Starting phenix.real_space_refine on Sun Jul 5 23:21:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vm3_65175/07_2026/9vm3_65175.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vm3_65175/07_2026/9vm3_65175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vm3_65175/07_2026/9vm3_65175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vm3_65175/07_2026/9vm3_65175.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vm3_65175/07_2026/9vm3_65175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vm3_65175/07_2026/9vm3_65175.map" } resolution = 4.52 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= 0.002 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 132 5.16 5 C 19000 2.51 5 N 5104 2.21 5 O 5484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 174 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29720 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1688, 13471 Classifications: {'peptide': 1688} Link IDs: {'PCIS': 4, 'PTRANS': 99, 'TRANS': 1584} Chain breaks: 7 Chain: "B" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1389 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 12, 'TRANS': 165} Restraints were copied for chains: C, D Time building chain proxies: 21.70, per 1000 atoms: 0.73 Number of scatterers: 29720 At special positions: 0 Unit cell: (167.58, 148.96, 171.57, 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 132 16.00 O 5484 8.00 N 5104 7.00 C 19000 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: 2.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7128 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 20 sheets defined 56.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.688A pdb=" N GLU A 242 " --> pdb=" O ASP A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 4.072A pdb=" N LYS A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 468 through 480 Processing helix chain 'A' and resid 483 through 488 removed outlier: 4.043A pdb=" N ARG A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 483 through 488' Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.569A pdb=" N HIS A 703 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 699 through 704' Processing helix chain 'A' and resid 721 through 737 Processing helix chain 'A' and resid 752 through 764 removed outlier: 4.035A pdb=" N GLU A 756 " --> pdb=" O ASN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 767 No H-bonds generated for 'chain 'A' and resid 765 through 767' Processing helix chain 'A' and resid 768 through 789 removed outlier: 6.465A pdb=" N HIS A 777 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N HIS A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 819 Processing helix chain 'A' and resid 820 through 823 Processing helix chain 'A' and resid 829 through 838 Processing helix chain 'A' and resid 899 through 904 removed outlier: 4.051A pdb=" N LEU A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 919 removed outlier: 3.784A pdb=" N GLU A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 931 removed outlier: 3.628A pdb=" N HIS A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 950 Processing helix chain 'A' and resid 955 through 959 removed outlier: 3.888A pdb=" N ARG A 959 " --> pdb=" O ARG A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 982 Processing helix chain 'A' and resid 986 through 1006 removed outlier: 3.838A pdb=" N SER A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1029 Processing helix chain 'A' and resid 1033 through 1050 removed outlier: 4.357A pdb=" N LEU A1037 " --> pdb=" O ASN A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1059 removed outlier: 3.676A pdb=" N TYR A1054 " --> pdb=" O HIS A1051 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A1055 " --> pdb=" O GLU A1052 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A1058 " --> pdb=" O VAL A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1097 Processing helix chain 'A' and resid 1100 through 1107 Processing helix chain 'A' and resid 1107 through 1122 Processing helix chain 'A' and resid 1128 through 1149 Processing helix chain 'A' and resid 1150 through 1153 Processing helix chain 'A' and resid 1154 through 1164 removed outlier: 3.674A pdb=" N LEU A1164 " --> pdb=" O ARG A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1176 removed outlier: 4.232A pdb=" N SER A1170 " --> pdb=" O LEU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1179 No H-bonds generated for 'chain 'A' and resid 1177 through 1179' Processing helix chain 'A' and resid 1246 through 1263 Processing helix chain 'A' and resid 1265 through 1275 Processing helix chain 'A' and resid 1277 through 1295 removed outlier: 3.678A pdb=" N PHE A1295 " --> pdb=" O CYS A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1307 removed outlier: 3.709A pdb=" N ALA A1302 " --> pdb=" O LYS A1298 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A1303 " --> pdb=" O GLY A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1404 Processing helix chain 'A' and resid 1408 through 1426 removed outlier: 4.193A pdb=" N VAL A1412 " --> pdb=" O ALA A1408 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A1426 " --> pdb=" O TYR A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1447 Processing helix chain 'A' and resid 1448 through 1453 Processing helix chain 'A' and resid 1456 through 1471 Processing helix chain 'A' and resid 1474 through 1497 Processing helix chain 'A' and resid 1500 through 1517 Processing helix chain 'A' and resid 1521 through 1538 Processing helix chain 'A' and resid 1540 through 1545 removed outlier: 3.842A pdb=" N ARG A1543 " --> pdb=" O MET A1540 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A1544 " --> pdb=" O GLY A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1571 Processing helix chain 'A' and resid 1574 through 1589 Processing helix chain 'A' and resid 1592 through 1611 Processing helix chain 'A' and resid 1612 through 1635 Processing helix chain 'A' and resid 1644 through 1648 Processing helix chain 'A' and resid 1651 through 1658 removed outlier: 3.515A pdb=" N VAL A1654 " --> pdb=" O SER A1651 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A1655 " --> pdb=" O SER A1652 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A1658 " --> pdb=" O LEU A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1697 Processing helix chain 'A' and resid 1699 through 1717 removed outlier: 3.927A pdb=" N VAL A1703 " --> pdb=" O LEU A1699 " (cutoff:3.500A) Proline residue: A1712 - end of helix Processing helix chain 'A' and resid 1719 through 1741 Processing helix chain 'A' and resid 1758 through 1765 removed outlier: 6.085A pdb=" N ASP A1763 " --> pdb=" O HIS A1760 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1793 removed outlier: 3.712A pdb=" N ILE A1782 " --> pdb=" O LYS A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1809 through 1813 removed outlier: 3.507A pdb=" N LYS A1812 " --> pdb=" O ASP A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1837 Processing helix chain 'A' and resid 1839 through 1844 Processing helix chain 'A' and resid 1865 through 1869 Processing helix chain 'A' and resid 1900 through 1922 Processing helix chain 'A' and resid 1926 through 1939 removed outlier: 3.551A pdb=" N LEU A1930 " --> pdb=" O ASP A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1945 through 1955 Processing helix chain 'A' and resid 1960 through 1992 removed outlier: 3.629A pdb=" N ARG A1965 " --> pdb=" O PRO A1961 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS A1966 " --> pdb=" O LYS A1962 " (cutoff:3.500A) Processing helix chain 'A' and resid 1995 through 2015 removed outlier: 4.305A pdb=" N TYR A1999 " --> pdb=" O ASP A1995 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 61 through 67 removed outlier: 4.037A pdb=" N TYR B 64 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 66 