Starting phenix.real_space_refine on Thu Sep 18 11:38:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b80_44330/09_2025/9b80_44330.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b80_44330/09_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_44330/09_2025/9b80_44330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b80_44330/09_2025/9b80_44330.map" model { file = "/net/cci-nas-00/data/ceres_data/9b80_44330/09_2025/9b80_44330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b80_44330/09_2025/9b80_44330.cif" } 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 13, 'ARG:plan': 11, 'ASP:plan': 8, 'PHE:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 245 Restraints were copied for chains: B Time building chain proxies: 7.99, per 1000 atoms: 0.49 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: 1.07 Conformation dependent library (CDL) restraints added in 505.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.95 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: 3.55 Time building geometry restraints manager: 1.39 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: 0.03 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: 3.750 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.380 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.560 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.19), 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 ARG 0.004 0.000 ARG A1462 TYR 0.019 0.001 TYR B 991 PHE 0.009 0.001 PHE A1117 TRP 0.016 0.001 TRP B1807 HIS 0.003 0.001 HIS A1093 Details of bonding type rmsd covalent geometry : bond 0.00277 (16486) covalent geometry : angle 0.55847 (22452) hydrogen bonds : bond 0.20305 ( 694) hydrogen bonds : angle 6.68379 ( 1968) *********************** 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 : 0.575 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.4880 time to fit residues: 38.1477 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 : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.107939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.064831 restraints weight = 37251.263| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.35 r_work: 0.2902 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 16486 Z= 0.221 Angle : 0.593 7.362 22452 Z= 0.312 Chirality : 0.045 0.172 2614 Planarity : 0.004 0.044 2902 Dihedral : 4.263 19.964 2336 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.37 % Allowed : 6.28 % Favored : 93.35 % 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: -0.29 (0.18), residues: 2168 helix: 0.52 (0.20), residues: 736 sheet: 0.34 (0.27), residues: 386 loop : -0.88 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 942 TYR 0.018 0.002 TYR B 991 PHE 0.020 0.002 PHE A1785 TRP 0.021 0.001 TRP A1807 HIS 0.006 0.001 HIS B1093 Details of bonding type rmsd covalent geometry : bond 0.00527 (16486) covalent geometry : angle 0.59265 (22452) hydrogen bonds : bond 0.04749 ( 694) hydrogen bonds : angle 4.90076 ( 1968) *********************** 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 65 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.614 Fit side-chains REVERT: A 1516 HIS cc_start: 0.8335 (t-90) cc_final: 0.8008 (t70) REVERT: A 1843 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.7959 (ttt) REVERT: B 1516 HIS cc_start: 0.8353 (t-90) cc_final: 0.7405 (t70) outliers start: 6 outliers final: 0 residues processed: 61 average time/residue: 0.5141 time to fit residues: 36.2110 Evaluate side-chains 56 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 107 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 161 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1763 HIS A1938 GLN A1970 ASN B1122 HIS B1763 HIS B1938 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.109400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.065707 restraints weight = 37436.446| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.20 r_work: 0.2970 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16486 Z= 0.109 Angle : 0.485 7.138 22452 Z= 0.253 Chirality : 0.041 0.164 2614 Planarity : 0.003 0.042 2902 Dihedral : 3.937 19.572 2336 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.80 % Allowed : 8.31 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.19), residues: 2168 helix: 0.76 (0.20), residues: 744 sheet: 0.28 (0.27), residues: 386 loop : -0.76 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2043 TYR 0.014 0.001 TYR A 991 PHE 0.009 0.001 PHE A1785 TRP 0.016 0.001 TRP B1807 HIS 0.004 0.001 HIS B1093 Details of bonding type rmsd covalent geometry : bond 0.00255 (16486) covalent geometry : angle 0.48544 (22452) hydrogen bonds : bond 0.03594 ( 694) hydrogen bonds : angle 4.44834 ( 1968) *********************** 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 75 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.599 Fit side-chains REVERT: A 1516 HIS cc_start: 0.8154 (t-90) cc_final: 0.7921 (t70) REVERT: B 1072 LYS cc_start: 0.9365 (mmmm) cc_final: 0.9134 (mppt) REVERT: B 1503 MET cc_start: 0.6580 (OUTLIER) cc_final: 0.5538 (mpt) REVERT: B 1516 HIS cc_start: 0.8243 (t-90) cc_final: 0.7394 (t70) outliers start: 13 outliers final: 4 residues processed: 73 average time/residue: 0.4955 time to fit residues: 41.7165 Evaluate side-chains 59 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1503 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 93 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 28 optimal weight: 40.0000 chunk 81 