Starting phenix.real_space_refine on Sat Jun 14 18:41:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b80_44330/06_2025/9b80_44330.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b80_44330/06_2025/9b80_44330.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b80_44330/06_2025/9b80_44330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b80_44330/06_2025/9b80_44330.map" model { file = "/net/cci-nas-00/data/ceres_data/9b80_44330/06_2025/9b80_44330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b80_44330/06_2025/9b80_44330.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 10262 2.51 5 N 2838 2.21 5 O 2992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16154 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8077 Classifications: {'peptide': 1096} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 54, 'TRANS': 1041} Chain breaks: 5 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 390 Unresolved non-hydrogen angles: 488 Unresolved non-hydrogen dihedrals: 322 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 245 Restraints were copied for chains: B Time building chain proxies: 19.20, per 1000 atoms: 1.19 Number of scatterers: 16154 At special positions: 0 Unit cell: (127.755, 204.575, 88.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2992 8.00 N 2838 7.00 C 10262 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: 3.88 Conformation dependent library (CDL) restraints added in 2.1 seconds 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 26 sheets defined 36.9% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 872 through 876 Processing helix chain 'A' and resid 887 through 904 removed outlier: 3.868A pdb=" N TYR A 891 " --> pdb=" O PRO A 887 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 892 " --> pdb=" O ALA A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 965 through 970 Processing helix chain 'A' and resid 987 through 998 Processing helix chain 'A' and resid 1003 through 1006 Processing helix chain 'A' and resid 1025 through 1041 removed outlier: 3.943A pdb=" N GLY A1040 " --> pdb=" O MET A1036 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1065 Processing helix chain 'A' and resid 1132 through 1144 removed outlier: 3.736A pdb=" N GLU A1136 " --> pdb=" O ALA A1132 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN A1139 " --> pdb=" O GLN A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1235 removed outlier: 4.417A pdb=" N LYS A1225 " --> pdb=" O SER A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1254 Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1282 through 1287 Processing helix chain 'A' and resid 1380 through 1385 removed outlier: 3.519A pdb=" N VAL A1384 " --> pdb=" O LEU A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1422 removed outlier: 4.203A pdb=" N PHE A1422 " --> pdb=" O ASP A1419 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1419 through 1422' Processing helix chain 'A' and resid 1423 through 1432 removed outlier: 4.167A pdb=" N SER A1427 " --> pdb=" O ARG A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1462 removed outlier: 4.021A pdb=" N ARG A1462 " --> pdb=" O ASN A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1499 removed outlier: 3.802A pdb=" N LYS A1495 " --> pdb=" O ALA A1491 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A1496 " --> pdb=" O GLU A1492 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A1499 " --> pdb=" O LYS A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1581 Processing helix chain 'A' and resid 1584 through 1588 Processing helix chain 'A' and resid 1629 through 1631 No H-bonds generated for 'chain 'A' and resid 1629 through 1631' Processing helix chain 'A' and resid 1641 through 1646 Processing helix chain 'A' and resid 1648 through 1660 Processing helix chain 'A' and resid 1678 through 1692 Processing helix chain 'A' and resid 1701 through 1712 Processing helix chain 'A' and resid 1716 through 1718 No H-bonds generated for 'chain 'A' and resid 1716 through 1718' Processing helix chain 'A' and resid 1726 through 1736 removed outlier: 4.292A pdb=" N GLN A1730 " --> pdb=" O THR A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1752 through 1758 Processing helix chain 'A' and resid 1771 through 1776 Processing helix chain 'A' and resid 1783 through 1788 Processing helix chain 'A' and resid 1795 through 1801 removed outlier: 3.798A pdb=" N ALA A1798 " --> pdb=" O LEU A1795 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A1801 " --> pdb=" O ALA A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1820 removed outlier: 3.828A pdb=" N TRP A1807 " --> pdb=" O SER A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1845 removed outlier: 3.752A pdb=" N GLN A1845 " --> pdb=" O ARG A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1907 removed outlier: 3.832A pdb=" N GLU A1899 " --> pdb=" O GLY A1895 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1935 Processing helix chain 'A' and resid 1948 through 1963 removed outlier: 3.626A pdb=" N LEU A1962 " --> pdb=" O GLU A1958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1980 through 1984 Processing helix chain 'A' and resid 1985 through 1992 removed outlier: 3.614A pdb=" N GLN A1989 " --> pdb=" O PRO A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1993 through 2010 removed outlier: 4.027A pdb=" N SER A1997 " --> pdb=" O LYS A1993 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR A1999 " --> pdb=" O LYS A1995 " (cutoff:3.500A) Processing helix chain 'A' and resid 2023 through 2025 No H-bonds generated for 'chain 'A' and resid 2023 through 2025' Processing helix chain 'A' and resid 2031 through 2051 removed outlier: 3.513A pdb=" N ALA A2040 " --> pdb=" O PHE A2036 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS A2045 " --> pdb=" O MET A2041 " (cutoff:3.500A) Processing helix chain 'A' and resid 2087 through 2100 removed outlier: 3.918A pdb=" N ASN A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 Processing helix chain 'B' and resid 887 through 904 removed outlier: 3.867A pdb=" N TYR B 891 " --> pdb=" O PRO B 887 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU B 892 " --> pdb=" O ALA B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 965 through 970 Processing helix chain 'B' and resid 987 through 998 Processing helix chain 'B' and resid 1003 through 1006 Processing helix chain 'B' and resid 1025 through 1041 removed outlier: 3.942A pdb=" N GLY B1040 " --> pdb=" O MET B1036 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER B1041 " --> pdb=" O SER B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1065 Processing helix chain 'B' and resid 1132 through 1144 removed outlier: 3.735A pdb=" N GLU B1136 " --> pdb=" O ALA B1132 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B1139 " --> pdb=" O GLN B1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 1221 through 1235 removed outlier: 4.417A pdb=" N LYS B1225 " --> pdb=" O SER B1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 1251 through 1254 Processing helix chain 'B' and resid 1255 through 1260 Processing helix chain 'B' and resid 1282 through 1287 Processing helix chain 'B' and resid 1380 through 1385 removed outlier: 3.518A pdb=" N VAL B1384 " --> pdb=" O LEU B1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 1423 through 1432 removed outlier: 4.167A pdb=" N SER B1427 " --> pdb=" O ARG B1423 " (cutoff:3.500A) Processing helix chain 'B' and resid 1452 through 1462 removed outlier: 4.021A pdb=" N ARG B1462 " --> pdb=" O ASN B1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 1489 through 1499 removed outlier: 3.803A pdb=" N LYS B1495 " --> pdb=" O ALA B1491 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B1496 " --> pdb=" O GLU B1492 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY B1499 " --> pdb=" O LYS B1495 " (cutoff:3.500A) Processing helix chain 'B' and resid 1572 through 1581 Processing helix chain 'B' and resid 1584 through 1588 Processing helix chain 'B' and resid 1629 through 1631 No H-bonds generated for 'chain 'B' and resid 1629 through 1631' Processing helix chain 'B' and resid 1641 through 1646 Processing helix chain 'B' and resid 1648 through 1660 Processing helix chain 'B' and resid 1678 through 1692 Processing helix chain 'B' and resid 1701 through 1712 Processing helix chain 'B' and resid 1716 through 1718 No H-bonds generated for 'chain 'B' and resid 1716 through 1718' Processing helix chain 'B' and resid 1726 through 1736 removed outlier: 4.292A pdb=" N GLN B1730 " --> pdb=" O THR B1726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1752 through 1758 Processing helix chain 'B' and resid 1771 through 1776 Processing helix chain 'B' and resid 1783 through 1788 Processing helix chain 'B' and resid 1795 through 1801 removed outlier: 3.798A pdb=" N ALA B1798 " --> pdb=" O LEU B1795 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B1801 " --> pdb=" O ALA B1798 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1820 removed outlier: 3.827A pdb=" N TRP B1807 " --> pdb=" O SER B1803 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1845 removed outlier: 3.752A pdb=" N GLN B1845 " --> pdb=" O ARG B1841 " (cutoff:3.500A) Processing helix chain 'B' and resid 1895 through 1907 removed outlier: 3.832A pdb=" N GLU B1899 " --> pdb=" O GLY B1895 " (cutoff:3.500A) Processing helix chain 'B' and resid 1922 through 1935 Processing helix chain 'B' and resid 1948 through 1963 removed outlier: 3.627A pdb=" N LEU B1962 " --> pdb=" O GLU B1958 " (cutoff:3.500A) Processing helix chain 'B' and resid 1980 through 1984 Processing helix chain 'B' and resid 1985 through 1992 removed outlier: 3.614A pdb=" N GLN B1989 " --> pdb=" O PRO B1985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1993 through 2010 removed outlier: 4.026A pdb=" N SER B1997 " --> pdb=" O LYS B1993 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B1999 " --> pdb=" O LYS B1995 " (cutoff:3.500A) Processing helix chain 'B' and resid 2023 through 2025 No H-bonds generated for 'chain 'B' and resid 2023 through 2025' Processing helix chain 'B' and resid 2031 through 2051 removed outlier: 3.514A pdb=" N ALA B2040 " --> pdb=" O PHE B2036 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS B2045 " --> pdb=" O MET B2041 " (cutoff:3.500A) Processing helix chain 'B' and resid 2087 through 2100 removed outlier: 3.918A pdb=" N ASN B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 860 through 864 removed outlier: 3.613A pdb=" N VAL A 931 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE A 944 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER A 955 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 946 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS A 957 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASP A 916 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR A 959 " --> pdb=" O PHE A 914 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE A 914 " --> pdb=" O TYR A 959 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR A1053 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A 918 " --> pdb=" O ARG A1051 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG A1051 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 985 through 986 removed outlier: 6.628A pdb=" N ILE A1008 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A1021 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A1010 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLU A1100 " --> pdb=" O PRO A1049 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 878 through 879 removed