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 86 through 96 removed outlier: 3.522A pdb=" N PHE B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.512A pdb=" N ILE B 101 " --> pdb=" O TRP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.541A pdb=" N ALA B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 178 Processing helix chain 'C' and resid 55 through 63 Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 106 through 118 Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 138 through 147 Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 211 through 224 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.687A pdb=" N GLU C 242 " --> pdb=" O ASP C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 removed outlier: 4.072A pdb=" N LYS C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 381 through 387 Processing helix chain 'C' and resid 401 through 409 Processing helix chain 'C' and resid 468 through 480 Processing helix chain 'C' and resid 483 through 488 removed outlier: 4.044A pdb=" N ARG C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 488 " --> pdb=" O SER C 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 483 through 488' Processing helix chain 'C' and resid 699 through 704 removed outlier: 3.570A pdb=" N HIS C 703 " --> pdb=" O TRP C 699 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS C 704 " --> pdb=" O VAL C 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 699 through 704' Processing helix chain 'C' and resid 721 through 737 Processing helix chain 'C' and resid 752 through 764 removed outlier: 4.035A pdb=" N GLU C 756 " --> pdb=" O ASN C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 765 through 767 No H-bonds generated for 'chain 'C' and resid 765 through 767' Processing helix chain 'C' and resid 768 through 789 removed outlier: 6.464A pdb=" N HIS C 777 " --> pdb=" O VAL C 773 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N HIS C 778 " --> pdb=" O ALA C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 819 Processing helix chain 'C' and resid 820 through 823 Processing helix chain 'C' and resid 829 through 838 Processing helix chain 'C' and resid 899 through 904 removed outlier: 4.051A pdb=" N LEU C 903 " --> pdb=" O VAL C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 919 removed outlier: 3.784A pdb=" N GLU C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 931 removed outlier: 3.628A pdb=" N HIS C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 950 Processing helix chain 'C' and resid 955 through 959 removed outlier: 3.888A pdb=" N ARG C 959 " --> pdb=" O ARG C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 982 Processing helix chain 'C' and resid 986 through 1006 removed outlier: 3.838A pdb=" N SER C1006 " --> pdb=" O SER C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1029 Processing helix chain 'C' and resid 1033 through 1050 removed outlier: 4.357A pdb=" N LEU C1037 " --> pdb=" O ASN C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1059 removed outlier: 3.676A pdb=" N TYR C1054 " --> pdb=" O HIS C1051 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL C1055 " --> pdb=" O GLU C1052 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C1058 " --> pdb=" O VAL C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1092 through 1097 Processing helix chain 'C' and resid 1100 through 1107 Processing helix chain 'C' and resid 1107 through 1122 Processing helix chain 'C' and resid 1128 through 1149 Processing helix chain 'C' and resid 1150 through 1153 Processing helix chain 'C' and resid 1154 through 1164 removed outlier: 3.672A pdb=" N LEU C1164 " --> pdb=" O ARG C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1176 removed outlier: 4.232A pdb=" N SER C1170 " --> pdb=" O LEU C1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1246 through 1263 Processing helix chain 'C' and resid 1265 through 1275 Processing helix chain 'C' and resid 1277 through 1295 removed outlier: 3.677A pdb=" N PHE C1295 " --> pdb=" O CYS C1291 " (cutoff:3.500A) Processing helix chain 'C' and resid 1298 through 1307 removed outlier: 3.709A pdb=" N ALA C1302 " --> pdb=" O LYS C1298 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C1303 " --> pdb=" O GLY C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1370 through 1404 Processing helix chain 'C' and resid 1408 through 1426 removed outlier: 4.193A pdb=" N VAL C1412 " --> pdb=" O ALA C1408 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C1426 " --> pdb=" O TYR C1422 " (cutoff:3.500A) Processing helix chain 'C' and resid 1429 through 1447 Processing helix chain 'C' and resid 1448 through 1453 Processing helix chain 'C' and resid 1456 through 1471 Processing helix chain 'C' and resid 1474 through 1497 Processing helix chain 'C' and resid 1500 through 1517 Processing helix chain 'C' and resid 1521 through 1538 Processing helix chain 'C' and resid 1540 through 1545 removed outlier: 3.842A pdb=" N ARG C1543 " --> pdb=" O MET C1540 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP C1544 " --> pdb=" O GLY C1541 " (cutoff:3.500A) Processing helix chain 'C' and resid 1546 through 1571 Processing helix chain 'C' and resid 1574 through 1589 Processing helix chain 'C' and resid 1592 through 1611 Processing helix chain 'C' and resid 1612 through 1635 Processing helix chain 'C' and resid 1644 through 1648 Processing helix chain 'C' and resid 1651 through 1658 removed outlier: 3.515A pdb=" N VAL C1654 " --> pdb=" O SER C1651 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C1655 " --> pdb=" O SER C1652 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C1658 " --> pdb=" O LEU C1655 " (cutoff:3.500A) Processing helix chain 'C' and resid 1679 through 1697 Processing helix chain 'C' and resid 1699 through 1717 removed outlier: 3.927A pdb=" N VAL C1703 " --> pdb=" O LEU C1699 " (cutoff:3.500A) Proline residue: C1712 - end of helix Processing helix chain 'C' and resid 1719 through 1741 Processing helix chain 'C' and resid 1758 through 1765 removed outlier: 6.085A pdb=" N ASP C1763 " --> pdb=" O HIS C1760 " (cutoff:3.500A) Processing helix chain 'C' and resid 1778 through 1793 removed outlier: 3.713A pdb=" N ILE C1782 " --> pdb=" O LYS C1778 " (cutoff:3.500A) Processing helix chain 'C' and resid 1809 through 1813 removed outlier: 3.506A pdb=" N LYS C1812 " --> pdb=" O ASP C1809 " (cutoff:3.500A) Processing helix chain 'C' and resid 1830 through 1837 Processing helix chain 'C' and resid 1839 through 1844 Processing helix chain 'C' and resid 1865 through 1869 Processing helix chain 'C' and resid 1900 through 1922 Processing helix chain 'C' and resid 1926 through 1939 removed outlier: 3.552A pdb=" N LEU C1930 " --> pdb=" O ASP C1926 " (cutoff:3.500A) Processing helix chain 'C' and resid 1945 through 1955 Processing helix chain 'C' and resid 1960 through 1992 removed outlier: 3.629A pdb=" N ARG C1965 " --> pdb=" O PRO C1961 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS C1966 " --> pdb=" O LYS C1962 " (cutoff:3.500A) Processing helix chain 'C' and resid 1995 through 2015 removed outlier: 4.306A pdb=" N TYR C1999 " --> pdb=" O ASP C1995 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 25 Processing helix chain 'D' and resid 61 through 67 removed outlier: 4.037A pdb=" N TYR D 64 " --> pdb=" O GLN D 61 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 66 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 86 through 96 removed outlier: 3.522A pdb=" N PHE D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 removed outlier: 3.511A pdb=" N ILE D 101 " --> pdb=" O TRP D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.541A pdb=" N ALA D 142 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 178 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 86 Processing sheet with id=AA2, first strand: chain 'A' and resid 498 through 502 