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.108186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.064591 restraints weight = 37168.475| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.08 r_work: 0.2935 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16486 Z= 0.153 Angle : 0.507 6.465 22452 Z= 0.265 Chirality : 0.042 0.162 2614 Planarity : 0.003 0.041 2902 Dihedral : 3.991 19.978 2336 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.23 % Allowed : 9.17 % Favored : 89.59 % 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: -0.08 (0.19), residues: 2168 helix: 0.78 (0.20), residues: 746 sheet: 0.28 (0.27), residues: 382 loop : -0.75 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2043 TYR 0.018 0.002 TYR A 991 PHE 0.011 0.001 PHE A1785 TRP 0.017 0.001 TRP B1807 HIS 0.004 0.001 HIS A1093 Details of bonding type rmsd covalent geometry : bond 0.00361 (16486) covalent geometry : angle 0.50699 (22452) hydrogen bonds : bond 0.03775 ( 694) hydrogen bonds : angle 4.38023 ( 1968) *********************** 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 76 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.574 Fit side-chains REVERT: A 989 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8752 (pm20) REVERT: A 1516 HIS cc_start: 0.8033 (t-90) cc_final: 0.7790 (t70) REVERT: A 1843 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.7742 (ttt) REVERT: B 989 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8753 (pm20) outliers start: 20 outliers final: 10 residues processed: 72 average time/residue: 0.4743 time to fit residues: 39.3515 Evaluate side-chains 67 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 1843 MET 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 2105 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 108 optimal weight: 3.9990 chunk 155 optimal weight: 30.0000 chunk 136 optimal weight: 30.0000 chunk 159 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 214 optimal weight: 10.0000 chunk 36 optimal weight: 50.0000 chunk 105 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.106694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.062747 restraints weight = 36969.443| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.21 r_work: 0.2891 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16486 Z= 0.213 Angle : 0.563 7.305 22452 Z= 0.294 Chirality : 0.044 0.170 2614 Planarity : 0.004 0.040 2902 Dihedral : 4.245 20.038 2336 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.42 % Allowed : 10.41 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.18), residues: 2168 helix: 0.71 (0.20), residues: 746 sheet: 0.18 (0.27), residues: 374 loop : -0.82 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2048 TYR 0.021 0.002 TYR A 991 PHE 0.015 0.001 PHE A1785 TRP 0.019 0.002 TRP B1807 HIS 0.006 0.001 HIS B1093 Details of bonding type rmsd covalent geometry : bond 0.00509 (16486) covalent geometry : angle 0.56274 (22452) hydrogen bonds : bond 0.04364 ( 694) hydrogen bonds : angle 4.48999 ( 1968) *********************** 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 79 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.680 Fit side-chains REVERT: A 989 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8778 (pm20) REVERT: A 1516 HIS cc_start: 0.7894 (t-90) cc_final: 0.7628 (t70) REVERT: A 1873 MET cc_start: 0.8003 (ttp) cc_final: 0.7642 (ptm) REVERT: B 989 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8809 (pm20) outliers start: 23 outliers final: 11 residues processed: 75 average time/residue: 0.4979 time to fit residues: 43.4172 Evaluate side-chains 65 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 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 2105 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 101 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 156 optimal weight: 40.0000 chunk 211 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1970 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.106808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.063266 restraints weight = 36790.764| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.06 r_work: 0.2900 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16486 Z= 0.203 Angle : 0.546 7.159 22452 Z= 0.285 Chirality : 0.043 0.168 2614 Planarity : 0.004 0.040 2902 Dihedral : 4.218 20.181 2336 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.72 % Allowed : 11.21 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.18), residues: 2168 helix: 0.76 (0.20), residues: 744 sheet: -0.03 (0.27), residues: 388 loop : -0.84 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2048 TYR 0.020 0.002 TYR B 991 PHE 0.013 0.001 PHE B1785 TRP 0.019 0.002 TRP B1424 HIS 0.005 0.001 HIS B1516 Details of bonding type rmsd covalent geometry : bond 0.00487 (16486) covalent geometry : angle 0.54594 (22452) hydrogen bonds : bond 0.04091 ( 694) hydrogen bonds : angle 4.38889 ( 1968) *********************** 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 85 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.543 Fit side-chains REVERT: A 989 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8754 (pm20) REVERT: A 1070 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8286 (pp30) REVERT: A 1516 HIS cc_start: 0.7877 (t-90) cc_final: 0.7630 (t70) REVERT: A 1873 MET cc_start: 0.7949 (ttp) cc_final: 0.7617 (ptm) REVERT: B 989 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8767 (pm20) REVERT: B 1503 MET cc_start: 0.6930 (mpt) cc_final: 0.6666 (mmt) outliers start: 28 