASP Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1940 GLN Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1048 LEU Chi-restraints excluded: chain F residue 1052 VAL Chi-restraints excluded: chain F residue 1428 LEU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1789 VAL Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1843 MET Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1872 LEU Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 197 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 135 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2059 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.083163 restraints weight = 23815.567| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.47 r_work: 0.2892 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15745 Z= 0.209 Angle : 0.594 12.303 21502 Z= 0.295 Chirality : 0.044 0.177 2470 Planarity : 0.004 0.051 2754 Dihedral : 7.467 166.224 2279 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.57 % Allowed : 22.63 % Favored : 74.80 % 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: 0.10 (0.20), residues: 2012 helix: 0.75 (0.20), residues: 712 sheet: -0.90 (0.27), residues: 390 loop : 0.16 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F1515 TYR 0.027 0.002 TYR E 991 PHE 0.010 0.001 PHE F1791 TRP 0.037 0.001 TRP F1442 HIS 0.005 0.001 HIS F1553 Details of bonding type rmsd covalent geometry : bond 0.00504 (15745) covalent geometry : angle 0.59441 (21502) hydrogen bonds : bond 0.03278 ( 660) hydrogen bonds : angle 4.55138 ( 2013) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9228 (t0) cc_final: 0.8949 (t0) REVERT: E 1458 ASN cc_start: 0.8961 (m-40) cc_final: 0.8618 (m110) REVERT: E 1515 ARG cc_start: 0.7957 (mmm-85) cc_final: 0.7712 (mmt-90) REVERT: E 1518 LEU cc_start: 0.9110 (mt) cc_final: 0.8673 (tm) REVERT: E 1596 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8420 (m-30) REVERT: E 1614 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.7122 (pp-130) REVERT: E 1725 ASP cc_start: 0.7997 (t70) cc_final: 0.7740 (m-30) REVERT: E 1797 ASP cc_start: 0.8860 (p0) cc_final: 0.8640 (p0) REVERT: E 1835 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: E 1996 TYR cc_start: 0.8152 (t80) cc_final: 0.7946 (t80) REVERT: E 2012 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8398 (mp0) REVERT: F 1023 LYS cc_start: 0.8929 (mtmt) cc_final: 0.8623 (mtmm) REVERT: F 1071 ASP cc_start: 0.8684 (t0) cc_final: 0.8264 (t0) REVERT: F 1240 MET cc_start: 0.6637 (tpp) cc_final: 0.6061 (tpp) REVERT: F 1432 LEU cc_start: 0.9325 (mm) cc_final: 0.8860 (mm) REVERT: F 1666 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7699 (mmp80) REVERT: F 1835 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7269 (mt0) REVERT: F 1989 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: F 2071 GLU cc_start: 0.7768 (pp20) cc_final: 0.7477 (pp20) outliers start: 39 outliers final: 29 residues processed: 167 average time/residue: 0.6203 time to fit residues: 115.8220 Evaluate side-chains 166 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 1505 VAL Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1557 THR Chi-restraints excluded: chain E residue 1562 GLN Chi-restraints excluded: chain E residue 1596 ASP Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1940 GLN Chi-restraints excluded: chain E residue 1974 VAL Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1048 LEU Chi-restraints excluded: chain F residue 1052 VAL Chi-restraints excluded: chain F residue 1428 LEU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1602 GLU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1782 MET Chi-restraints excluded: chain F residue 1789 VAL Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1872 LEU Chi-restraints excluded: chain F residue 1974 VAL Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.5878 > 50: distance: 76 - 118: 26.990 distance: 79 - 115: 34.217 distance: 105 - 107: 16.193 distance: 107 - 108: 13.273 distance: 108 - 109: 12.581 distance: 108 - 111: 11.883 distance: 109 - 110: 39.164 distance: 109 - 115: 34.454 distance: 111 - 112: 11.555 distance: 112 - 113: 11.826 distance: 112 - 114: 14.908 distance: 115 - 116: 9.640 distance: 116 - 117: 43.534 distance: 116 - 119: 8.534 distance: 117 - 118: 14.355 distance: 117 - 125: 10.880 distance: 119 - 120: 32.205 distance: 120 - 121: 38.732 distance: 120 - 122: 10.812 distance: 121 - 123: 18.387 distance: 122 - 124: 13.608 distance: 123 - 124: 26.397 distance: 125 - 126: 3.611 distance: 126 - 127: 12.587 distance: 126 - 129: 12.395 distance: 127 - 128: 12.171 distance: 127 - 132: 6.456 distance: 129 - 130: 20.672 distance: 129 - 131: 32.202 distance: 132 - 133: 12.342 distance: 133 - 134: 31.089 distance: 133 - 136: 10.965 distance: 134 - 135: 7.747 distance: 134 - 141: 20.457 distance: 136 - 137: 26.350 distance: 137 - 138: 21.929 distance: 138 - 139: 17.782 distance: 138 - 140: 15.690 distance: 141 - 142: 4.212 distance: 142 - 143: 21.606 distance: 142 - 145: 20.715 distance: 143 - 144: 14.465 distance: 143 - 147: 7.771 distance: 145 - 146: 13.435 distance: 147 - 148: 12.773 distance: 148 - 149: 14.556 distance: 148 - 151: 17.788 distance: 149 - 150: 14.612 distance: 149 - 152: 14.322 distance: 152 - 153: 17.003 distance: 152 - 158: 14.473 distance: 153 - 154: 6.157 distance: 153 - 156: 6.417 distance: 154 - 155: 18.455 distance: 154 - 159: 13.291 distance: 156 - 157: 21.038 distance: 157 - 158: 8.135 distance: 159 - 160: 12.221 distance: 160 - 161: 15.125 distance: 160 - 163: 12.033 distance: 161 - 162: 11.834 distance: 161 - 170: 7.739 distance: 164 - 165: 6.220 distance: 165 - 166: 5.795 distance: 166 - 167: 8.691 distance: 167 - 168: 10.768 distance: 167 - 169: 12.148 distance: 170 - 171: 8.775 distance: 171 - 172: 6.905 distance: 171 - 174: 7.500 distance: 172 - 173: 14.148 distance: 172 - 181: 11.112 distance: 174 - 175: 7.044 distance: 175 - 176: 6.543 distance: 176 - 177: 5.650 distance: 177 - 178: 8.693 distance: 178 - 179: 9.479 distance: 178 - 180: 9.373 distance: 182 - 183: 12.728 distance: 182 - 185: 17.716 distance: 183 - 184: 8.448 distance: 183 - 186: 8.979