removed outlier: 6.370A pdb=" N LEU A 511 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 293 removed outlier: 3.965A pdb=" N ILE A 292 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU A 283 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY A 279 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 3.965A pdb=" N ILE A 292 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU A 283 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE A 336 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS A 400 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 338 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA A 398 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 340 " --> pdb=" O TRP A 396 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TRP A 396 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU A 342 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP A 396 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 460 " --> pdb=" O TRP A 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 619 through 622 Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 603 removed outlier: 3.824A pdb=" N ALA A 602 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 574 " --> pdb=" O ALA A 602 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 741 through 742 Processing sheet with id=AA8, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AA9, first strand: chain 'A' and resid 1819 through 1824 removed outlier: 3.812A pdb=" N PHE A1752 " --> pdb=" O TYR A1771 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU A1768 " --> pdb=" O VAL A1891 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N ILE A1889 " --> pdb=" O ALA A1881 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N ALA A1881 " --> pdb=" O ILE A1889 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N VAL A1891 " --> pdb=" O ASP A1879 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP A1879 " --> pdb=" O VAL A1891 " (cutoff:3.500A) removed outlier: 11.356A pdb=" N THR A1874 " --> pdb=" O PRO A1855 " (cutoff:3.500A) removed outlier: 12.350A pdb=" N LEU A1876 " --> pdb=" O CYS A1853 " (cutoff:3.500A) removed outlier: 11.833A pdb=" N CYS A1853 " --> pdb=" O LEU A1876 " (cutoff:3.500A) removed outlier: 12.754A pdb=" N THR A1878 " --> pdb=" O LEU A1851 " (cutoff:3.500A) removed outlier: 12.980A pdb=" N LEU A1851 " --> pdb=" O THR A1878 " (cutoff:3.500A) removed outlier: 11.696A pdb=" N HIS A1880 " --> pdb=" O THR A1849 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR A1849 " --> pdb=" O HIS A1880 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 41 through 46 removed outlier: 9.068A pdb=" N VAL B 77 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS B 5 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU B 79 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL B 7 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N CYS B 81 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 9 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N SER B 83 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE B 78 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL B 113 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL B 80 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR B 115 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE B 82 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N VAL B 155 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU B 112 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 83 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 498 through 502 removed outlier: 6.370A pdb=" N LEU C 511 " --> pdb=" O GLU C 531 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 290 through 293 removed outlier: 3.964A pdb=" N ILE C 292 " --> pdb=" O LEU C 283 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU C 283 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 279 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 290 through 293 removed outlier: 3.964A pdb=" N ILE C 292 " --> pdb=" O LEU C 283 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU C 283 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE C 336 " --> pdb=" O HIS C 400 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS C 400 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 338 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA C 398 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE C 340 " --> pdb=" O TRP C 396 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TRP C 396 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU C 342 " --> pdb=" O PHE C 394 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP C 396 " --> pdb=" O PHE C 460 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 460 " --> pdb=" O TRP C 396 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 619 through 622 Processing sheet with id=AB7, first strand: chain 'C' and resid 602 through 603 removed outlier: 3.824A pdb=" N ALA C 602 " --> pdb=" O VAL C 574 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 574 " --> pdb=" O ALA C 602 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 741 through 742 Processing sheet with id=AB9, first strand: chain 'C' and resid 792 through 793 Processing sheet with id=AC1, first strand: chain 'C' and resid 1819 through 1824 removed outlier: 3.812A pdb=" N PHE C1752 " --> pdb=" O TYR C1771 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU C1768 " --> pdb=" O VAL C1891 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N ILE C1889 " --> pdb=" O ALA C1881 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N ALA C1881 " --> pdb=" O ILE C1889 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N VAL C1891 " --> pdb=" O ASP C1879 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP C1879 " --> pdb=" O VAL C1891 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N THR C1874 " --> pdb=" O PRO C1855 " (cutoff:3.500A) removed outlier: 12.350A pdb=" N LEU C1876 " --> pdb=" O CYS C1853 " (cutoff:3.500A) removed outlier: 11.833A pdb=" N CYS C1853 " --> pdb=" O LEU C1876 " (cutoff:3.500A) removed outlier: 12.754A pdb=" N THR C1878 " --> pdb=" O LEU C1851 " (cutoff:3.500A) removed outlier: 12.980A pdb=" N LEU C1851 " --> pdb=" O THR C1878 " (cutoff:3.500A) removed outlier: 11.696A pdb=" N HIS C1880 " --> pdb=" O THR C1849 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C1849 " --> pdb=" O HIS C1880 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 41 through 46 removed outlier: 9.068A pdb=" N VAL D 77 " --> pdb=" O THR D 3 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS D 5 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU D 79 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL D 7 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N CYS D 81 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL D 9 " --> pdb=" O CYS D 81 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N SER D 83 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE D 78 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL D 113 " --> pdb=" O PHE D 78 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL D 80 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR D 115 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE D 82 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N VAL D 155 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU D 112 " --> pdb=" O VAL D 155 " (cutoff:3.500A) 1592 hydrogen bonds defined for protein. 