outliers final: 10 residues processed: 81 average time/residue: 0.4571 time to fit residues: 42.8531 Evaluate side-chains 65 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 1384 VAL Chi-restraints excluded: chain A residue 1447 ASN 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 2105 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 99 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 217 optimal weight: 0.0770 chunk 156 optimal weight: 50.0000 chunk 28 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 37 optimal weight: 0.0030 overall best weight: 0.5550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1855 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.108907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.065627 restraints weight = 36476.539| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.17 r_work: 0.2963 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16486 Z= 0.093 Angle : 0.483 8.311 22452 Z= 0.250 Chirality : 0.041 0.159 2614 Planarity : 0.003 0.040 2902 Dihedral : 3.867 19.487 2336 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.29 % Allowed : 12.13 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.19), residues: 2168 helix: 0.99 (0.20), residues: 742 sheet: 0.12 (0.27), residues: 376 loop : -0.68 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1255 TYR 0.013 0.001 TYR A 991 PHE 0.008 0.001 PHE B1117 TRP 0.018 0.001 TRP B1807 HIS 0.004 0.001 HIS B1516 Details of bonding type rmsd covalent geometry : bond 0.00212 (16486) covalent geometry : angle 0.48324 (22452) hydrogen bonds : bond 0.02916 ( 694) hydrogen bonds : angle 4.03394 ( 1968) *********************** 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 75 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.687 Fit side-chains REVERT: A 1070 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8145 (pp30) REVERT: A 1516 HIS cc_start: 0.7780 (t-90) cc_final: 0.7540 (t70) REVERT: A 1622 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8926 (tt) REVERT: A 1873 MET cc_start: 0.7962 (ttp) cc_final: 0.7669 (ptm) REVERT: B 1070 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8159 (pp30) REVERT: B 1622 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8940 (tt) REVERT: B 1843 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8042 (ttt) outliers start: 21 outliers final: 8 residues processed: 72 average time/residue: 0.5306 time to fit residues: 43.2706 Evaluate side-chains 63 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1088 VAL 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 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 1622 LEU Chi-restraints excluded: chain B residue 1843 MET 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 197 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 161 optimal weight: 0.0030 chunk 151 optimal weight: 10.0000 chunk 82 optimal weight: 0.0570 chunk 78 optimal weight: 0.0060 chunk 54 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.3324 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.109950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066614 restraints weight = 36712.623| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.18 r_work: 0.2999 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2524 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= 0.083 Angle : 0.464 7.226 22452 Z= 0.240 Chirality : 0.040 0.157 2614 Planarity : 0.003 0.040 2902 Dihedral : 3.661 19.229 2336 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.17 % Allowed : 12.25 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.19), residues: 2168 helix: 1.12 (0.20), residues: 744 sheet: 0.10 (0.26), residues: 394 loop : -0.64 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1694 TYR 0.014 0.001 TYR A 991 PHE 0.008 0.001 PHE B1117 TRP 0.015 0.001 TRP B1807 HIS 0.005 0.001 HIS A 920 Details of bonding type rmsd covalent geometry : bond 0.00187 (16486) covalent geometry : angle 0.46424 (22452) hydrogen bonds : bond 0.02581 ( 694) hydrogen bonds : angle 3.86571 ( 1968) *********************** 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 75 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.506 Fit side-chains REVERT: A 989 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8718 (pm20) REVERT: A 1516 HIS cc_start: 0.7596 (t-90) cc_final: 0.7373 (t70) REVERT: A 1622 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8956 (tp) REVERT: A 1644 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8949 (pm20) REVERT: B 989 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8720 (pm20) REVERT: B 1070 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8158 (pp30) REVERT: B 1503 MET cc_start: 0.6648 (mmt) cc_final: 0.6215 (mmt) REVERT: B 1622 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8954 (tp) REVERT: B 1644 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.9008 (pm20) REVERT: B 2060 TRP cc_start: 0.8685 (m100) cc_final: 0.8359 (m100) outliers start: 19 outliers final: 8 residues processed: 74 average time/residue: 0.5189 time to fit residues: 43.8993 Evaluate side-chains 64 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1622 LEU Chi-restraints excluded: chain A residue 1644 GLU Chi-restraints excluded: chain A residue 2105 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 1622 LEU Chi-restraints excluded: chain B residue 1644 GLU 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 11 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 202 