outlier: 3.925A pdb=" N THR A 879 " --> pdb=" O ASP A1000 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A1000 " --> pdb=" O THR A 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1113 through 1116 removed outlier: 5.778A pdb=" N SER A1886 " --> pdb=" O VAL A1965 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A1967 " --> pdb=" O SER A1886 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1113 through 1116 removed outlier: 4.617A pdb=" N VAL A2110 " --> pdb=" O LEU A2084 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1118 through 1121 removed outlier: 7.606A pdb=" N TYR A1506 " --> pdb=" O LEU A1473 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER A1475 " --> pdb=" O TYR A1506 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL A1441 " --> pdb=" O ARG A1470 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A1472 " --> pdb=" O VAL A1441 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A1476 " --> pdb=" O ALA A1445 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A1413 " --> pdb=" O TRP A1442 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LYS A1444 " --> pdb=" O ILE A1413 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU A1415 " --> pdb=" O LYS A1444 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1123 through 1127 removed outlier: 5.462A pdb=" N THR A1123 " --> pdb=" O VAL A1389 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A1391 " --> pdb=" O THR A1123 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLU A1125 " --> pdb=" O LEU A1391 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS A1393 " --> pdb=" O GLU A1125 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU A1402 " --> pdb=" O VAL A1389 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A1391 " --> pdb=" O LEU A1400 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A1400 " --> pdb=" O LEU A1391 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS A1315 " --> pdb=" O PHE A1401 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1239 through 1245 Processing sheet with id=AA9, first strand: chain 'A' and resid 1525 through 1528 Processing sheet with id=AB1, first strand: chain 'A' and resid 1531 through 1535 Processing sheet with id=AB2, first strand: chain 'A' and resid 1625 through 1628 removed outlier: 6.767A pdb=" N SER A1604 " --> pdb=" O TYR A1567 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA A1569 " --> pdb=" O GLU A1602 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLU A1602 " --> pdb=" O ALA A1569 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1625 through 1628 removed outlier: 5.866A pdb=" N THR A1829 " --> pdb=" O VAL A1853 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLN A1855 " --> pdb=" O THR A1829 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE A1831 " --> pdb=" O GLN A1855 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1720 through 1722 removed outlier: 8.154A pdb=" N ALA A1721 " --> pdb=" O VAL A1695 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR A1697 " --> pdb=" O ALA A1721 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A1670 " --> pdb=" O LEU A1743 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LEU A1745 " --> pdb=" O THR A1670 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A1672 " --> pdb=" O LEU A1745 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP A1742 " --> pdb=" O ARG A1765 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU A1767 " --> pdb=" O ASP A1742 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A1744 " --> pdb=" O LEU A1767 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N THR A1790 " --> pdb=" O THR A1762 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY A1764 " --> pdb=" O THR A1790 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N HIS A1792 " --> pdb=" O GLY A1764 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE A1766 " --> pdb=" O HIS A1792 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N THR B1790 " --> pdb=" O THR B1762 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY B1764 " --> pdb=" O THR B1790 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N HIS B1792 " --> pdb=" O GLY B1764 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE B1766 " --> pdb=" O HIS B1792 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP B1742 " --> pdb=" O ARG B1765 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU B1767 " --> pdb=" O ASP B1742 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL B1744 " --> pdb=" O LEU B1767 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B1670 " --> pdb=" O LEU B1743 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N LEU B1745 " --> pdb=" O THR B1670 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B1672 " --> pdb=" O LEU B1745 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ALA B1721 " --> pdb=" O VAL B1695 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR B1697 " --> pdb=" O ALA B1721 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1779 through 1781 Processing sheet with id=AB6, first strand: chain 'B' and resid 860 through 864 removed outlier: 3.613A pdb=" N VAL B 931 " --> pdb=" O ILE B 864 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE B 944 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER B 955 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL B 946 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS B 957 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASP B 916 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR B 959 " --> pdb=" O PHE B 914 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE B 914 " --> pdb=" O TYR B 959 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR B1053 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 918 " --> pdb=" O ARG B1051 