4500 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: 7.33 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9808 1.34 - 1.46: 6546 1.46 - 1.58: 13864 1.58 - 1.70: 0 1.70 - 1.82: 194 Bond restraints: 30412 Sorted by residual: bond pdb=" CA ILE A1711 " pdb=" CB ILE A1711 " ideal model delta sigma weight residual 1.539 1.521 0.018 5.40e-03 3.43e+04 1.16e+01 bond pdb=" CA ILE C1711 " pdb=" CB ILE C1711 " ideal model delta sigma weight residual 1.539 1.521 0.018 5.40e-03 3.43e+04 1.10e+01 bond pdb=" CA SER C1006 " pdb=" C SER C1006 " ideal model delta sigma weight residual 1.524 1.468 0.055 2.25e-02 1.98e+03 6.00e+00 bond pdb=" CA SER A1006 " pdb=" C SER A1006 " ideal model delta sigma weight residual 1.524 1.469 0.055 2.25e-02 1.98e+03 5.99e+00 bond pdb=" CB MET A1738 " pdb=" CG MET A1738 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.33e+00 ... (remaining 30407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 40566 2.76 - 5.51: 606 5.51 - 8.27: 80 8.27 - 11.02: 14 11.02 - 13.78: 10 Bond angle restraints: 41276 Sorted by residual: angle pdb=" C LYS C1446 " pdb=" N PHE C1447 " pdb=" CA PHE C1447 " ideal model delta sigma weight residual 122.52 116.59 5.93 1.16e+00 7.43e-01 2.61e+01 angle pdb=" C LYS A1446 " pdb=" N PHE A1447 " pdb=" CA PHE A1447 " ideal model delta sigma weight residual 122.52 116.60 5.92 1.16e+00 7.43e-01 2.61e+01 angle pdb=" N VAL A1139 " pdb=" CA VAL A1139 " pdb=" C VAL A1139 " ideal model delta sigma weight residual 110.30 105.73 4.57 9.70e-01 1.06e+00 2.22e+01 angle pdb=" CB MET C1620 " pdb=" CG MET C1620 " pdb=" SD MET C1620 " ideal model delta sigma weight residual 112.70 99.18 13.52 3.00e+00 1.11e-01 2.03e+01 angle pdb=" CB MET A1620 " pdb=" CG MET A1620 " pdb=" SD MET A1620 " ideal model delta sigma weight residual 112.70 99.18 13.52 3.00e+00 1.11e-01 2.03e+01 ... (remaining 41271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 16643 18.00 - 35.99: 1580 35.99 - 53.99: 213 53.99 - 71.98: 28 71.98 - 89.98: 24 Dihedral angle restraints: 18488 sinusoidal: 7530 harmonic: 10958 Sorted by residual: dihedral pdb=" CA PHE C 560 " pdb=" C PHE C 560 " pdb=" N SER C 561 " pdb=" CA SER C 561 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PHE A 560 " pdb=" C PHE A 560 " pdb=" N SER A 561 " pdb=" CA SER A 561 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PHE C 960 " pdb=" C PHE C 960 " pdb=" N PRO C 961 " pdb=" CA PRO C 961 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 18485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3289 0.046 - 0.092: 1079 0.092 - 0.138: 275 0.138 - 0.184: 19 0.184 - 0.231: 6 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CG LEU C 780 " pdb=" CB LEU C 780 " pdb=" CD1 LEU C 780 " pdb=" CD2 LEU C 780 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CG LEU A 780 " pdb=" CB LEU A 780 " pdb=" CD1 LEU A 780 " pdb=" CD2 LEU A 780 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU A1730 " pdb=" CB LEU A1730 " pdb=" CD1 LEU A1730 " pdb=" CD2 LEU A1730 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 4665 not shown) Planarity restraints: 5344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C1993 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO C1994 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C1994 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C1994 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A1993 " 0.039 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A1994 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A1994 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A1994 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 670 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO A 671 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 671 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 671 " -0.028 5.00e-02 4.00e+02 ... (remaining 5341 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 671 2.61 - 3.18: 31769 3.18 - 3.75: 51426 3.75 - 4.33: 69917 4.33 - 4.90: 104098 Nonbonded interactions: 257881 Sorted by model distance: nonbonded pdb=" O THR A1531 " pdb=" OG1 THR A1534 " model vdw 2.037 3.040 nonbonded pdb=" O THR C1531 " pdb=" OG1 THR C1534 " model vdw 2.037 3.040 nonbonded pdb=" O ILE C1650 " pdb=" OH TYR C1845 " model vdw 2.040 3.040 nonbonded pdb=" O ILE A1650 " pdb=" OH TYR A1845 " model vdw 2.041 3.040 nonbonded pdb=" OD2 ASP C 82 " pdb=" OG SER C1006 " model vdw 2.046 3.040 ... (remaining 257876 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 3.380 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 43.150 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.007 0.069 30412 Z= 0.334 Angle : 0.923 13.776 41276 Z= 0.499 Chirality : 0.047 0.231 4668 Planarity : 0.006 0.060 5344 Dihedral : 14.035 89.979 11360 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 36.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 are not related in a simple way. whole: -2.38 (0.13), residues: 3696 helix: -1.33 (0.11), residues: 1826 sheet: -1.44 (0.24), residues: 440 loop : -1.74 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1478 TYR 0.024 0.003 TYR A1720 PHE 0.032 0.003 PHE A1678 TRP 0.021 0.002 TRP A1272 HIS 0.015 0.002 HIS C1613 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.33 (30412) covalent geometry : angle 0.92289 / 0.50 (41276) hydrogen bonds : bond 0.15599 / 10.10 ( 1588) hydrogen bonds : angle 7.60983 / 5.32 ( 4500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: -0.0219 (ttm) cc_final: -0.0732 (ttm) REVERT: A 658 TRP cc_start: 0.8712 (p90) cc_final: 0.7794 (p90) REVERT: A 935 PHE cc_start: 0.9309 (m-80) cc_final: 0.9029 (m-80) REVERT: A 1057 LEU cc_start: 0.9096 (mt) cc_final: 0.8879 (mt) REVERT: A 1096 MET cc_start: 0.7266 (mpp) cc_final: 0.7008 (mpp) REVERT: A 1103 PHE cc_start: 0.8840 (t80) cc_final: 0.8589 (t80) REVERT: A 1535 TYR cc_start: 0.9432 (m-80) cc_final: 0.9072 (m-80) REVERT: A 1620 MET cc_start: 0.8898 (ptm) cc_final: 0.8684 (ppp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0895 time to fit residues: 15.8818 Evaluate side-chains 78 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.511 Evaluate side-chains 11 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.056 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0268 time to fit residues: 0.4351 Evaluate side-chains 6 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN A 994 ASN A1020 HIS ** A1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1727 HIS A1996 GLN B 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.060434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.038794 restraints weight = 86010.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.040209 restraints weight = 63127.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.041158 restraints weight = 50866.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.041846 restraints weight = 43800.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.042341 restraints weight = 39405.666| |-----------------------------------------------------------------------------| r_work (final): 0.3164 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.054407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.044965 restraints weight = 14532.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.045735 restraints weight = 11952.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.046332 restraints weight = 10241.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.046783 restraints weight = 9037.