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.109643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066138 restraints weight = 36667.739| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.15 r_work: 0.2988 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16486 Z= 0.089 Angle : 0.466 8.273 22452 Z= 0.240 Chirality : 0.040 0.159 2614 Planarity : 0.003 0.040 2902 Dihedral : 3.618 18.888 2336 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.92 % Allowed : 12.50 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.18), residues: 2168 helix: 1.10 (0.20), residues: 746 sheet: 0.18 (0.27), residues: 380 loop : -0.55 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2043 TYR 0.015 0.001 TYR A 991 PHE 0.009 0.001 PHE B1117 TRP 0.021 0.001 TRP A2060 HIS 0.003 0.001 HIS B1516 Details of bonding type rmsd covalent geometry : bond 0.00204 (16486) covalent geometry : angle 0.46559 (22452) hydrogen bonds : bond 0.02694 ( 694) hydrogen bonds : angle 3.83614 ( 1968) *********************** 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 70 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.685 Fit side-chains REVERT: A 989 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8744 (pm20) REVERT: A 1070 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8201 (pp30) REVERT: A 1516 HIS cc_start: 0.7552 (t-90) cc_final: 0.7333 (t70) REVERT: A 1622 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8919 (tt) REVERT: B 989 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8740 (pm20) REVERT: B 1070 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8164 (pp30) REVERT: B 1503 MET cc_start: 0.6641 (mmt) cc_final: 0.6134 (mmt) REVERT: B 1622 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8909 (tt) outliers start: 15 outliers final: 8 residues processed: 70 average time/residue: 0.4504 time to fit residues: 36.4674 Evaluate side-chains 65 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1622 LEU Chi-restraints excluded: chain A residue 2105 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 1622 LEU 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 87 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.107396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.063714 restraints weight = 36859.186| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.17 r_work: 0.2915 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16486 Z= 0.171 Angle : 0.529 7.173 22452 Z= 0.273 Chirality : 0.042 0.162 2614 Planarity : 0.003 0.040 2902 Dihedral : 3.943 19.725 2336 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.92 % Allowed : 12.81 % Favored : 86.27 % 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 (0.18), residues: 2168 helix: 0.97 (0.20), residues: 744 sheet: -0.02 (0.26), residues: 392 loop : -0.53 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1612 TYR 0.022 0.002 TYR A 991 PHE 0.013 0.001 PHE A1785 TRP 0.019 0.001 TRP A2060 HIS 0.005 0.001 HIS B1093 Details of bonding type rmsd covalent geometry : bond 0.00406 (16486) covalent geometry : angle 0.52882 (22452) hydrogen bonds : bond 0.03749 ( 694) hydrogen bonds : angle 4.14232 ( 1968) ********************** 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 65 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.645 Fit side-chains REVERT: A 989 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8756 (pm20) REVERT: A 1070 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8210 (pp30) REVERT: A 1516 HIS cc_start: 0.7606 (t-90) cc_final: 0.7376 (t70) REVERT: B 989 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8760 (pm20) REVERT: B 1070 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8105 (pp30) REVERT: B 1503 MET cc_start: 0.6683 (mmt) cc_final: 0.6283 (mmt) outliers start: 15 outliers final: 10 residues processed: 65 average time/residue: 0.4881 time to fit residues: 36.5728 Evaluate side-chains 61 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1622 LEU Chi-restraints excluded: chain A residue 2105 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 1622 LEU 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 61 optimal weight: 3.9990 chunk 157 optimal weight: 0.0170 chunk 117 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 50.0000 chunk 49 optimal weight: 30.0000 chunk 192 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 43 optimal weight: 0.0170 chunk 73 optimal weight: 2.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.108086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064600 restraints weight = 36708.072| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.19 r_work: 0.2941 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16486 Z= 0.119 Angle : 0.491 6.845 22452 Z= 0.254 Chirality : 0.041 0.159 2614 Planarity : 0.003 0.040 2902 Dihedral : 3.836 19.495 2336 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.99 % Allowed : 12.93 % Favored : 86.08 % 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: 0.13 (0.18), residues: 2168 helix: 1.04 (0.20), residues: 744 sheet: -0.02 (0.26), residues: 392 loop : -0.50 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B2048 TYR 0.017 0.001 TYR B 991 PHE 0.009 0.001 PHE B 944 TRP 0.018 0.001 TRP A2060 HIS 0.004 0.001 HIS B1093 Details of bonding type rmsd covalent geometry : bond 0.00283 (16486) covalent geometry : angle 0.49142 (22452) hydrogen bonds : bond 0.03139 ( 694) hydrogen bonds : angle 4.00419 ( 1968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7297.07 seconds wall clock time: 124 minutes 27.97 seconds (7467.97 seconds total)