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG B1051 " --> pdb=" O VAL B 918 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 985 through 986 removed outlier: 6.627A pdb=" N ILE B1008 " --> pdb=" O LEU B1021 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B1021 " --> pdb=" O ILE B1008 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B1010 " --> pdb=" O ARG B1019 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLU B1100 " --> pdb=" O PRO B1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 878 through 879 removed outlier: 3.924A pdb=" N THR B 879 " --> pdb=" O ASP B1000 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B1000 " --> pdb=" O THR B 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 1113 through 1116 removed outlier: 5.778A pdb=" N SER B1886 " --> pdb=" O VAL B1965 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B1967 " --> pdb=" O SER B1886 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1113 through 1116 removed outlier: 4.617A pdb=" N VAL B2110 " --> pdb=" O LEU B2084 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1118 through 1121 removed outlier: 7.606A pdb=" N TYR B1506 " --> pdb=" O LEU B1473 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER B1475 " --> pdb=" O TYR B1506 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B1441 " --> pdb=" O ARG B1470 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B1472 " --> pdb=" O VAL B1441 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN B1476 " --> pdb=" O ALA B1445 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B1413 " --> pdb=" O TRP B1442 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LYS B1444 " --> pdb=" O ILE B1413 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU B1415 " --> pdb=" O LYS B1444 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1123 through 1127 removed outlier: 5.461A pdb=" N THR B1123 " --> pdb=" O VAL B1389 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B1391 " --> pdb=" O THR B1123 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLU B1125 " --> pdb=" O LEU B1391 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS B1393 " --> pdb=" O GLU B1125 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU B1402 " --> pdb=" O VAL B1389 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU B1391 " --> pdb=" O LEU B1400 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B1400 " --> pdb=" O LEU B1391 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS B1315 " --> pdb=" O PHE B1401 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1239 through 1245 Processing sheet with id=AC5, first strand: chain 'B' and resid 1525 through 1528 Processing sheet with id=AC6, first strand: chain 'B' and resid 1531 through 1535 Processing sheet with id=AC7, first strand: chain 'B' and resid 1625 through 1628 removed outlier: 6.767A pdb=" N SER B1604 " --> pdb=" O TYR B1567 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA B1569 " --> pdb=" O GLU B1602 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLU B1602 " --> pdb=" O ALA B1569 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1625 through 1628 removed outlier: 5.866A pdb=" N THR B1829 " --> pdb=" O VAL B1853 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLN B1855 " --> pdb=" O THR B1829 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE B1831 " --> pdb=" O GLN B1855 " (cutoff:3.500A) 734 hydrogen bonds defined for protein. 1968 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: 6.93 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5400 1.34 - 1.46: 3543 1.46 - 1.58: 7453 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 16486 Sorted by residual: bond pdb=" N MET A1235 " pdb=" CA MET A1235 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.30e-02 5.92e+03 6.96e+00 bond pdb=" N MET B1235 " pdb=" CA MET B1235 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.30e-02 5.92e+03 6.88e+00 bond pdb=" N ASN B1234 " pdb=" CA ASN B1234 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.30e-02 5.92e+03 6.35e+00 bond pdb=" N ASN A1234 " pdb=" CA ASN A1234 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.30e-02 5.92e+03 6.30e+00 bond pdb=" N SER A1394 " pdb=" CA SER A1394 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.17e-02 7.31e+03 6.14e+00 ... (remaining 16481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 21755 1.35 - 2.71: 558 2.71 - 4.06: 107 4.06 - 5.42: 24 5.42 - 6.77: 8 Bond angle restraints: 22452 Sorted by residual: angle pdb=" N PHE A1395 " pdb=" CA PHE A1395 " pdb=" C PHE A1395 " ideal model delta sigma weight residual 113.02 107.40 5.62 1.20e+00 6.94e-01 2.19e+01 angle pdb=" N PHE B1395 " pdb=" CA PHE B1395 " pdb=" C PHE B1395 " ideal model delta sigma weight residual 113.02 107.41 5.61 1.20e+00 6.94e-01 2.19e+01 angle pdb=" N TYR A1396 " pdb=" CA TYR A1396 " pdb=" C TYR A1396 " ideal model delta sigma weight residual 113.17 108.69 4.48 1.26e+00 6.30e-01 1.27e+01 angle pdb=" C GLU A1750 " pdb=" N GLU A1751 " pdb=" CA GLU A1751 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C GLU B1750 " pdb=" N GLU B1751 " pdb=" CA GLU B1751 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.25e+01 ... (remaining 22447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 8972 16.40 - 32.79: 590 32.79 - 49.19: 130 49.19 - 65.59: 38 65.59 - 81.98: 20 Dihedral angle restraints: 9750 sinusoidal: 3500 harmonic: 6250 Sorted by residual: dihedral pdb=" CA VAL A1648 " pdb=" C VAL A1648 " pdb=" N PRO A1649 " pdb=" CA PRO A1649 " ideal model delta harmonic sigma weight residual 180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA VAL B1648 " pdb=" C VAL B1648 " pdb=" N PRO B1649 " pdb=" CA PRO B1649 " ideal model delta harmonic sigma weight residual -180.00 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP A1418 " pdb=" CB ASP A1418 " pdb=" CG ASP A1418 " pdb=" OD1 ASP A1418 " ideal model delta sinusoidal sigma weight residual -30.00 -89.37 59.37 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 9747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1803 0.036 - 0.071: 552 0.071 - 0.107: 191 0.107 - 0.142: 56 0.142 - 0.178: 12 Chirality restraints: 2614 Sorted by residual: chirality pdb=" CA TYR A1396 " pdb=" N TYR A1396 " pdb=" C TYR A1396 " pdb=" CB TYR A1396 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA TYR B1396 " pdb=" N TYR B1396 " pdb=" C TYR B1396 " pdb=" CB TYR B1396 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA PRO A1649 " pdb=" N PRO A1649 " pdb=" C PRO A1649 " pdb=" CB PRO A1649 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 2611 not shown) Planarity restraints: 2902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B1393 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C LYS B1393 " 0.038 2.00e-02 2.50e+03 pdb=" O LYS B1393 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B1394 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1393 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C LYS A1393 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS A1393 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A1394 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1212 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A1213 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1213 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1213 " 0.026 5.00e-02 4.00e+02 ... (remaining 2899 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3117 2.78 - 3.31: 14917 3.31 - 3.84: 25956 3.84 - 4.37: 29268 4.37 - 4.90: 51565 Nonbonded interactions: 124823 Sorted by model distance: nonbonded pdb=" O HIS B1516 " pdb=" ND1 HIS B1516 " model vdw 2.249 3.120 nonbonded pdb=" O HIS A1516 " pdb=" ND1 HIS A1516 " model vdw 2.249 3.120 nonbonded pdb=" OD1 ASN A2001 " pdb=" NH2 ARG A2004 " model vdw 2.271 3.120 nonbonded pdb=" OD1 ASN B2001 " pdb=" NH2 ARG B2004 " model vdw 2.271 3.120 nonbonded pdb=" OG SER B 867 " pdb=" OG SER B 870 " model vdw 2.313 3.040 ... (remaining 124818 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 49.750 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.003 0.043 16486 Z= 0.160 Angle : 0.558 6.771 22452 Z= 0.329 Chirality : 0.042 0.178 2614 Planarity : 0.003 0.047 2902 Dihedral : 12.820 81.985 5730 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 2168 helix: 0.65 (0.20), residues: 726 sheet: 0.50 (0.28), residues: 408 loop : -1.00 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1807 HIS 0.003 0.001 HIS A1093 PHE 0.009 0.001 PHE A1117 TYR 0.019 0.001 TYR B 991 ARG 0.004 0.000 ARG A1462 Details of bonding type rmsd hydrogen bonds : bond 0.20305 ( 694) hydrogen bonds : angle 6.68379 ( 1968) covalent geometry : bond 0.00277 (16486) covalent geometry : angle 0.55847 (22452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.758 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 1.0518 time to fit residues: 83.2717 Evaluate side-chains 52 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 HIS B1763 HIS ** B1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.109362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066504 restraints weight = 37108.681| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.35 r_work: 0.2944 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16486 Z= 0.160 Angle : 0.536 6.602 22452 Z= 0.283 Chirality : 0.042 0.169 2614 Planarity : 0.004 0.044 2902 Dihedral : 4.007 19.768 2336 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.25 % Allowed : 5.36 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 2168 helix: 0.65 (0.20), residues: 738 sheet: 0.29 (0.28), residues: 392 loop : -0.83 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1807 HIS 0.006 0.001 HIS A1098 PHE 0.015 0.001 PHE B 969 TYR 0.016 0.002 TYR B 991 ARG 0.003 0.000 ARG A2043 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 694) hydrogen bonds : angle 4.80157 ( 1968) covalent geometry : bond 0.00369 (16486) covalent geometry : angle 0.53629 (22452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 1.594 Fit side-chains REVERT: A 1516 HIS cc_start: 0.8323 (t-90) cc_final: 0.7931 (t70) REVERT: A 1843 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8005 (ttt) REVERT: B 1516 HIS cc_start: 0.8392 (t-90) cc_final: 0.7342 (t70) outliers start: 4 outliers final: 0 residues processed: 62 average time/residue: 1.0368 time to fit residues: 75.4539 Evaluate side-chains 55 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1843 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 79 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 126 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 35 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 30.0000 chunk 193 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1763 HIS ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1970 ASN B1122 HIS ** B1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.109171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065399 restraints weight = 36807.164| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.19 r_work: 0.2961 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 16486 Z= 0.131 Angle : 0.496 7.169 22452 Z= 0.258 Chirality : 0.041 0.158 2614 Planarity : 0.003 0.042 2902 Dihedral : 3.908 19.626 2336 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.11 % Allowed : 7.70 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 2168 helix: 0.81 (0.20), residues: 744 sheet: 0.24 (0.27), residues: 392 loop : -0.75 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1807 HIS 0.005 0.001 HIS B1093 PHE 0.011 0.001 PHE A1785 TYR 0.015 0.001 TYR A 991 ARG 0.003 