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.047183 restraints weight = 8242.149| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30412 Z= 0.153 Angle : 0.671 9.867 41276 Z= 0.346 Chirality : 0.042 0.159 4668 Planarity : 0.005 0.052 5344 Dihedral : 5.572 26.195 4060 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 are not related in a simple way. whole: -1.39 (0.13), residues: 3696 helix: -0.29 (0.11), residues: 1884 sheet: -1.22 (0.25), residues: 444 loop : -1.56 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1478 TYR 0.020 0.002 TYR C1845 PHE 0.038 0.002 PHE C1547 TRP 0.013 0.002 TRP C1599 HIS 0.011 0.002 HIS A1717 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (30412) covalent geometry : angle 0.67103 / 0.35 (41276) hydrogen bonds : bond 0.04628 / 3.08 ( 1588) hydrogen bonds : angle 6.00022 / 4.16 ( 4500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 781 ASP cc_start: 0.9353 (t70) cc_final: 0.8961 (m-30) REVERT: C 1042 MET cc_start: 0.9188 (ppp) cc_final: 0.8925 (ppp) REVERT: C 1096 MET cc_start: 0.7373 (mpp) cc_final: 0.7077 (mpp) REVERT: C 1535 TYR cc_start: 0.9411 (m-80) cc_final: 0.8975 (m-80) REVERT: C 1577 MET cc_start: 0.8842 (mmm) cc_final: 0.8512 (mmm) REVERT: C 1620 MET cc_start: 0.9095 (ptm) cc_final: 0.8639 (ppp) REVERT: C 1751 TYR cc_start: 0.8799 (m-80) cc_final: 0.8414 (m-10) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.0869 time to fit residues: 16.8870 Evaluate side-chains 81 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.532 Evaluate side-chains 15 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.057 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0303 time to fit residues: 0.6328 Evaluate side-chains 10 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 251 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 47 optimal weight: 0.0030 chunk 295 optimal weight: 3.9990 chunk 316 optimal weight: 0.0010 chunk 252 optimal weight: 8.9990 chunk 258 optimal weight: 5.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1505 GLN C1639 HIS ** C1653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1727 HIS ** C1988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.059826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.038593 restraints weight = 86217.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.039928 restraints weight = 64040.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.040801 restraints weight = 51965.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.041491 restraints weight = 45067.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.041944 restraints weight = 40520.701| |-----------------------------------------------------------------------------| r_work (final): 0.3155 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.054424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.045143 restraints weight = 14629.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.046000 restraints weight = 11805.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.046612 restraints weight = 9976.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.047157 restraints weight = 8758.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.047511 restraints weight = 7829.500| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 30412 Z= 0.171 Angle : 0.666 10.492 41276 Z= 0.337 Chirality : 0.041 0.236 4668 Planarity : 0.005 0.051 5344 Dihedral : 5.250 22.032 4060 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 are not related in a simple way. whole: -1.14 (0.14), residues: 3696 helix: -0.04 (0.11), residues: 1888 sheet: -1.26 (0.24), residues: 466 loop : -1.44 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1441 TYR 0.013 0.002 TYR A1845 PHE 0.026 0.002 PHE C 475 TRP 0.011 0.001 TRP A1599 HIS 0.007 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (30412) covalent geometry : angle 0.66553 / 0.34 (41276) hydrogen bonds : bond 0.04236 / 2.84 ( 1588) hydrogen bonds : angle 5.79589 / 4.02 ( 4500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 551 LEU cc_start: 0.9396 (tp) cc_final: 0.8925 (pp) REVERT: C 577 MET cc_start: 0.7734 (tpt) cc_final: 0.7527 (tpt) REVERT: C 781 ASP cc_start: 0.9324 (t70) cc_final: 0.8928 (m-30) REVERT: C 805 PHE cc_start: 0.7828 (t80) cc_final: 0.7453 (t80) REVERT: C 1042 MET cc_start: 0.9198 (ppp) cc_final: 0.8909 (ppp) REVERT: C 1096 MET cc_start: 0.7395 (mpp) cc_final: 0.7068 (mpp) REVERT: C 1508 MET cc_start: 0.9044 (mtp) cc_final: 0.8835 (mtp) REVERT: C 1535 TYR cc_start: 0.9340 (m-80) cc_final: 0.8809 (m-80) REVERT: C 1577 MET cc_start: 0.8812 (mmm) cc_final: 0.8515 (mmm) REVERT: C 1582 MET cc_start: 0.9321 (mpp) cc_final: 0.9087 (mpp) REVERT: C 1751 TYR cc_start: 0.8683 (m-80) cc_final: 0.8446 (m-10) REVERT: C 1909 MET cc_start: 0.9211 (mmt) cc_final: 0.8251 (ttt) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.0971 time to fit residues: 19.1846 Evaluate side-chains 82 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.551 Evaluate side-chains 15 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.057 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0285 time to fit residues: 0.6016 Evaluate side-chains 10 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 286 optimal weight: 5.9990 chunk 183 optimal weight: 0.0370 chunk 217 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 338 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 236 optimal weight: 0.6980 chunk 186 optimal weight: 0.9990 overall best weight: 0.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.062390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.040258 restraints weight = 83973.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.041766 restraints weight = 62101.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.042763 restraints weight = 49751.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.043475 restraints weight = 42808.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.044017 restraints weight = 38486.385| |-----------------------------------------------------------------------------| r_work (final): 0.3220 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.056069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.046357 restraints weight = 13822.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.047223 restraints weight = 11111.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.047862 restraints weight = 9417.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.048381 restraints weight = 8289.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.048776 restraints weight = 7463.979| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30412 Z= 0.118 Angle : 0.616 10.651 41276 Z= 0.307 Chirality : 0.041 0.165 4668 Planarity : 0.004 0.049 5344 Dihedral : 4.883 20.612 4060 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.06 % Allowed : 2.94 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 are not related in a simple way. whole: -0.51 (0.14), residues: 3696 helix: 0.51 (0.12), residues: 1874 sheet: -1.21 (0.24), residues: 466 loop : -1.10 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 90 TYR 0.013 0.001 TYR A1845 PHE 0.020 0.001 PHE A1547 TRP 0.010 0.001 TRP C 120 HIS 0.006 0.001 HIS A1146 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (30412) covalent geometry : angle 0.61555 / 0.31 (41276) hydrogen bonds : bond 0.03739 / 2.52 ( 1588) hydrogen bonds : angle 5.40105 / 3.74 ( 4500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 551 LEU cc_start: 0.9389 (tp) cc_final: 0.8968 (pp) REVERT: C 781 ASP cc_start: 0.9339 (t70) cc_final: 0.8941 (m-30) REVERT: C 805 PHE cc_start: 0.7883 (t80) cc_final: 0.7604 (t80) REVERT: C 1096 MET cc_start: 0.7943 (mpp) cc_final: 0.7501 (mpp) REVERT: C 1259 TRP cc_start: 0.8560 (t60) cc_final: 0.8101 (t60) REVERT: C 1535 TYR cc_start: 0.9239 (m-80) cc_final: 0.8622 (m-80) REVERT: C 1620 MET cc_start: 0.9244 (ptm) cc_final: 0.8843 (ppp) REVERT: C 1738 MET cc_start: 0.8675 (mmp) cc_final: 0.8431 (mmt) REVERT: C 1751 TYR cc_start: 0.8590 (m-80) cc_final: 0.8381 (m-10) REVERT: C 1909 MET cc_start: 0.9192 (mmt) cc_final: 0.8309 (ttt) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.1043 time to fit residues: 21.5426 Evaluate side-chains 95 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.529 Evaluate side-chains 14 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.057 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0285 time to fit residues: 0.5665 Evaluate side-chains 11 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 38 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 11 optimal weight: 0.0270 chunk 354 optimal weight: 9.9990 chunk 143 optimal weight: 0.6980 chunk 365 optimal weight: 2.9990 chunk 274 optimal weight: 0.0050 chunk 275 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 0.0040 overall best weight: 0.3466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1023 GLN ** C1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.063204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.041035 restraints weight = 82234.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.042462 restraints weight = 60423.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.043469 restraints weight = 48779.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.044234 restraints weight = 41855.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.044789 restraints weight = 37384.796| |-----------------------------------------------------------------------------| r_work (final): 0.3247 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.056700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.046895 restraints weight = 13980.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.047675 restraints weight = 11330.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.048358 restraints weight = 9655.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.048904 restraints weight = 8504.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.049298 restraints weight = 7625.651| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30412 Z= 0.114 Angle : 0.610 10.142 41276 Z= 0.303 Chirality : 0.041 0.159 4668 Planarity : 0.004 0.049 5344 Dihedral : 4.650 18.849 4060 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 are not related in a simple way. whole: -0.29 (0.14), residues: 3696 helix: 0.70 (0.12), residues: 1862 sheet: -1.09 (0.24), residues: 462 loop : -1.01 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 802 TYR 0.014 0.001 TYR A 297 PHE 0.018 0.001 PHE C1000 TRP 0.007 0.001 TRP C 120 HIS 0.006 0.001 HIS A1146 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (30412) covalent geometry : angle 0.61024 / 0.30 (41276) hydrogen bonds : bond 0.03587 / 2.42 ( 1588) hydrogen bonds : angle 5.27800 / 3.66 ( 4500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 551 LEU cc_start: 0.9374 (tp) cc_final: 0.8967 (pp) REVERT: C 781 ASP cc_start: 0.9285 (t70) cc_final: 0.8892 (m-30) REVERT: C 805 PHE cc_start: 0.7856 (t80) cc_final: 0.7601 (t80) REVERT: C 1042 MET cc_start: 0.9196 (ppp) cc_final: 0.8922 (ppp) REVERT: C 1096 MET cc_start: 0.7188 (mpp) cc_final: 0.6899 (mpp) REVERT: C 1140 HIS cc_start: 0.8856 (t70) cc_final: 0.8453 (t70) REVERT: C 1465 ARG cc_start: 0.9223 (mtt180) cc_final: 0.8966 (mtp85) REVERT: C 1535 TYR cc_start: 0.9183 (m-80) cc_final: 0.8505 (m-80) REVERT: C 1582 MET cc_start: 0.9430 (mpp) cc_final: 0.9223 (mpp) REVERT: C 1620 MET cc_start: 0.9147 (ptm) cc_final: 0.8653 (ppp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1101 time to fit residues: 23.3445 Evaluate side-chains 97 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.527 Evaluate side-chains 17 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.063 Fit side-chains REVERT: B 11 ASP cc_start: 0.7076 (p0) cc_final: 0.6838 (t0) REVERT: B 79 LEU cc_start: 0.8835 (mt) cc_final: 0.8629 (mt) REVERT: B 118 ASP cc_start: 0.8306 (p0) cc_final: 0.7962 (p0) REVERT: B 121 ASP cc_start: 0.7963 (m-30) cc_final: 0.7246 (p0) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0314 time to fit residues: 0.7204 Evaluate side-chains 9 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 311 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 333 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 292 optimal weight: 7.9990 chunk 314 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1023 GLN ** C1653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1709 ASN ** C1988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.061506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.040035 restraints weight = 83695.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.041397 restraints weight = 62571.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.042357 restraints weight = 50787.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.042930 restraints weight = 43702.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.043490 restraints weight = 39748.848| |-----------------------------------------------------------------------------| r_work (final): 0.3218 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.055536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.046057 restraints weight = 13949.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.046883 restraints weight = 11087.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.047508 restraints weight = 9349.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.048008 restraints weight = 8209.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.048305 restraints weight = 7381.611| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 30412 Z= 0.149 Angle : 0.610 10.661 41276 Z= 0.306 Chirality : 0.040 0.266 4668 Planarity : 0.005 0.065 5344 Dihedral : 4.613 18.256 4060 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 are not related in a simple way. whole: -0.28 (0.14), residues: 3696 helix: 0.68 (0.12), residues: 1880 sheet: -1.05 (0.24), residues: 462 loop : -0.97 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 802 TYR 0.015 0.001 TYR A1751 PHE 0.025 0.001 PHE A 728 TRP 0.008 0.001 TRP A1259 HIS 0.006 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (30412) covalent geometry : angle 0.60961 / 0.31 (41276) hydrogen bonds : bond 0.03522 / 2.36 ( 1588) hydrogen bonds : angle 5.30722 / 3.70 ( 4500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 577 MET cc_start: 0.7604 (tpt) cc_final: 0.7364 (tpt) REVERT: C 781 ASP cc_start: 0.9115 (t70) cc_final: 0.8714 (m-30) REVERT: C 805 PHE cc_start: 0.7955 (t80) cc_final: 0.7700 (t80) REVERT: C 1096 MET cc_start: 0.7305 (mpp) cc_final: 0.6605 (mpp) REVERT: C 1140 HIS cc_start: 0.8933 (t70) cc_final: 0.8598 (t70) REVERT: C 1174 ASP cc_start: 0.9029 (m-30) cc_final: 0.8745 (p0) REVERT: C 1259 TRP cc_start: 0.8635 (t60) cc_final: 0.8166 (t60) REVERT: C 1287 LEU cc_start: 0.9272 (tp) cc_final: 0.9071 (tp) REVERT: C 1465 ARG cc_start: 0.9197 (mtt180) cc_final: 0.8895 (mtp180) REVERT: C 1535 TYR cc_start: 0.9151 (m-80) cc_final: 0.8635 (m-80) REVERT: C 1582 MET cc_start: 0.9444 (mpp) cc_final: 0.9189 (mpp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1082 time to fit residues: 22.3646 Evaluate side-chains 95 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.653 Evaluate side-chains 13 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.073 Fit side-chains REVERT: B 79 LEU cc_start: 0.8749 (mt) cc_final: 0.8529 (mt) REVERT: B 118 ASP cc_start: 0.8170 (p0) cc_final: 0.7825 (p0) REVERT: B 121 ASP cc_start: 0.7947 (m-30) cc_final: 0.7287 (p0) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0542 time to fit residues: 0.8811 Evaluate side-chains 7 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 335 optimal weight: 4.9990 chunk 339 optimal weight: 0.0570 chunk 244 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 1 optimal weight: 0.0170 chunk 166 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 311 optimal weight: 0.0000 chunk 69 optimal weight: 0.0370 chunk 120 optimal weight: 0.5980 overall best weight: 0.1418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.064072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.041744 restraints weight = 80789.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.043248 restraints weight = 59865.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.044286 restraints weight = 48332.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.045085 restraints weight = 41339.