0.000 ARG A2043 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 694) hydrogen bonds : angle 4.42891 ( 1968) covalent geometry : bond 0.00317 (16486) covalent geometry : angle 0.49594 (22452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 1.781 Fit side-chains REVERT: A 1070 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8200 (pp30) REVERT: A 1503 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6826 (mmt) REVERT: A 1516 HIS cc_start: 0.8177 (t-90) cc_final: 0.7932 (t70) REVERT: B 1072 LYS cc_start: 0.9356 (mmmm) cc_final: 0.9135 (mppt) REVERT: B 1516 HIS cc_start: 0.8228 (t-90) cc_final: 0.7329 (t70) outliers start: 18 outliers final: 3 residues processed: 74 average time/residue: 1.2155 time to fit residues: 105.1808 Evaluate side-chains 60 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 1503 MET Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 1260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 89 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 169 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 27 optimal weight: 30.0000 chunk 116 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 157 optimal weight: 30.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 HIS B1938 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.106542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.062728 restraints weight = 36909.026| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.14 r_work: 0.2887 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16486 Z= 0.243 Angle : 0.590 6.635 22452 Z= 0.309 Chirality : 0.045 0.173 2614 Planarity : 0.004 0.041 2902 Dihedral : 4.335 20.379 2336 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.42 % Allowed : 9.11 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2168 helix: 0.63 (0.20), residues: 748 sheet: 0.25 (0.28), residues: 360 loop : -0.88 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1807 HIS 0.005 0.001 HIS A1093 PHE 0.017 0.002 PHE A1785 TYR 0.022 0.002 TYR B1567 ARG 0.003 0.001 ARG B1841 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 694) hydrogen bonds : angle 4.69861 ( 1968) covalent geometry : bond 0.00581 (16486) covalent geometry : angle 0.59041 (22452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 1.969 Fit side-chains REVERT: A 989 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8803 (pm20) REVERT: A 1503 MET cc_start: 0.7054 (mpt) cc_final: 0.6703 (mmt) REVERT: A 1516 HIS cc_start: 0.8044 (t-90) cc_final: 0.7787 (t70) REVERT: A 1873 MET cc_start: 0.7982 (ttp) cc_final: 0.7682 (ttm) REVERT: B 989 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8835 (pm20) REVERT: B 1072 LYS cc_start: 0.9325 (mmmm) cc_final: 0.9118 (mppt) outliers start: 23 outliers final: 13 residues processed: 73 average time/residue: 1.0627 time to fit residues: 92.1286 Evaluate side-chains 69 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1773 ASP Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1773 ASP Chi-restraints excluded: chain B residue 2105 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 43 optimal weight: 20.0000 chunk 175 optimal weight: 0.0770 chunk 145 optimal weight: 0.0020 chunk 180 optimal weight: 0.0170 chunk 148 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 210 optimal weight: 0.2980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1855 GLN A1938 GLN B1855 GLN B1970 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.109473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066069 restraints weight = 37106.454| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.15 r_work: 0.2979 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16486 Z= 0.087 Angle : 0.469 7.144 22452 Z= 0.244 Chirality : 0.040 0.163 2614 Planarity : 0.003 0.040 2902 Dihedral : 3.820 19.316 2336 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.23 % Allowed : 9.91 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 2168 helix: 0.96 (0.20), residues: 744 sheet: 0.23 (0.27), residues: 370 loop : -0.65 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1424 HIS 0.003 0.001 HIS B1731 PHE 0.008 0.001 PHE B1422 TYR 0.012 0.001 TYR A 991 ARG 0.003 0.000 ARG A2043 Details of bonding type rmsd hydrogen bonds : bond 0.02866 ( 694) hydrogen bonds : angle 4.12628 ( 1968) covalent geometry : bond 0.00194 (16486) covalent geometry : angle 0.46932 (22452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 1.705 Fit side-chains REVERT: A 1070 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8175 (pp30) REVERT: A 1503 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6665 (mmt) REVERT: A 1516 HIS cc_start: 0.7793 (t-90) cc_final: 0.7514 (t70) REVERT: A 1873 MET cc_start: 0.7900 (ttp) cc_final: 0.7657 (ttm) outliers start: 20 outliers final: 10 residues processed: 72 average time/residue: 1.0722 time to fit residues: 91.3881 Evaluate side-chains 64 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1503 MET Chi-restraints excluded: chain A residue 1773 ASP Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1773 ASP Chi-restraints excluded: chain B residue 2105 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 49 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.107801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064023 restraints weight = 36829.295| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.17 r_work: 0.2925 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16486 Z= 0.157 Angle : 0.509 7.085 22452 Z= 0.264 Chirality : 0.042 0.162 2614 Planarity : 0.003 0.040 2902 Dihedral : 3.944 20.131 2336 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.60 % Allowed : 10.34 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 2168 helix: 0.93 (0.20), residues: 744 sheet: 0.18 (0.26), residues: 394 loop : -0.65 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1424 HIS 0.005 0.001 HIS A1093 PHE 0.012 0.001 PHE A1785 TYR 0.020 0.002 TYR B 991 ARG 0.002 0.000 ARG B2048 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 694) hydrogen bonds : angle 4.23906 ( 1968) covalent geometry : bond 0.00375 (16486) covalent geometry : angle 0.50852 (22452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 1.656 Fit side-chains REVERT: A 989 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8745 (pm20) REVERT: A 1070 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8199 (pp30) REVERT: A 1503 MET cc_start: 0.6962 (mpt) cc_final: 0.6657 (mmt) REVERT: A 1516 HIS cc_start: 0.7772 (t-90) cc_final: 0.7527 (t70) REVERT: A 1873 MET cc_start: 0.7951 (ttp) cc_final: 0.7658 (ttm) REVERT: B 989 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8753 (pm20) REVERT: B 1500 ASP cc_start: 0.8232 (p0) cc_final: 0.7943 (t70) REVERT: B 1503 MET cc_start: 0.6683 (mpt) cc_final: 0.6465 (mmt) outliers start: 26 outliers final: 16 residues processed: 79 average time/residue: 1.0579 time to fit residues: 97.3417 Evaluate side-chains 72 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1447 ASN Chi-restraints excluded: chain A residue 1622 LEU Chi-restraints excluded: chain A residue 1773 ASP Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1622 LEU Chi-restraints excluded: chain B residue 1773 ASP Chi-restraints excluded: chain B residue 2105 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 167 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 161 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.106540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062572 restraints weight = 37176.470| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.22 r_work: 0.2889 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16486 Z= 0.208 Angle : 0.561 7.037 22452 Z= 0.291 Chirality : 0.044 0.169 2614 Planarity : 0.004 0.040 2902 Dihedral : 4.227 19.903 2336 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.60 % Allowed : 11.02 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2168 helix: 0.80 (0.20), residues: 748 sheet: -0.01 (0.27), residues: 388 loop : -0.77 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1807 HIS 0.005 0.001 HIS B1093 PHE 0.015 0.001 PHE B1785 TYR 0.021 0.002 TYR A 991 ARG 0.003 0.000 ARG A1612 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 694) hydrogen bonds : angle 4.39434 ( 1968) covalent geometry : bond 0.00497 (16486) covalent geometry : angle 0.56078 (22452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 1.785 Fit side-chains REVERT: A 989 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8802 (pm20) REVERT: A 1516 HIS cc_start: 0.7736 (t-90) cc_final: 0.7509 (t70) REVERT: A 1873 MET cc_start: 0.7967 (ttp) cc_final: 0.7661 (ttm) REVERT: B 989 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8781 (pm20) REVERT: B 1070 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8226 (pp30) REVERT: B 1503 MET cc_start: 0.6738 (mpt) cc_final: 0.6514 (mmt) outliers start: 26 outliers final: 13 residues processed: 83 average time/residue: 1.0406 time to fit residues: 100.4309 Evaluate side-chains 68 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1447 ASN Chi-restraints excluded: chain A residue 1773 ASP Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1773 ASP Chi-restraints excluded: chain B residue 2105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 135 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 158 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.105794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.062079 restraints weight = 36672.613| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.24 r_work: 0.2870 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16486 Z= 0.255 Angle : 0.599 6.715 22452 Z= 0.312 Chirality : 0.045 0.173 2614 Planarity : 0.004 0.044 2902 Dihedral : 4.441 20.551 2336 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.72 % Allowed : 11.51 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.18), residues: 2168 helix: 0.64 (0.20), residues: 748 sheet: -0.21 (0.26), residues: 384 loop : -0.87 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1807 HIS 0.006 0.001 HIS A1093 PHE 0.016 0.002 PHE A1785 TYR 0.024 0.002 TYR A 991 ARG 0.003 0.001 ARG B1612 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 694) hydrogen bonds : angle 4.53965 ( 1968) covalent geometry : bond 0.00608 (16486) covalent geometry : angle 0.59920 (22452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 1.803 Fit side-chains REVERT: A 989 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8807 (pm20) REVERT: A 1070 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8245 (pp30) REVERT: A 1516 HIS cc_start: 0.7803 (t-90) cc_final: 0.7546 (t70) REVERT: A 1873 MET cc_start: 0.7928 (ttp) cc_final: 0.7601 (ttm) REVERT: B 989 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8818 (pm20) REVERT: B 1070 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8300 (pp30) REVERT: B 1235 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6639 (tmt) outliers start: 28 outliers final: 12 residues processed: 81 average time/residue: 1.0078 time to fit residues: 95.2842 Evaluate side-chains 68 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1447 ASN Chi-restraints excluded: chain A residue 1773 ASP Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1235 MET Chi-restraints excluded: chain B residue 1665 VAL Chi-restraints excluded: chain B residue 1773 ASP Chi-restraints excluded: chain B residue 2105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 4 optimal weight: 0.9990 chunk 145 optimal weight: 0.0070 chunk 42 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 135 optimal weight: 20.0000 