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.045645 restraints weight = 36765.023| |-----------------------------------------------------------------------------| r_work (final): 0.3274 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.056381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.046377 restraints weight = 14117.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.047243 restraints weight = 11392.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.047921 restraints weight = 9594.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.048462 restraints weight = 8412.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.048826 restraints weight = 7526.580| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30412 Z= 0.115 Angle : 0.623 9.616 41276 Z= 0.307 Chirality : 0.041 0.224 4668 Planarity : 0.004 0.057 5344 Dihedral : 4.473 18.500 4060 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 are not related in a simple way. whole: -0.10 (0.14), residues: 3696 helix: 0.85 (0.12), residues: 1876 sheet: -0.97 (0.24), residues: 452 loop : -0.93 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 802 TYR 0.018 0.001 TYR D 51 PHE 0.020 0.001 PHE A1000 TRP 0.007 0.001 TRP C 120 HIS 0.007 0.001 HIS C1727 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (30412) covalent geometry : angle 0.62292 / 0.31 (41276) hydrogen bonds : bond 0.03416 / 2.29 ( 1588) hydrogen bonds : angle 5.11882 / 3.55 ( 4500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 781 ASP cc_start: 0.9158 (t70) cc_final: 0.8761 (m-30) REVERT: C 1042 MET cc_start: 0.9216 (ppp) cc_final: 0.8922 (ppp) REVERT: C 1096 MET cc_start: 0.7374 (mpp) cc_final: 0.6818 (mpp) REVERT: C 1140 HIS cc_start: 0.8977 (t70) cc_final: 0.8526 (t70) REVERT: C 1174 ASP cc_start: 0.8987 (m-30) cc_final: 0.8690 (p0) REVERT: C 1259 TRP cc_start: 0.8516 (t60) cc_final: 0.8104 (t60) REVERT: C 1535 TYR cc_start: 0.9104 (m-80) cc_final: 0.8590 (m-80) REVERT: C 1582 MET cc_start: 0.9445 (mpp) cc_final: 0.9118 (mpp) REVERT: C 1684 VAL cc_start: 0.9745 (t) cc_final: 0.9464 (t) REVERT: C 1738 MET cc_start: 0.8445 (mmp) cc_final: 0.8208 (mmt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1032 time to fit residues: 22.6282 Evaluate side-chains 94 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.560 Evaluate side-chains 16 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.058 Fit side-chains REVERT: B 1 MET cc_start: 0.3961 (tpt) cc_final: 0.3547 (ppp) REVERT: B 118 ASP cc_start: 0.8168 (p0) cc_final: 0.7806 (p0) REVERT: B 121 ASP cc_start: 0.7943 (m-30) cc_final: 0.7278 (p0) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0291 time to fit residues: 0.6376 Evaluate side-chains 9 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 131 optimal weight: 0.0670 chunk 196 optimal weight: 0.0020 chunk 344 optimal weight: 0.0170 chunk 291 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 230 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 21 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 chunk 360 optimal weight: 7.9990 overall best weight: 0.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 915 GLN ** C1653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.064363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.042225 restraints weight = 81282.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.043674 restraints weight = 59677.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.044733 restraints weight = 48165.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.045507 restraints weight = 41181.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.046083 restraints weight = 36633.548| |-----------------------------------------------------------------------------| r_work (final): 0.3286 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.056214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.046548 restraints weight = 14479.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.047448 restraints weight = 11354.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.048167 restraints weight = 9481.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.048697 restraints weight = 8211.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.049122 restraints weight = 7337.875| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30412 Z= 0.110 Angle : 0.604 7.712 41276 Z= 0.302 Chirality : 0.041 0.205 4668 Planarity : 0.004 0.052 5344 Dihedral : 4.371 17.264 4060 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 are not related in a simple way. whole: 0.08 (0.14), residues: 3696 helix: 0.99 (0.12), residues: 1864 sheet: -0.80 (0.24), residues: 454 loop : -0.85 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 802 TYR 0.014 0.001 TYR A1751 PHE 0.013 0.001 PHE A1547 TRP 0.007 0.001 TRP A 120 HIS 0.010 0.001 HIS C1727 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (30412) covalent geometry : angle 0.60370 / 0.30 (41276) hydrogen bonds : bond 0.03301 / 2.22 ( 1588) hydrogen bonds : angle 5.11667 / 3.57 ( 4500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 577 MET cc_start: 0.7194 (tpt) cc_final: 0.6928 (tpt) REVERT: C 781 ASP cc_start: 0.9160 (t70) cc_final: 0.8788 (m-30) REVERT: C 1042 MET cc_start: 0.9154 (ppp) cc_final: 0.8874 (ppp) REVERT: C 1096 MET cc_start: 0.7251 (mpp) cc_final: 0.6697 (mpp) REVERT: C 1140 HIS cc_start: 0.8957 (t70) cc_final: 0.8496 (t70) REVERT: C 1174 ASP cc_start: 0.8961 (m-30) cc_final: 0.8701 (p0) REVERT: C 1535 TYR cc_start: 0.8978 (m-80) cc_final: 0.8432 (m-80) REVERT: C 1577 MET cc_start: 0.9210 (mmm) cc_final: 0.8726 (mmm) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1030 time to fit residues: 20.9930 Evaluate side-chains 97 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.549 Evaluate side-chains 16 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.060 Fit side-chains REVERT: B 1 MET cc_start: 0.3903 (tpt) cc_final: 0.3577 (ppp) REVERT: B 79 LEU cc_start: 0.8819 (mt) cc_final: 0.8599 (mt) REVERT: B 118 ASP cc_start: 0.8258 (p0) cc_final: 0.7880 (p0) REVERT: B 121 ASP cc_start: 0.7981 (m-30) cc_final: 0.7188 (p0) REVERT: B 166 LYS cc_start: 0.3402 (mttt) cc_final: 0.3189 (mttt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0462 time to fit residues: 0.9262 Evaluate side-chains 14 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 95 optimal weight: 0.0980 chunk 137 optimal weight: 4.9990 chunk 267 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 chunk 238 optimal weight: 0.0050 chunk 148 optimal weight: 3.9990 chunk 183 optimal weight: 0.0770 chunk 348 optimal weight: 8.9990 chunk 272 optimal weight: 0.9990 chunk 201 optimal weight: 20.0000 chunk 292 optimal weight: 3.9990 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1622 HIS ** C1639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1653 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.064682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.042297 restraints weight = 82055.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.043788 restraints weight = 60129.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.044718 restraints weight = 48481.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.045549 restraints weight = 41985.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.046066 restraints weight = 37479.138| |-----------------------------------------------------------------------------| r_work (final): 0.3282 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.056624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.046745 restraints weight = 14279.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.047643 restraints weight = 11478.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.048314 restraints weight = 9667.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.048889 restraints weight = 8459.