chunk 52 optimal weight: 0.0270 chunk 169 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.108518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065406 restraints weight = 36795.875| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.14 r_work: 0.2964 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16486 Z= 0.093 Angle : 0.489 7.312 22452 Z= 0.253 Chirality : 0.041 0.161 2614 Planarity : 0.003 0.040 2902 Dihedral : 3.951 19.130 2336 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.11 % Allowed : 12.13 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 2168 helix: 1.01 (0.20), residues: 744 sheet: 0.04 (0.26), residues: 388 loop : -0.67 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1807 HIS 0.004 0.001 HIS B1516 PHE 0.009 0.001 PHE B1632 TYR 0.012 0.001 TYR A1996 ARG 0.002 0.000 ARG B2043 Details of bonding type rmsd hydrogen bonds : bond 0.02842 ( 694) hydrogen bonds : angle 4.01915 ( 1968) covalent geometry : bond 0.00208 (16486) covalent geometry : angle 0.48941 (22452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 1.613 Fit side-chains REVERT: A 1070 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8123 (pp30) REVERT: A 1516 HIS cc_start: 0.7673 (t-90) cc_final: 0.7415 (t70) REVERT: A 1622 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9029 (tp) REVERT: A 1644 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8896 (pm20) REVERT: A 1873 MET cc_start: 0.7879 (ttp) cc_final: 0.7597 (ttm) REVERT: B 1070 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8122 (pp30) outliers start: 18 outliers final: 13 residues processed: 71 average time/residue: 0.9889 time to fit residues: 81.6278 Evaluate side-chains 67 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1447 ASN Chi-restraints excluded: chain A residue 1622 LEU Chi-restraints excluded: chain A residue 1644 GLU Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain A residue 1773 ASP Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1384 VAL Chi-restraints excluded: chain B residue 1665 VAL Chi-restraints excluded: chain B residue 1773 ASP Chi-restraints excluded: chain B residue 2105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 84 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.108325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065046 restraints weight = 37072.524| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.17 r_work: 0.2948 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16486 Z= 0.105 Angle : 0.487 6.549 22452 Z= 0.251 Chirality : 0.041 0.158 2614 Planarity : 0.003 0.040 2902 Dihedral : 3.869 19.682 2336 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.17 % Allowed : 12.32 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2168 helix: 1.08 (0.20), residues: 744 sheet: 0.02 (0.26), residues: 394 loop : -0.63 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B2060 HIS 0.003 0.001 HIS B1516 PHE 0.009 0.001 PHE B1117 TYR 0.017 0.001 TYR A 991 ARG 0.002 0.000 ARG A2043 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 694) hydrogen bonds : angle 4.00587 ( 1968) covalent geometry : bond 0.00247 (16486) covalent geometry : angle 0.48697 (22452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 1.645 Fit side-chains REVERT: A 1070 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8226 (pp30) REVERT: A 1516 HIS cc_start: 0.7601 (t-90) cc_final: 0.7344 (t70) REVERT: A 1622 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8942 (tt) REVERT: A 1644 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8907 (pm20) REVERT: A 1873 MET cc_start: 0.7911 (ttp) cc_final: 0.7594 (ttm) REVERT: B 1070 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8166 (pp30) REVERT: B 1235 MET cc_start: 0.7063 (ttp) cc_final: 0.6829 (tmt) REVERT: B 1622 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8915 (tt) outliers start: 19 outliers final: 12 residues processed: 66 average time/residue: 1.0040 time to fit residues: 77.3643 Evaluate side-chains 62 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1447 ASN Chi-restraints excluded: chain A residue 1622 LEU Chi-restraints excluded: chain A residue 1644 GLU Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain A residue 1773 ASP Chi-restraints excluded: chain A residue 2105 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1384 VAL Chi-restraints excluded: chain B residue 1622 LEU Chi-restraints excluded: chain B residue 1773 ASP Chi-restraints excluded: chain B residue 2105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 105 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 34 optimal weight: 30.0000 chunk 26 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 185 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.106502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.063046 restraints weight = 36981.406| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.14 r_work: 0.2898 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16486 Z= 0.195 Angle : 0.549 6.436 22452 Z= 0.284 Chirality : 0.043 0.170 2614 Planarity : 0.004 0.041 2902 Dihedral : 4.137 19.474 2336 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.23 % Allowed : 12.32 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2168 helix: 0.90 (0.20), residues: 750 sheet: -0.03 (0.26), residues: 392 loop : -0.69 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1807 HIS 0.006 0.001 HIS B1093 PHE 0.013 0.001 PHE A1785 TYR 0.023 0.002 TYR B 991 ARG 0.003 0.000 ARG A2048 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 694) hydrogen bonds : angle 4.25775 ( 1968) covalent geometry : bond 0.00469 (16486) covalent geometry : angle 0.54886 (22452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15793.43 seconds wall clock time: 275 minutes 47.56 seconds (16547.56 seconds total)