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.049301 restraints weight = 7561.355| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30412 Z= 0.107 Angle : 0.604 9.018 41276 Z= 0.300 Chirality : 0.040 0.195 4668 Planarity : 0.004 0.054 5344 Dihedral : 4.290 19.128 4060 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 are not related in a simple way. whole: 0.23 (0.14), residues: 3696 helix: 1.10 (0.12), residues: 1864 sheet: -0.68 (0.25), residues: 450 loop : -0.78 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1478 TYR 0.013 0.001 TYR A1751 PHE 0.014 0.001 PHE A1000 TRP 0.016 0.001 TRP C1259 HIS 0.011 0.001 HIS C1717 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (30412) covalent geometry : angle 0.60427 / 0.30 (41276) hydrogen bonds : bond 0.03222 / 2.16 ( 1588) hydrogen bonds : angle 5.01963 / 3.50 ( 4500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 479 MET cc_start: 0.0021 (mtt) cc_final: -0.0369 (mtm) REVERT: C 577 MET cc_start: 0.7190 (tpt) cc_final: 0.6900 (tpt) REVERT: C 781 ASP cc_start: 0.9056 (t70) cc_final: 0.8740 (m-30) REVERT: C 1042 MET cc_start: 0.9181 (ppp) cc_final: 0.8888 (ppp) REVERT: C 1096 MET cc_start: 0.7288 (mpp) cc_final: 0.6751 (mpp) REVERT: C 1140 HIS cc_start: 0.8949 (t70) cc_final: 0.8495 (t70) REVERT: C 1174 ASP cc_start: 0.8992 (m-30) cc_final: 0.8704 (p0) REVERT: C 1259 TRP cc_start: 0.8546 (t60) cc_final: 0.8138 (t60) REVERT: C 1465 ARG cc_start: 0.9159 (mtt180) cc_final: 0.8947 (mtp85) REVERT: C 1535 TYR cc_start: 0.8991 (m-80) cc_final: 0.8471 (m-80) REVERT: C 1577 MET cc_start: 0.9214 (mmm) cc_final: 0.8718 (mmm) REVERT: C 1582 MET cc_start: 0.9387 (mpp) cc_final: 0.9065 (mtt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0844 time to fit residues: 18.2046 Evaluate side-chains 94 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.501 Evaluate side-chains 14 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.3946 (tpt) cc_final: 0.3694 (ppp) REVERT: B 79 LEU cc_start: 0.8752 (mt) cc_final: 0.8506 (mt) REVERT: B 166 LYS cc_start: 0.3135 (mttt) cc_final: 0.2900 (mttt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0480 time to fit residues: 0.8196 Evaluate side-chains 11 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 87 optimal weight: 0.0000 chunk 53 optimal weight: 7.9990 chunk 351 optimal weight: 0.5980 chunk 330 optimal weight: 0.8980 chunk 348 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 203 optimal weight: 0.0870 chunk 31 optimal weight: 0.0980 chunk 91 optimal weight: 10.0000 chunk 218 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 overall best weight: 0.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 295 ASN ** C1996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.064027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.042583 restraints weight = 82755.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.044120 restraints weight = 60107.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.045181 restraints weight = 48026.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.045955 restraints weight = 40971.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.046563 restraints weight = 36392.459| |-----------------------------------------------------------------------------| r_work (final): 0.3293 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.056993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.047029 restraints weight = 14261.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.047954 restraints weight = 11455.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.048663 restraints weight = 9626.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.049213 restraints weight = 8360.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.049557 restraints weight = 7471.617| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30412 Z= 0.104 Angle : 0.601 10.105 41276 Z= 0.296 Chirality : 0.040 0.185 4668 Planarity : 0.004 0.054 5344 Dihedral : 4.242 18.724 4060 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 are not related in a simple way. whole: 0.37 (0.14), residues: 3696 helix: 1.20 (0.12), residues: 1850 sheet: -0.55 (0.25), residues: 450 loop : -0.69 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1478 TYR 0.011 0.001 TYR A1751 PHE 0.013 0.001 PHE A1000 TRP 0.011 0.001 TRP C1259 HIS 0.011 0.001 HIS A1717 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (30412) covalent geometry : angle 0.60121 / 0.30 (41276) hydrogen bonds : bond 0.03143 / 2.11 ( 1588) hydrogen bonds : angle 4.98948 / 3.48 ( 4500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 577 MET cc_start: 0.7179 (tpt) cc_final: 0.6876 (tpt) REVERT: C 781 ASP cc_start: 0.9167 (t70) cc_final: 0.8845 (m-30) REVERT: C 1042 MET cc_start: 0.9168 (ppp) cc_final: 0.8889 (ppp) REVERT: C 1140 HIS cc_start: 0.8998 (t70) cc_final: 0.8546 (t70) REVERT: C 1174 ASP cc_start: 0.9045 (m-30) cc_final: 0.8671 (p0) REVERT: C 1259 TRP cc_start: 0.8575 (t60) cc_final: 0.8202 (t60) REVERT: C 1535 TYR cc_start: 0.8976 (m-80) cc_final: 0.8471 (m-80) REVERT: C 1577 MET cc_start: 0.9241 (mmm) cc_final: 0.8724 (mmm) REVERT: C 1582 MET cc_start: 0.9334 (mpp) cc_final: 0.9065 (mtt) REVERT: C 1738 MET cc_start: 0.8700 (mmp) cc_final: 0.8441 (mmt) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.0918 time to fit residues: 20.2732 Evaluate side-chains 97 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.544 Evaluate side-chains 16 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.3918 (tpt) cc_final: 0.3710 (ppp) REVERT: B 118 ASP cc_start: 0.8237 (p0) cc_final: 0.7832 (p0) REVERT: B 121 ASP cc_start: 0.7849 (m-30) cc_final: 0.7096 (p0) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0460 time to fit residues: 0.9302 Evaluate side-chains 15 residues out of total 158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 148 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 chunk 140 optimal weight: 0.9980 chunk 325 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.063683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.042008 restraints weight = 80256.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.043466 restraints weight = 59533.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.044389 restraints weight = 47980.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.045213 restraints weight = 41469.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.045803 restraints weight = 36807.950| |-----------------------------------------------------------------------------| r_work (final): 0.3281 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.057039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.047263 restraints weight = 14495.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.048195 restraints weight = 11501.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.048937 restraints weight = 9585.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.049478 restraints weight = 8275.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.049901 restraints weight = 7360.583| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30412 Z= 0.111 Angle : 0.605 8.877 41276 Z= 0.299 Chirality : 0.040 0.185 4668 Planarity : 0.004 0.054 5344 Dihedral : 4.203 22.738 4060 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 are not related in a simple way. whole: 0.43 (0.14), residues: 3696 helix: 1.20 (0.12), residues: 1872 sheet: -0.53 (0.25), residues: 446 loop : -0.61 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1478 TYR 0.010 0.001 TYR C1751 PHE 0.022 0.001 PHE C1000 TRP 0.012 0.001 TRP C1259 HIS 0.010 0.001 HIS C1717 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (30412) covalent geometry : angle 0.60459 / 0.30 (41276) hydrogen bonds : bond 0.03091 / 2.08 ( 1588) hydrogen bonds : angle 5.00914 / 3.49 ( 4500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3537.17 seconds wall clock time: 63 minutes 1.51 seconds (3781.51 seconds total)